1
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Shum C, Han SY, Thiruvahindrapuram B, Wang Z, de Rijke J, Zhang B, Sundberg M, Chen C, Buttermore ED, Makhortova N, Howe J, Sahin M, Scherer SW. Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs. Comput Struct Biotechnol J 2024; 23:638-647. [PMID: 38283851 PMCID: PMC10819409 DOI: 10.1016/j.csbj.2023.12.036] [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: 10/31/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/30/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas nucleases and human induced pluripotent stem cell (iPSC) technology can reveal deep insight into the genetic and molecular bases of human biology and disease. Undesired editing outcomes, both on-target (at the edited locus) and off-target (at other genomic loci) hinder the application of CRISPR-Cas nucleases. We developed Off-flow, a Nextflow-coded bioinformatic workflow that takes a specific guide sequence and Cas protein input to call four separate off-target prediction programs (CHOPCHOP, Cas-Offinder, CRISPRitz, CRISPR-Offinder) to output a comprehensive list of predicted off-target sites. We applied it to whole genome sequencing (WGS) data to investigate the occurrence of unintended effects in human iPSCs that underwent repair or insertion of disease-related variants by homology-directed repair. Off-flow identified a 3-base-pair-substitution and a mono-allelic genomic deletion at the target loci, KCNQ2, in 2 clones. Unbiased WGS analysis further identified off-target missense variants and a mono-allelic genomic deletion at the targeted locus, GNAQ, in 10 clones. On-target substitution and deletions had escaped standard PCR and Sanger sequencing analysis, while missense variants at other genomic loci were not detected by Off-flow. We used these results to filter out iPSC clones for subsequent functional experiments. Off-flow, which we make publicly available, works for human and mouse genomes currently and can be adapted for other genomes. Off-flow and WGS analysis can improve the integrity of studies using CRISPR/Cas-edited cells and animal models.
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Affiliation(s)
- Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sang Yeon Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Benjamin Zhang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Sundberg
- Department of Neurology, FM Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cidi Chen
- Human Neuron Core, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Nina Makhortova
- Human Neuron Core, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mustafa Sahin
- Department of Neurology, FM Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
- Lead contact
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McKay L, Petrelli B, Pind M, Reynolds JN, Wintle RF, Chudley AE, Drögemöller B, Fainsod A, Scherer SW, Hanlon-Dearman A, Hicks GG. Risk and Resilience Variants in the Retinoic Acid Metabolic and Developmental Pathways Associated with Risk of FASD Outcomes. Biomolecules 2024; 14:569. [PMID: 38785976 PMCID: PMC11117505 DOI: 10.3390/biom14050569] [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: 04/04/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Fetal Alcohol Spectrum Disorder (FASD) is a common neurodevelopmental disorder that affects an estimated 2-5% of North Americans. FASD is induced by prenatal alcohol exposure (PAE) during pregnancy and while there is a clear genetic contribution, few genetic factors are currently identified or understood. In this study, using a candidate gene approach, we performed a genetic variant analysis of retinoic acid (RA) metabolic and developmental signaling pathway genes on whole exome sequencing data of 23 FASD-diagnosed individuals. We found risk and resilience alleles in ADH and ALDH genes known to normally be involved in alcohol detoxification at the expense of RA production, causing RA deficiency, following PAE. Risk and resilience variants were also identified in RA-regulated developmental pathway genes, especially in SHH and WNT pathways. Notably, we also identified significant variants in the causative genes of rare neurodevelopmental disorders sharing comorbidities with FASD, including STRA6 (Matthew-Wood), SOX9 (Campomelic Dysplasia), FDG1 (Aarskog), and 22q11.2 deletion syndrome (TBX1). Although this is a small exploratory study, the findings support PAE-induced RA deficiency as a major etiology underlying FASD and suggest risk and resilience variants may be suitable biomarkers to determine the risk of FASD outcomes following PAE.
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Affiliation(s)
- Leo McKay
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Berardino Petrelli
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Molly Pind
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - James N. Reynolds
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 2V7, Canada
| | - Richard F. Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Albert E. Chudley
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Britt Drögemöller
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Centre on Aging, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, P.O. Box 12271, Jerusalem 9112102, Israel
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ana Hanlon-Dearman
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Geoffrey G. Hicks
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
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3
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Deneault E. Recent Therapeutic Gene Editing Applications to Genetic Disorders. Curr Issues Mol Biol 2024; 46:4147-4185. [PMID: 38785523 PMCID: PMC11119904 DOI: 10.3390/cimb46050255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Recent years have witnessed unprecedented progress in therapeutic gene editing, revolutionizing the approach to treating genetic disorders. In this comprehensive review, we discuss the progression of milestones leading to the emergence of the clustered regularly interspaced short palindromic repeats (CRISPR)-based technology as a powerful tool for precise and targeted modifications of the human genome. CRISPR-Cas9 nuclease, base editing, and prime editing have taken center stage, demonstrating remarkable precision and efficacy in targeted ex vivo and in vivo genomic modifications. Enhanced delivery systems, including viral vectors and nanoparticles, have further improved the efficiency and safety of therapeutic gene editing, advancing their clinical translatability. The exploration of CRISPR-Cas systems beyond the commonly used Cas9, such as the development of Cas12 and Cas13 variants, has expanded the repertoire of gene editing tools, enabling more intricate modifications and therapeutic interventions. Outstandingly, prime editing represents a significant leap forward, given its unparalleled versatility and minimization of off-target effects. These innovations have paved the way for therapeutic gene editing in a multitude of previously incurable genetic disorders, ranging from monogenic diseases to complex polygenic conditions. This review highlights the latest innovative studies in the field, emphasizing breakthrough technologies in preclinical and clinical trials, and their applications in the realm of precision medicine. However, challenges such as off-target effects and ethical considerations remain, necessitating continued research to refine safety profiles and ethical frameworks.
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Affiliation(s)
- Eric Deneault
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
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Pradeepan KS, McCready FP, Wei W, Khaki M, Zhang W, Salter MW, Ellis J, Martinez-Trujillo J. Calcium-Dependent Hyperexcitability in Human Stem Cell-Derived Rett Syndrome Neuronal Networks. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100290. [PMID: 38420187 PMCID: PMC10899066 DOI: 10.1016/j.bpsgos.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/20/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Background Mutations in MECP2 predominantly cause Rett syndrome and can be modeled in vitro using human stem cell-derived neurons. Patients with Rett syndrome have signs of cortical hyperexcitability, such as seizures. Human stem cell-derived MECP2 null excitatory neurons have smaller soma size and reduced synaptic connectivity but are also hyperexcitable due to higher input resistance. Paradoxically, networks of MECP2 null neurons show a decrease in the frequency of network bursts consistent with a hypoconnectivity phenotype. Here, we examine this issue. Methods We reanalyzed multielectrode array data from 3 isogenic MECP2 cell line pairs recorded over 6 weeks (n = 144). We used a custom burst detection algorithm to analyze network events and isolated a phenomenon that we termed reverberating super bursts (RSBs). To probe potential mechanisms of RSBs, we conducted pharmacological manipulations using bicuculline, EGTA-AM, and DMSO on 1 cell line (n = 34). Results RSBs, often misidentified as single long-duration bursts, consisted of a large-amplitude initial burst followed by several high-frequency, low-amplitude minibursts. Our analysis revealed that MECP2 null networks exhibited increased frequency of RSBs, which produced increased bursts compared with isogenic controls. Bicuculline or DMSO treatment did not affect RSBs. EGTA-AM selectively eliminated RSBs and rescued network burst dynamics. Conclusions During early development, MECP2 null neurons are hyperexcitable and produce hyperexcitable networks. This may predispose them to the emergence of hypersynchronic states that potentially translate into seizures. Network hyperexcitability depends on asynchronous neurotransmitter release that is likely driven by presynaptic Ca2+ and can be rescued by EGTA-AM to restore typical network dynamics.
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Affiliation(s)
- Kartik S. Pradeepan
- Graduate Program in Neuroscience, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Fraser P. McCready
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Milad Khaki
- Robarts Research Institute, Western University, London, Ontario, Canada
| | - Wenbo Zhang
- Neuroscience & Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael W. Salter
- Neuroscience & Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julio Martinez-Trujillo
- Graduate Program in Neuroscience, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Robarts Research Institute, Western University, London, Ontario, Canada
- Western Institute for Neuroscience, Western University, London, Ontario, Canada
- Department of Physiology and Pharmacology, and Psychiatry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Psychiatry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
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5
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Rylaarsdam L, Rakotomamonjy J, Pope E, Guemez-Gamboa A. iPSC-derived models of PACS1 syndrome reveal transcriptional and functional deficits in neuron activity. Nat Commun 2024; 15:827. [PMID: 38280846 PMCID: PMC10821916 DOI: 10.1038/s41467-024-44989-7] [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: 05/13/2022] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
PACS1 syndrome is a neurodevelopmental disorder characterized by intellectual disability and distinct craniofacial abnormalities resulting from a de novo p.R203W variant in phosphofurin acidic cluster sorting protein 1 (PACS1). PACS1 is known to have functions in the endosomal pathway and nucleus, but how the p.R203W variant affects developing neurons is not fully understood. Here we differentiated stem cells towards neuronal models including cortical organoids to investigate the impact of the PACS1 syndrome-causing variant on neurodevelopment. While few deleterious effects were detected in PACS1(+/R203W) neural precursors, mature PACS1(+/R203W) glutamatergic neurons exhibited impaired expression of genes involved in synaptic signaling processes. Subsequent characterization of neural activity using calcium imaging and multielectrode arrays revealed the p.R203W PACS1 variant leads to a prolonged neuronal network burst duration mediated by an increased interspike interval. These findings demonstrate the impact of the PACS1 p.R203W variant on developing human neural tissue and uncover putative electrophysiological underpinnings of disease.
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Affiliation(s)
- Lauren Rylaarsdam
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jennifer Rakotomamonjy
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eleanor Pope
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alicia Guemez-Gamboa
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Khan SS, Jaimon E, Lin YE, Nikoloff J, Tonelli F, Alessi DR, Pfeffer SR. Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575737. [PMID: 38293195 PMCID: PMC10827083 DOI: 10.1101/2024.01.15.575737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Activating LRRK2 mutations cause Parkinson's disease. Previously, we showed that cholinergic interneurons and astrocytes but not medium spiny neurons of the dorsal striatum lose primary cilia in LRRK2 mutant mice. Single nucleus RNA sequencing shows that cilia loss in cholinergic interneurons correlates with higher LRRK2 expression and decreased glial derived neurotrophic factor transcription. Nevertheless, much higher LRRK2 expression is seen in medium spiny neurons that have normal cilia in mice and humans. In parallel with decreased striatal dopaminergic neurite density, LRRK2 G2019S neurons show increased autism-linked CNTN5 adhesion protein expression; glial cells show significant loss of ferritin heavy chain. Human striatal tissue from LRRK2 pathway mutation carriers and idiopathic Parkinson's disease show similar cilia loss in cholinergic interneurons and astrocytes and overall loss of such neurons. These data strongly suggest that loss of cilia in specific striatal cell types decreases neuroprotection for dopamine neurons in mice and human Parkinson's disease.
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Affiliation(s)
- Shahzad S. Khan
- Department of Biochemistry, Stanford University School of Medicine, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
- Current address: Departments of Cell Biology & Physiology and Neurology, University of North Carolina, Chapel Hill, United States
| | - Ebsy Jaimon
- Department of Biochemistry, Stanford University School of Medicine, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
| | - Yu-En Lin
- Department of Biochemistry, Stanford University School of Medicine, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
| | - Jonas Nikoloff
- Department of Biochemistry, Stanford University School of Medicine, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
| | - Francesca Tonelli
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom
| | - Dario R. Alessi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom
| | - Suzanne R. Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, United States
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7
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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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Namipashaki A, Pugsley K, Liu X, Abrehart K, Lim SM, Sun G, Herold MJ, Polo JM, Bellgrove MA, Hawi Z. Integration of xeno-free single-cell cloning in CRISPR-mediated DNA editing of human iPSCs improves homogeneity and methodological efficiency of cellular disease modeling. Stem Cell Reports 2023; 18:2515-2527. [PMID: 37977144 PMCID: PMC10724053 DOI: 10.1016/j.stemcr.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
The capability to generate induced pluripotent stem cell (iPSC) lines, in tandem with CRISPR-Cas9 DNA editing, offers great promise to understand the underlying genetic mechanisms of human disease. The low efficiency of available methods for homogeneous expansion of singularized CRISPR-transfected iPSCs necessitates the coculture of transfected cells in mixed populations and/or on feeder layers. Consequently, edited cells must be purified using labor-intensive screening and selection, culminating in inefficient editing. Here, we provide a xeno-free method for single-cell cloning of CRISPRed iPSCs achieving a clonal survival of up to 70% within 7-10 days. This is accomplished through improved viability of the transfected cells, paralleled with provision of an enriched environment for the robust establishment and proliferation of singularized iPSC clones. Enhanced cell survival was accompanied by a high transfection efficiency exceeding 97%, and editing efficiencies of 50%-65% for NHEJ and 10% for HDR, indicative of the method's utility in stem cell disease modeling.
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Affiliation(s)
- Atefeh Namipashaki
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kealan Pugsley
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Xiaodong Liu
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Kirra Abrehart
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Sue Mei Lim
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Guizhi Sun
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jose M Polo
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia; Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
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9
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Lv S, He E, Luo J, Liu Y, Liang W, Xu S, Zhang K, Yang Y, Wang M, Song Y, Wu Y, Cai X. Using Human-Induced Pluripotent Stem Cell Derived Neurons on Microelectrode Arrays to Model Neurological Disease: A Review. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301828. [PMID: 37863819 PMCID: PMC10667858 DOI: 10.1002/advs.202301828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/04/2023] [Indexed: 10/22/2023]
Abstract
In situ physiological signals of in vitro neural disease models are essential for studying pathogenesis and drug screening. Currently, an increasing number of in vitro neural disease models are established using human-induced pluripotent stem cell (hiPSC) derived neurons (hiPSC-DNs) to overcome interspecific gene expression differences. Microelectrode arrays (MEAs) can be readily interfaced with two-dimensional (2D), and more recently, three-dimensional (3D) neural stem cell-derived in vitro models of the human brain to monitor their physiological activity in real time. Therefore, MEAs are emerging and useful tools to model neurological disorders and disease in vitro using human iPSCs. This is enabling a real-time window into neuronal signaling at the network scale from patient derived. This paper provides a comprehensive review of MEA's role in analyzing neural disease models established by hiPSC-DNs. It covers the significance of MEA fabrication, surface structure and modification schemes for hiPSC-DNs culturing and signal detection. Additionally, this review discusses advances in the development and use of MEA technology to study in vitro neural disease models, including epilepsy, autism spectrum developmental disorder (ASD), and others established using hiPSC-DNs. The paper also highlights the application of MEAs combined with hiPSC-DNs in detecting in vitro neurotoxic substances. Finally, the future development and outlook of multifunctional and integrated devices for in vitro medical diagnostics and treatment are discussed.
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Affiliation(s)
- Shiya Lv
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Enhui He
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- The State Key Lab of Brain‐Machine IntelligenceZhejiang UniversityHangzhou321100China
| | - Jinping Luo
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yaoyao Liu
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Wei Liang
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Shihong Xu
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Kui Zhang
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yan Yang
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Mixia Wang
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yilin Song
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yirong Wu
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xinxia Cai
- State Key Laboratory of Transducer TechnologyAerospace Information Research InstituteChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
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10
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Molloy CJ, Cooke J, Gatford NJF, Rivera-Olvera A, Avazzadeh S, Homberg JR, Grandjean J, Fernandes C, Shen S, Loth E, Srivastava DP, Gallagher L. Bridging the translational gap: what can synaptopathies tell us about autism? Front Mol Neurosci 2023; 16:1191323. [PMID: 37441676 PMCID: PMC10333541 DOI: 10.3389/fnmol.2023.1191323] [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: 03/21/2023] [Accepted: 05/24/2023] [Indexed: 07/15/2023] Open
Abstract
Multiple molecular pathways and cellular processes have been implicated in the neurobiology of autism and other neurodevelopmental conditions. There is a current focus on synaptic gene conditions, or synaptopathies, which refer to clinical conditions associated with rare genetic variants disrupting genes involved in synaptic biology. Synaptopathies are commonly associated with autism and developmental delay and may be associated with a range of other neuropsychiatric outcomes. Altered synaptic biology is suggested by both preclinical and clinical studies in autism based on evidence of differences in early brain structural development and altered glutamatergic and GABAergic neurotransmission potentially perturbing excitatory and inhibitory balance. This review focusses on the NRXN-NLGN-SHANK pathway, which is implicated in the synaptic assembly, trans-synaptic signalling, and synaptic functioning. We provide an overview of the insights from preclinical molecular studies of the pathway. Concentrating on NRXN1 deletion and SHANK3 mutations, we discuss emerging understanding of cellular processes and electrophysiology from induced pluripotent stem cells (iPSC) models derived from individuals with synaptopathies, neuroimaging and behavioural findings in animal models of Nrxn1 and Shank3 synaptic gene conditions, and key findings regarding autism features, brain and behavioural phenotypes from human clinical studies of synaptopathies. The identification of molecular-based biomarkers from preclinical models aims to advance the development of targeted therapeutic treatments. However, it remains challenging to translate preclinical animal models and iPSC studies to interpret human brain development and autism features. We discuss the existing challenges in preclinical and clinical synaptopathy research, and potential solutions to align methodologies across preclinical and clinical research. Bridging the translational gap between preclinical and clinical studies will be necessary to understand biological mechanisms, to identify targeted therapies, and ultimately to progress towards personalised approaches for complex neurodevelopmental conditions such as autism.
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Affiliation(s)
- Ciara J. Molloy
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Jennifer Cooke
- Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Nicholas J. F. Gatford
- Kavli Institute for Nanoscience Discovery, Nuffield Department of Clinical Neurosciences, University of Oxford, Medical Sciences Division, Oxford, United Kingdom
| | - Alejandro Rivera-Olvera
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Sahar Avazzadeh
- Physiology and Cellular Physiology Research Laboratory, CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, Human Biology Building, University of Galway, Galway, Ireland
| | - Judith R. Homberg
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Joanes Grandjean
- Physiology and Cellular Physiology Research Laboratory, CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, Human Biology Building, University of Galway, Galway, Ireland
- Department of Medical Imaging, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Cathy Fernandes
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, University of Galway, Galway, Ireland
- FutureNeuro, The SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons, Dublin, Ireland
| | - Eva Loth
- Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Deepak P. Srivastava
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- The Hospital for SickKids, Toronto, ON, Canada
- The Peter Gilgan Centre for Research and Learning, SickKids Research Institute, Toronto, ON, Canada
- The Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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11
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Sandhu A, Kumar A, Rawat K, Gautam V, Sharma A, Saha L. Modernising autism spectrum disorder model engineering and treatment via CRISPR-Cas9: A gene reprogramming approach. World J Clin Cases 2023; 11:3114-3127. [PMID: 37274051 PMCID: PMC10237133 DOI: 10.12998/wjcc.v11.i14.3114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/13/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
A neurological abnormality called autism spectrum disorder (ASD) affects how a person perceives and interacts with others, leading to social interaction and communication issues. Limited and recurring behavioural patterns are another feature of the illness. Multiple mutations throughout development are the source of the neurodevelopmental disorder autism. However, a well-established model and perfect treatment for this spectrum disease has not been discovered. The rising era of the clustered regularly interspaced palindromic repeats (CRISPR)-associated protein 9 (Cas9) system can streamline the complexity underlying the pathogenesis of ASD. The CRISPR-Cas9 system is a powerful genetic engineering tool used to edit the genome at the targeted site in a precise manner. The major hurdle in studying ASD is the lack of appropriate animal models presenting the complex symptoms of ASD. Therefore, CRISPR-Cas9 is being used worldwide to mimic the ASD-like pathology in various systems like in vitro cell lines, in vitro 3D organoid models and in vivo animal models. Apart from being used in establishing ASD models, CRISPR-Cas9 can also be used to treat the complexities of ASD. The aim of this review was to summarize and critically analyse the CRISPR-Cas9-mediated discoveries in the field of ASD.
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Affiliation(s)
- Arushi Sandhu
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Anil Kumar
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Kajal Rawat
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Vipasha Gautam
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Antika Sharma
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
| | - Lekha Saha
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 0172, Chandigarh, India
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12
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Muzzi L, Di Lisa D, Falappa M, Pepe S, Maccione A, Pastorino L, Martinoia S, Frega M. Human-Derived Cortical Neurospheroids Coupled to Passive, High-Density and 3D MEAs: A Valid Platform for Functional Tests. Bioengineering (Basel) 2023; 10:bioengineering10040449. [PMID: 37106636 PMCID: PMC10136157 DOI: 10.3390/bioengineering10040449] [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: 03/03/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
With the advent of human-induced pluripotent stem cells (hiPSCs) and differentiation protocols, methods to create in-vitro human-derived neuronal networks have been proposed. Although monolayer cultures represent a valid model, adding three-dimensionality (3D) would make them more representative of an in-vivo environment. Thus, human-derived 3D structures are becoming increasingly used for in-vitro disease modeling. Achieving control over the final cell composition and investigating the exhibited electrophysiological activity is still a challenge. Thence, methodologies to create 3D structures with controlled cellular density and composition and platforms capable of measuring and characterizing the functional aspects of these samples are needed. Here, we propose a method to rapidly generate neurospheroids of human origin with control over cell composition that can be used for functional investigations. We show a characterization of the electrophysiological activity exhibited by the neurospheroids by using micro-electrode arrays (MEAs) with different types (i.e., passive, C-MOS, and 3D) and number of electrodes. Neurospheroids grown in free culture and transferred on MEAs exhibited functional activity that can be chemically and electrically modulated. Our results indicate that this model holds great potential for an in-depth study of signal transmission to drug screening and disease modeling and offers a platform for in-vitro functional testing.
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Affiliation(s)
- Lorenzo Muzzi
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genoa, 16145 Genoa, Italy
| | - Donatella Di Lisa
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genoa, 16145 Genoa, Italy
| | - Matteo Falappa
- 3Brain AG, 8808 Pfäffikon, Switzerland
- Corticale Srl., 16145 Genoa, Italy
| | - Sara Pepe
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
| | | | - Laura Pastorino
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genoa, 16145 Genoa, Italy
| | - Sergio Martinoia
- Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS), University of Genoa, 16145 Genoa, Italy
| | - Monica Frega
- Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, The Netherlands
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behaviour, 6500 HB Nijmegen, The Netherlands
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13
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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14
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Wendt FR, Pathak GA, Singh K, Stein MB, Koenen KC, Krystal JH, Gelernter J, Davis LK, Polimanti R. Sex-Specific Genetic and Transcriptomic Liability to Neuroticism. Biol Psychiatry 2023; 93:243-252. [PMID: 36244801 PMCID: PMC10508260 DOI: 10.1016/j.biopsych.2022.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/08/2022] [Accepted: 07/13/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND The presentation, etiology, and relative risk of psychiatric disorders are strongly influenced by biological sex. Neuroticism is a transdiagnostic feature of psychiatric disorders displaying prominent sex differences. We performed genome-wide association studies of neuroticism separately in males and females to identify sex-specific genetic and transcriptomic profiles. METHODS Neuroticism scores were derived from the Eysenck Personality Inventory Neuroticism scale. Genome-wide association studies were performed in 145,669 females and 129,229 males from the UK Biobank considering autosomal and X chromosomal variation. Two-sided z tests were used to test for sex-specific effects of discovered loci, genetic correlates (n = 673 traits), tissue and gene transcriptomic profiles, and polygenic associations across health outcomes in the Vanderbilt University Biobank (39,692 females and 31,268 males). RESULTS The single nucleotide polymorphism heritability of neuroticism was not statistically different between males (h2 = 10.6%) and females (h2 = 11.85%). Four female-specific (rs10736549-CNTN5, rs6507056-ASXL3, rs2087182-MMS22L, and rs72995548-HSPB2) and 2 male-specific (rs10507274-MED13L and rs7984597) neuroticism risk loci reached genome-wide significance. Male- and female-specific neuroticism polygenic scores were most significantly associated with mood disorders (males: odds ratio = 1.11, p = 1.40 × 10-9; females: odds ratio = 1.14, p = 6.05 × 10-22). They also associated with sex-specific laboratory measurements related to erythrocyte count, distribution, and hemoglobin concentration. Gene expression variation in the pituitary was enriched for neuroticism loci in males (male: b = 0.026, p = .002), and genetically regulated transcriptomic changes highlighted the effect of SHISHA9, TEX26, and NCOA6. CONCLUSIONS Through a comprehensive assessment of genetic risk for neuroticism and the associated biological processes, this study identified several molecular pathways that can partially explain the known sex differences in neurotic symptoms and their psychiatric comorbidities.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut; Department of Anthropology, University of Toronto, Mississauga, Ontario, Canada; Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut
| | - Kritika Singh
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, California; Department of Psychiatry, University of California, San Diego, San Diego, California; Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California
| | - Karestan C Koenen
- Stanley Center for Psychiatry Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatry and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; Department of Genetics, Yale School of Medicine, New Haven, Connecticut; Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut.
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15
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Faheem M, Deneault E, Alexandrova R, Rodrigues DC, Pellecchia G, Shum C, Zarrei M, Piekna A, Wei W, Howe JL, Thiruvahindrapuram B, Lamoureux S, Ross PJ, Bradley CA, Ellis J, Scherer SW. Disruption of DDX53 coding sequence has limited impact on iPSC-derived human NGN2 neurons. BMC Med Genomics 2023; 16:5. [PMID: 36635662 PMCID: PMC9837974 DOI: 10.1186/s12920-022-01425-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The X-linked PTCHD1 locus is strongly associated with autism spectrum disorder (ASD). Males who carry chromosome microdeletions of PTCHD1 antisense long non-coding RNA (PTCHD1-AS)/DEAD-box helicase 53 (DDX53) have ASD, or a sub-clinical form called Broader Autism Phenotype. If the deletion extends beyond PTCHD1-AS/DDX53 to the next gene, PTCHD1, which is protein-coding, the individuals typically have ASD and intellectual disability (ID). Three male siblings with a 90 kb deletion that affects only PTCHD1-AS (and not including DDX53) have ASD. We performed a functional analysis of DDX53 to examine its role in NGN2 neurons. METHODS We used the clustered regularly interspaced short palindromic repeats (CRISPR) gene editing strategy to knock out DDX53 protein by inserting 3 termination codons (3TCs) into two different induced pluripotent stem cell (iPSC) lines. DDX53 CRISPR-edited iPSCs were differentiated into cortical excitatory neurons by Neurogenin 2 (NGN-2) directed differentiation. The functional differences of DDX53-3TC neurons compared to isogenic control neurons with molecular and electrophysiological approaches were assessed. RESULTS Isogenic iPSC-derived control neurons exhibited low levels of DDX53 transcripts. Transcriptional analysis revealed the generation of excitatory cortical neurons and DDX53 protein was not detected in iPSC-derived control neurons by western blot. Control lines and DDX53-3TC neurons were active in the multi-electrode array, but no overt electrophysiological phenotype in either isogenic line was observed. CONCLUSION DDX53-3TC mutation does not alter NGN2 neuronal function in these experiments, suggesting that synaptic deficits causing ASD are unlikely in this cell type.
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Affiliation(s)
- Muhammad Faheem
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Eric Deneault
- grid.57544.370000 0001 2110 2143Centre for Oncology, Radiopharmaceuticals and Research; Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON Canada
| | - Roumiana Alexandrova
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Deivid C. Rodrigues
- grid.42327.300000 0004 0473 9646Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON Canada
| | - Giovanna Pellecchia
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Carole Shum
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Mehdi Zarrei
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Alina Piekna
- grid.42327.300000 0004 0473 9646Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON Canada
| | - Wei Wei
- grid.42327.300000 0004 0473 9646Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON Canada
| | - Jennifer L. Howe
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Bhooma Thiruvahindrapuram
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - Sylvia Lamoureux
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada
| | - P. Joel Ross
- grid.42327.300000 0004 0473 9646Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.139596.10000 0001 2167 8433Department of Biology, University of Prince Edward Island, Charlottetown, PE Canada
| | - Clarrisa A. Bradley
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646Neurosciences & Mental Health Program, Hospital for Sick Children, Toronto, ON Canada
| | - James Ellis
- grid.42327.300000 0004 0473 9646Developmental & Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646Genetics & Genome Biology Program, Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre, University of Toronto, Toronto, ON Canada
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16
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Van Nynatten LR, Slessarev M, Martin CM, Leligdowicz A, Miller MR, Patel MA, Daley M, Patterson EK, Cepinskas G, Fraser DD. Novel plasma protein biomarkers from critically ill sepsis patients. Clin Proteomics 2022; 19:50. [PMID: 36572854 PMCID: PMC9792322 DOI: 10.1186/s12014-022-09389-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite the high morbidity and mortality associated with sepsis, the relationship between the plasma proteome and clinical outcome is poorly understood. In this study, we used targeted plasma proteomics to identify novel biomarkers of sepsis in critically ill patients. METHODS Blood was obtained from 15 critically ill patients with suspected/confirmed sepsis (Sepsis-3.0 criteria) on intensive care unit (ICU) Day-1 and Day-3, as well as age- and sex-matched 15 healthy control subjects. A total of 1161 plasma proteins were measured with proximal extension assays. Promising sepsis biomarkers were narrowed with machine learning and then correlated with relevant clinical and laboratory variables. RESULTS The median age for critically ill sepsis patients was 56 (IQR 51-61) years. The median MODS and SOFA values were 7 (IQR 5.0-8.0) and 7 (IQR 5.0-9.0) on ICU Day-1, and 4 (IQR 3.5-7.0) and 6 (IQR 3.5-7.0) on ICU Day-3, respectively. Targeted proteomics, together with feature selection, identified the leading proteins that distinguished sepsis patients from healthy control subjects with ≥ 90% classification accuracy; 25 proteins on ICU Day-1 and 26 proteins on ICU Day-3 (6 proteins overlapped both ICU days; PRTN3, UPAR, GDF8, NTRK3, WFDC2 and CXCL13). Only 7 of the leading proteins changed significantly between ICU Day-1 and Day-3 (IL10, CCL23, TGFα1, ST2, VSIG4, CNTN5, and ITGAV; P < 0.01). Significant correlations were observed between a variety of patient clinical/laboratory variables and the expression of 15 proteins on ICU Day-1 and 14 proteins on ICU Day-3 (P < 0.05). CONCLUSIONS Targeted proteomics with feature selection identified proteins altered in critically ill sepsis patients relative to healthy control subjects. Correlations between protein expression and clinical/laboratory variables were identified, each providing pathophysiological insight. Our exploratory data provide a rationale for further hypothesis-driven sepsis research.
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Affiliation(s)
| | - Marat Slessarev
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Claudio M. Martin
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Aleks Leligdowicz
- grid.39381.300000 0004 1936 8884Medicine, Western University, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Michael R. Miller
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada
| | - Maitray A. Patel
- grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada
| | - Mark Daley
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Computer Science, Western University, London, ON N6A 3K7 Canada ,grid.494618.6The Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1 Canada
| | - Eric K. Patterson
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada
| | - Gediminas Cepinskas
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Medical Biophysics, Western University, London, ON N6A 3K7 Canada
| | - Douglas D. Fraser
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, London, ON Canada ,grid.39381.300000 0004 1936 8884Pediatrics, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Clinical Neurological Sciences, Western University, London, ON Canada ,grid.39381.300000 0004 1936 8884Physiology and Pharmacology, Western University, London, ON Canada ,grid.412745.10000 0000 9132 1600London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, London, ON N6A 5W9 Canada
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17
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Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Cell Rep 2022; 41:111678. [DOI: 10.1016/j.celrep.2022.111678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
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18
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Mok RSF, Zhang W, Sheikh TI, Pradeepan K, Fernandes IR, DeJong LC, Benigno G, Hildebrandt MR, Mufteev M, Rodrigues DC, Wei W, Piekna A, Liu J, Muotri AR, Vincent JB, Muller L, Martinez-Trujillo J, Salter MW, Ellis J. Wide spectrum of neuronal and network phenotypes in human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations. Transl Psychiatry 2022; 12:450. [PMID: 36253345 PMCID: PMC9576700 DOI: 10.1038/s41398-022-02216-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/19/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder primarily caused by heterozygous loss-of-function mutations in the X-linked gene MECP2 that is a global transcriptional regulator. Mutations in the methyl-CpG binding domain (MBD) of MECP2 disrupt its interaction with methylated DNA. Here, we investigate the effect of a novel MECP2 L124W missense mutation in the MBD of an atypical RTT patient with preserved speech in comparison to severe MECP2 null mutations. L124W protein had a limited ability to disrupt heterochromatic chromocenters due to decreased binding dynamics. We isolated two pairs of isogenic WT and L124W induced pluripotent stem cells. L124W induced excitatory neurons expressed stable protein, exhibited increased input resistance and decreased voltage-gated Na+ and K+ currents, and their neuronal dysmorphology was limited to decreased dendritic complexity. Three isogenic pairs of MECP2 null neurons had the expected more extreme morphological and electrophysiological phenotypes. We examined development and maturation of L124W and MECP2 null excitatory neural network activity using micro-electrode arrays. Relative to isogenic controls, L124W neurons had an increase in synchronous network burst frequency, in contrast to MECP2 null neurons that suffered a significant decrease in synchronous network burst frequency and a transient extension of network burst duration. A biologically motivated computational neural network model shows the observed changes in network dynamics are explained by changes in intrinsic Na+ and K+ currents in individual neurons. Our multilevel results demonstrate that RTT excitatory neurons show a wide spectrum of morphological, electrophysiological and circuitry phenotypes that are dependent on the severity of the MECP2 mutation.
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Grants
- R01 MH108528 NIMH NIH HHS
- MOP-133423 CIHR
- R01 MH109885 NIMH NIH HHS
- FDN-154336 CIHR
- R01 MH100175 NIMH NIH HHS
- Col Harland Sanders Rett Syndrome Research Fund at the University of Toronto (to J.E.), SFARI (Research grant #514918 to J.E. and J.M-T), CIHR (MOP-133423 to J.E. and M.W.S.; ERARE Team Grant ERT161303 to J.E.), CIHR foundation grant (FDN-154336 to M.W.S), Ontario Brain Institute (POND Network to J.E.), McLaughlin Centre Accelerator grant (to J.E.), John Evans Leadership Fund & Ontario Research Fund (to J.E), Canada Research Chair in Stem Cell Models of Childhood Disease (to J.E.), Beta Sigma Phi International Endowment Fund (to J.E.).
- BrainsCAN at Western University through the Canada First Research Excellence Fund (CFREF) (to GB, KP, LM, JMT). NSERC Postgraduate Scholarship–Doctoral (PGS-D) Scholarship to KP.
- Trainee support was provided by Restracomp (to LCD).
- National Institutes of Health (NIH) grants # R01MH108528, R01MH109885, and R01MH1000175 to ARM.
- Ontario Rett Syndrome Association to JBV.
- SFARI (Research grant #514918 to J.E. and J.M-T), BrainsCAN at Western University through the Canada First Research Excellence Fund (CFREF) (to GB, KP, LM, JMT)
- CIHR (MOP-133423 to J.E. and M.W.S.; CIHR foundation grant (FDN-154336 to M.W.S),
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Affiliation(s)
- Rebecca S F Mok
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wenbo Zhang
- Neurosciences & Mental Health Program, The Hospital for Sick Children, Toronto, M5G 0A4, ON, Canada
| | - Taimoor I Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Kartik Pradeepan
- Department of Physiology and Pharmacology, Department of Psychiatry, Neuroscience Graduate Program, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Isabella R Fernandes
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
| | - Leah C DeJong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Gabriel Benigno
- Department of Applied Mathematics, Robarts Research Institute, Brain and Mind Institute, Western University, London, ON, N6A 5B7, Canada
| | - Matthew R Hildebrandt
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Marat Mufteev
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jiajie Liu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alysson R Muotri
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA, 92037-0695, USA
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, Center for Academic Research and Training in Anthropogeny, Archealization Center, Kavli Institute, University of California San Diego, La Jolla, CA, 92037, USA
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Lyle Muller
- Department of Applied Mathematics, Robarts Research Institute, Brain and Mind Institute, Western University, London, ON, N6A 5B7, Canada
| | - Julio Martinez-Trujillo
- Department of Physiology and Pharmacology, Department of Psychiatry, Neuroscience Graduate Program, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5B7, Canada
| | - Michael W Salter
- Neurosciences & Mental Health Program, The Hospital for Sick Children, Toronto, M5G 0A4, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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19
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Langlie J, Mittal R, Finberg A, Bencie NB, Mittal J, Omidian H, Omidi Y, Eshraghi AA. Unraveling pathological mechanisms in neurological disorders: the impact of cell-based and organoid models. Neural Regen Res 2022; 17:2131-2140. [PMID: 35259819 PMCID: PMC9083150 DOI: 10.4103/1673-5374.335836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell-based models are a promising tool in deciphering the molecular mechanisms underlying the pathogenesis of neurological disorders as well as aiding in the discovery and development of future drug therapies. The greatest challenge is creating cell-based models that encapsulate the vast phenotypic presentations as well as the underlying genotypic etiology of these conditions. In this article, we discuss the recent advancements in cell-based models for understanding the pathophysiology of neurological disorders. We reviewed studies discussing the progression of cell-based models to the advancement of three-dimensional models and organoids that provide a more accurate model of the pathophysiology of neurological disorders in vivo. The better we understand how to create more precise models of the neurological system, the sooner we will be able to create patient-specific models and large libraries of these neurological disorders. While three-dimensional models can be used to discover the linking factors to connect the varying phenotypes, such models will also help to understand the early pathophysiology of these neurological disorders and how they are affected by their environment. The three-dimensional cell models will allow us to create more specific treatments and uncover potentially preventative measures in neurological disorders such as autism spectrum disorder, Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis.
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Affiliation(s)
- Jake Langlie
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rahul Mittal
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ariel Finberg
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nathalie B Bencie
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeenu Mittal
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hossein Omidian
- College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Yadollah Omidi
- College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Adrien A Eshraghi
- Department of Otolaryngology, Hearing Research and Communication Disorders Laboratory; Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami; Department of Biomedical Engineering, University of Miami, Coral Gables; Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, USA
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20
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Jiang CC, Lin LS, Long S, Ke XY, Fukunaga K, Lu YM, Han F. Signalling pathways in autism spectrum disorder: mechanisms and therapeutic implications. Signal Transduct Target Ther 2022; 7:229. [PMID: 35817793 PMCID: PMC9273593 DOI: 10.1038/s41392-022-01081-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent and complex neurodevelopmental disorder which has strong genetic basis. Despite the rapidly rising incidence of autism, little is known about its aetiology, risk factors, and disease progression. There are currently neither validated biomarkers for diagnostic screening nor specific medication for autism. Over the last two decades, there have been remarkable advances in genetics, with hundreds of genes identified and validated as being associated with a high risk for autism. The convergence of neuroscience methods is becoming more widely recognized for its significance in elucidating the pathological mechanisms of autism. Efforts have been devoted to exploring the behavioural functions, key pathological mechanisms and potential treatments of autism. Here, as we highlight in this review, emerging evidence shows that signal transduction molecular events are involved in pathological processes such as transcription, translation, synaptic transmission, epigenetics and immunoinflammatory responses. This involvement has important implications for the discovery of precise molecular targets for autism. Moreover, we review recent insights into the mechanisms and clinical implications of signal transduction in autism from molecular, cellular, neural circuit, and neurobehavioural aspects. Finally, the challenges and future perspectives are discussed with regard to novel strategies predicated on the biological features of autism.
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Affiliation(s)
- Chen-Chen Jiang
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Li-Shan Lin
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Sen Long
- Department of Pharmacy, Hangzhou Seventh People's Hospital, Mental Health Center Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Xiao-Yan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Kohji Fukunaga
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Feng Han
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China. .,Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China. .,Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, China.
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21
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Girardin S, Clément B, Ihle SJ, Weaver S, Petr JB, Mateus JC, Duru J, Krubner M, Forró C, Ruff T, Fruh I, Müller M, Vörös J. Topologically controlled circuits of human iPSC-derived neurons for electrophysiology recordings. LAB ON A CHIP 2022; 22:1386-1403. [PMID: 35253810 PMCID: PMC8963377 DOI: 10.1039/d1lc01110c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/18/2022] [Indexed: 06/01/2023]
Abstract
Bottom-up neuroscience, which consists of building and studying controlled networks of neurons in vitro, is a promising method to investigate information processing at the neuronal level. However, in vitro studies tend to use cells of animal origin rather than human neurons, leading to conclusions that might not be generalizable to humans and limiting the possibilities for relevant studies on neurological disorders. Here we present a method to build arrays of topologically controlled circuits of human induced pluripotent stem cell (iPSC)-derived neurons. The circuits consist of 4 to 50 neurons with well-defined connections, confined by microfabricated polydimethylsiloxane (PDMS) membranes. Such circuits were characterized using optical imaging and microelectrode arrays (MEAs), suggesting the formation of functional connections between the neurons of a circuit. Electrophysiology recordings were performed on circuits of human iPSC-derived neurons for at least 4.5 months. We believe that the capacity to build small and controlled circuits of human iPSC-derived neurons holds great promise to better understand the fundamental principles of information processing and storing in the brain.
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Affiliation(s)
- Sophie Girardin
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Blandine Clément
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Stephan J Ihle
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Sean Weaver
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Jana B Petr
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - José C Mateus
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Portugal
| | - Jens Duru
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Magdalena Krubner
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Csaba Forró
- Cui Laboratory, S285 290 Jane Stanford Way Stanford, Stanford, CA 94305, USA
| | - Tobias Ruff
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
| | - Isabelle Fruh
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Matthias Müller
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Gloriastrasse 35, 8092 Zurich, Switzerland.
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22
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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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23
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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: 10] [Impact Index Per Article: 5.0] [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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24
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Avazzadeh S, Quinlan LR, Reilly J, McDonagh K, Jalali A, Wang Y, McInerney V, Krawczyk J, Ding Y, Fitzgerald J, O'Sullivan M, Forman EB, Lynch SA, Ennis S, Feerick N, Reilly R, Li W, Shen X, Yang G, Lu Y, Peeters H, Dockery P, O'Brien T, Shen S, Gallagher L. NRXN1α +/- is associated with increased excitability in ASD iPSC-derived neurons. BMC Neurosci 2021; 22:56. [PMID: 34525970 PMCID: PMC8442436 DOI: 10.1186/s12868-021-00661-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
Background NRXN1 deletions are identified as one of major rare risk factors for autism spectrum disorder (ASD) and other neurodevelopmental disorders. ASD has 30% co-morbidity with epilepsy, and the latter is associated with excessive neuronal firing. NRXN1 encodes hundreds of presynaptic neuro-adhesion proteins categorized as NRXN1α/β/γ. Previous studies on cultured cells show that the short NRXN1β primarily exerts excitation effect, whereas the long NRXN1α which is more commonly deleted in patients involves in both excitation and inhibition. However, patient-derived models are essential for understanding functional consequences of NRXN1α deletions in human neurons. We recently derived induced pluripotent stem cells (iPSCs) from five controls and three ASD patients carrying NRXN1α+/- and showed increased calcium transients in patient neurons. Methods In this study we investigated the electrophysiological properties of iPSC-derived cortical neurons in control and ASD patients carrying NRXN1α+/- using patch clamping. Whole genome RNA sequencing was carried out to further understand the potential underlying molecular mechanism. Results NRXN1α+/- cortical neurons were shown to display larger sodium currents, higher AP amplitude and accelerated depolarization time. RNASeq analyses revealed transcriptomic changes with significant upregulation glutamatergic synapse and ion channels/transporter activity including voltage-gated potassium channels (GRIN1, GRIN3B, SLC17A6, CACNG3, CACNA1A, SHANK1), which are likely to couple with the increased excitability in NRXN1α+/- cortical neurons. Conclusions Together with recent evidence of increased calcium transients, our results showed that human NRXN1α+/- isoform deletions altered neuronal excitability and non-synaptic function, and NRXN1α+/- patient iPSCs may be used as an ASD model for therapeutic development with calcium transients and excitability as readouts. Supplementary Information The online version contains supplementary material available at 10.1186/s12868-021-00661-0.
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Affiliation(s)
- Sahar Avazzadeh
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland
| | - Leo R Quinlan
- Physiology and Cellular Physiology Research Laboratory, School of Medicine, CÚRAM SFI Centre for Research in Medical Devices, National University of Ireland (NUI), Galway, Ireland
| | - Jamie Reilly
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland
| | - Katya McDonagh
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland
| | | | - Yanqin Wang
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland.,Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Veronica McInerney
- HRB Clinical Research Facility, National University of Ireland (NUI), Galway, Ireland
| | - Janusz Krawczyk
- Department of Haematology, Galway University Hospital, Galway, Ireland
| | - Yicheng Ding
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland
| | | | - Matthew O'Sullivan
- Trinity Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Eva B Forman
- Children's University Hospital, Temple Street, Dublin, Ireland
| | - Sally A Lynch
- Children's University Hospital, Temple Street, Dublin, Ireland.,Department of Clinical Genetics, OLCHC, Dublin 12, Ireland
| | - Sean Ennis
- School of Medicine and Medical Science, UCD Academic Centre On Rare Diseases, University College Dublin, Dublin, Ireland
| | - Niamh Feerick
- Centre for Bioengineering, Trinity College Institute of Neuroscience, School of Medicine, School of Engineering, Trinity College Dublin, Dublin, Ireland
| | - Richard Reilly
- Centre for Bioengineering, Trinity College Institute of Neuroscience, School of Medicine, School of Engineering, Trinity College Dublin, Dublin, Ireland
| | - Weidong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Shen
- School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China
| | - Guangming Yang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yin Lu
- College of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Hilde Peeters
- Centre for Human Genetics, University Hospital Leuven, KU Leuven, 3000, Leuven, Belgium
| | - Peter Dockery
- Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | - Timothy O'Brien
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland
| | - Sanbing Shen
- School of Medicine, Regenerative Medicine Institute, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Ireland. .,FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, D02, Ireland.
| | - Louise Gallagher
- Trinity Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
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25
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Deneault E, Chaineau M, Nicouleau M, Castellanos Montiel MJ, Franco Flores AK, Haghi G, Chen CXQ, Abdian N, Shlaifer I, Beitel LK, Durcan TM. A streamlined CRISPR workflow to introduce mutations and generate isogenic iPSCs for modeling amyotrophic lateral sclerosis. Methods 2021; 203:297-310. [PMID: 34500068 DOI: 10.1016/j.ymeth.2021.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/28/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) represents a complex neurodegenerative disorder with significant genetic heterogeneity. To date, both the genetic etiology and the underlying molecular mechanisms driving this disease remain poorly understood, although in recent years several studies have highlighted a number of genetic mutations causative for ALS. With these mutations pointing to potential pathways that may be affected within individuals with ALS, having the ability to generate human neurons and other disease relevant cells containing these mutations becomes even more critical if new therapies are to emerge. Recent developments with the advent of induced pluripotent stem cells (iPSCs) and clustered regularly interspaced short palindromic repeats (CRISPR) gene editing fields gave us the tools to introduce or correct a specific mutation at any site within the genome of an iPSC, and thus model the specific contribution of risk mutations. In this study we describe a rapid and efficient way to either introduce a mutation into a control line, or to correct an allele-specific mutation, generating an isogenic control line from patient-derived iPSCs with a given mutation. The mutations introduced were the G94A (also known as G93A) mutation into SOD1 or H517Q into FUS, and the mutation corrected was a patient iPSC line with I114T mutation in SOD1. A combination of small molecules and growth factors were used to guide a stepwise differentiation of the edited cells into motor neurons in order to demonstrate that disease-relevant cells could be generated for downstream applications. Through a combination of iPSCs and CRISPR editing, the cells generated here will provide fundamental insights into the molecular mechanisms underlying neuron degeneration in ALS.
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Affiliation(s)
- Eric Deneault
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Mathilde Chaineau
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Michael Nicouleau
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Maria José Castellanos Montiel
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Anna Kristyna Franco Flores
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Ghazal Haghi
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Carol X-Q Chen
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Narges Abdian
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Irina Shlaifer
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Lenore K Beitel
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, Quebec H3A 2B4, Canada.
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26
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Nakazawa T. Modeling schizophrenia with iPS cell technology and disease mouse models. Neurosci Res 2021; 175:46-52. [PMID: 34411680 DOI: 10.1016/j.neures.2021.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022]
Abstract
Induced pluripotent stem cell (iPSC) technology, which enables the direct analysis of neuronal cells with the same genetic background as patients, has recently garnered significant attention in schizophrenia research. This technology is important because it enables a comprehensive interpretation using mice and human clinical research and cross-species verification. Here I review recent advances in modeling schizophrenia using iPSC technology, alongside the utility of disease mouse models.
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Affiliation(s)
- Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.
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27
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Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System. Microorganisms 2021; 9:microorganisms9081723. [PMID: 34442802 PMCID: PMC8399841 DOI: 10.3390/microorganisms9081723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/26/2022] Open
Abstract
Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders defined by impaired social interactions and communication with repetitive behaviors, activities, or interests. Gastrointestinal (GI) disturbances and gut microbiota dysbiosis are frequently associated with ASD in childhood. However, it is not known whether microbiota dysbiosis in ASD patients also occurs in adulthood. Further, the consequences of altered gut microbiota on digestive functions and the enteric nervous system (ENS) remain unexplored. Therefore, we studied, in mice, the ability offecal supernatant (FS) from adult ASD patients to induce GI dysfunctions and ENS remodeling. First, the analyses of the fecal microbiota composition in adult ASD patients indicated a reduced α-diversity and increased abundance of three bacterial 16S rRNA gene amplicon sequence variants compared to healthy controls (HC). The transfer of FS from ASD patients (FS-ASD) to mice decreased colonic barrier permeability by 29% and 58% compared to FS-HC for paracellular and transcellular permeability, respectively. These effects are associated with the reduced expression of the tight junction proteins JAM-A, ZO-2, cingulin, and proinflammatory cytokines TNFα and IL1β. In addition, the expression of glial and neuronal molecules was reduced by FS-ASD as compared to FS-HC in particular for those involved in neuronal connectivity (βIII-tubulin and synapsin decreased by 31% and 67%, respectively). Our data suggest that changes in microbiota composition in ASD may contribute to GI alterations, and in part, via ENS remodeling.
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28
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Canals I, Quist E, Ahlenius H. Transcription Factor-Based Strategies to Generate Neural Cell Types from Human Pluripotent Stem Cells. Cell Reprogram 2021; 23:206-220. [PMID: 34388027 DOI: 10.1089/cell.2021.0045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the last years, the use of pluripotent stem cells in studies of human biology has grown exponentially. These cells represent an infinite source for differentiation into several human cell types facilitating the investigation on biological processes, functionality of cells, or diseases mechanisms in relevant human models. In the neurobiology field, pluripotent stem cells have been extensively used to generate the main neuronal and glial cells of the brain. Traditionally, protocols following developmental cues have been applied to pluripotent stem cells to drive differentiation toward different cell lineages; however, these protocols give rise to populations with mixed identities. Interestingly, new protocols applying overexpression of lineage-specific transcription factors (TFs) have emerged and facilitated the generation of highly pure populations of specific subtypes of neurons and glial cells in an easy, reproducible, and rapid manner. In this study, we review protocols based on this strategy to generate excitatory, inhibitory, dopaminergic, and motor neurons as well as astrocytes, oligodendrocytes, and microglia. In addition, we will discuss the main applications for cells generated with these protocols, including disease modeling, drug screening, and mechanistic studies. Finally, we will discuss the advantages and disadvantages of TF-based protocols and present our view of the future in this field.
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Affiliation(s)
- Isaac Canals
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
| | - Ella Quist
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
| | - Henrik Ahlenius
- Stem Cells, Aging and Neurodegeneration Group, Faculty of Medicine, Lund University, Lund, Sweden.,Division of Neurology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund, Sweden
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29
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Mossink B, Verboven AHA, van Hugte EJH, Klein Gunnewiek TM, Parodi G, Linda K, Schoenmaker C, Kleefstra T, Kozicz T, van Bokhoven H, Schubert D, Nadif Kasri N, Frega M. Human neuronal networks on micro-electrode arrays are a highly robust tool to study disease-specific genotype-phenotype correlations in vitro. Stem Cell Reports 2021; 16:2182-2196. [PMID: 34329594 PMCID: PMC8452490 DOI: 10.1016/j.stemcr.2021.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/16/2023] Open
Abstract
Micro-electrode arrays (MEAs) are increasingly used to characterize neuronal network activity of human induced pluripotent stem cell (hiPSC)-derived neurons. Despite their gain in popularity, MEA recordings from hiPSC-derived neuronal networks are not always used to their full potential in respect to experimental design, execution, and data analysis. Therefore, we benchmarked the robustness of MEA-derived neuronal activity patterns from ten healthy individual control lines, and uncover comparable network phenotypes. To achieve standardization, we provide recommendations on experimental design and analysis. With such standardization, MEAs can be used as a reliable platform to distinguish (disease-specific) network phenotypes. In conclusion, we show that MEAs are a powerful and robust tool to uncover functional neuronal network phenotypes from hiPSC-derived neuronal networks, and provide an important resource to advance the hiPSC field toward the use of MEAs for disease phenotyping and drug discovery. MEAs are a robust tool to model neuronal network functioning Neuronal networks from different healthy donors show comparable network activity MEAs are able to distinguish disease-specific neuronal network phenotypes We provide recommendations to standardize neuronal network recordings on MEA
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Clinical Neurophysiology, University of Twente, 7522 NB Enschede, the Netherlands
| | - Anouk H A Verboven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboudumc, Radboud Institute for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; ACE Kempenhaeghe, Department of Epileptology, 5591 VE Heeze, the Netherlands
| | - Teun M Klein Gunnewiek
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Medical Imaging, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Giulia Parodi
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Katrin Linda
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Chantal Schoenmaker
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Tamas Kozicz
- Department of Medical Imaging, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Dirk Schubert
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Monica Frega
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, 6500 HB Nijmegen, the Netherlands; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA.
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30
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Transcriptome analysis of MBD5-associated neurodevelopmental disorder (MAND) neural progenitor cells reveals dysregulation of autism-associated genes. Sci Rep 2021; 11:11295. [PMID: 34050248 PMCID: PMC8163803 DOI: 10.1038/s41598-021-90798-z] [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: 06/24/2020] [Accepted: 04/20/2021] [Indexed: 11/30/2022] Open
Abstract
MBD5-associated neurodevelopmental disorder (MAND) is an autism spectrum disorder (ASD) characterized by intellectual disability, motor delay, speech impairment and behavioral problems; however, the biological role of methyl-CpG-binding domain 5, MBD5, in neurodevelopment and ASD remains largely undefined. Hence, we created neural progenitor cells (NPC) derived from individuals with chromosome 2q23.1 deletion and conducted RNA-seq to identify differentially expressed genes (DEGs) and the biological processes and pathways altered in MAND. Primary skin fibroblasts from three unrelated individuals with MAND and four unrelated controls were converted into induced pluripotent stem cell (iPSC) lines, followed by directed differentiation of iPSC to NPC. Transcriptome analysis of MAND NPC revealed 468 DEGs (q < 0.05), including 20 ASD-associated genes. Comparison of DEGs in MAND with SFARI syndromic autism genes revealed a striking significant overlap in biological processes commonly altered in neurodevelopmental phenotypes, with TGFβ, Hippo signaling, DNA replication, and cell cycle among the top enriched pathways. Overall, these transcriptome deviations provide potential connections to the overlapping neurocognitive and neuropsychiatric phenotypes associated with key high-risk ASD genes, including chromatin modifiers and epigenetic modulators, that play significant roles in these disease states.
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31
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Dunbar EK, Saloman JL, Phillips AE, Whitcomb DC. Severe Pain in Chronic Pancreatitis Patients: Considering Mental Health and Associated Genetic Factors. J Pain Res 2021; 14:773-784. [PMID: 33762844 PMCID: PMC7982558 DOI: 10.2147/jpr.s274276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/20/2021] [Indexed: 12/24/2022] Open
Abstract
Pain is the most distressing and disruptive feature of recurrent acute pancreatitis (RAP) and chronic pancreatitis (CP) resulting in low quality of life (QOL) and disabilities. There is no single, characteristic pain pattern in patients with RAP and CP. Abdominal imaging features of CP accurately reflect morphologic features but they do not correlate with pain. Pain is the major driver of poor quality of life (QOL) and it is the constant pain, rather than intermittent pain that drives poor QOL. Furthermore, the most severe constant pain experience in CP is also a complex condition. The ability to target the etiopathogenesis of severe pain requires new methods to detect the exact pain mechanisms in an individual at cellular, tissue, system and psychiatric levels. In patients with complex and severe disease, it is likely that multiple overlapping mechanisms are simultaneously driving pain, anxiety and depression. Quantitative sensory testing (QST) shows promise in detecting alterations in central processing of pain signals and to classify patients for mechanistic and therapeutic studies. New genetic research suggests that genetic loci for severe pain in CP overlap with genetic loci for depression and other psychiatric disorders, providing additional insights and therapeutic targets for individual patients with severe CP pain. Well-designed clinical trials that integrate clinical features, QST, genetics and psychological assessments with targeted treatment and assessment of responses are required for a quantum leap forward. A better understanding of the context and mechanisms contributing to severe pain experiences in individual patients is predicted to lead to better therapies and quality of life.
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Affiliation(s)
- Ellyn K Dunbar
- Departments of Human Genetics and Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jami L Saloman
- Departments of Neurobiology and Medicine, Division of Gastroenterology, Hepatology and Nutrition, Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anna Evans Phillips
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - David C Whitcomb
- Departments of Human Genetics, Cell Biology and Molecular Physiology, and Medicine, Division of Gastroenterology, Hepatology and Nutrition, Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, PA, USA
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32
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Pintacuda G, Martín JM, Eggan KC. Mind the translational gap: using iPS cell models to bridge from genetic discoveries to perturbed pathways and therapeutic targets. Mol Autism 2021; 12:10. [PMID: 33557935 PMCID: PMC7869517 DOI: 10.1186/s13229-021-00417-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a group of neurodevelopmental disorders characterized by impaired social interactions as well as the presentation of restrictive and repetitive behaviors. ASD is highly heritable but genetically heterogenous with both common and rare genetic variants collaborating to predispose individuals to the disorder. In this review, we synthesize recent efforts to develop human induced pluripotent stem cell (iPSC)-derived models of ASD-related phenotypes. We firstly address concerns regarding the relevance and validity of available neuronal iPSC-derived models. We then critically evaluate the robustness of various differentiation and cell culture protocols used for producing cell types of relevance to ASD. By exploring iPSC models of ASD reported thus far, we examine to what extent cellular and neuronal phenotypes with potential relevance to ASD can be linked to genetic variants found to underlie it. Lastly, we outline promising strategies by which iPSC technology can both enhance the power of genetic studies to identify ASD risk factors and nominate pathways that are disrupted across groups of ASD patients that might serve as common points for therapeutic intervention.
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Affiliation(s)
- Greta Pintacuda
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Jacqueline M Martín
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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33
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Canals I, Ahlenius H. CRISPR/Cas9 Genome Engineering in Human Pluripotent Stem Cells for Modeling of Neurological Disorders. Methods Mol Biol 2021; 2352:237-251. [PMID: 34324191 DOI: 10.1007/978-1-0716-1601-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Recent advances in genome editing have brought new hopes for personalized and precision medicine but have also dramatically facilitated disease modeling studies. Combined with reprogramming approaches, stem cells and differentiation toward neural lineages, genome engineering holds great potential for regenerative approaches and to model neurological disorders. The use of patient-specific induced pluripotent stem cells combined with neural differentiation allows studying the effect of specific mutations in different brain cells. New genome editing tools such as CRISPR/Cas9 represent a step further by facilitating the introduction or correction of specific mutations within the same cell line, thus eliminating variability due to differences in the genetic background. Here, we present a step-by-step protocol from design to generation of human pluripotent stem cell lines with specific mutations introduced or corrected with CRISPR/Cas9 gene editing that can be used in combination with transcription factor-based protocols to dissect underlying mechanisms of neurological disorders.
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Affiliation(s)
- Isaac Canals
- Stem Cells, Aging and Neurodegeneration group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Henrik Ahlenius
- Stem Cells, Aging and Neurodegeneration group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurology, Lund Stem Cell Center, Lund University, Lund, Sweden.
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34
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Experimental Models to Study Autism Spectrum Disorders: hiPSCs, Rodents and Zebrafish. Genes (Basel) 2020; 11:genes11111376. [PMID: 33233737 PMCID: PMC7699923 DOI: 10.3390/genes11111376] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorders (ASD) affect around 1.5% of the global population, which manifest alterations in communication and socialization, as well as repetitive behaviors or restricted interests. ASD is a complex disorder with known environmental and genetic contributors; however, ASD etiology is far from being clear. In the past decades, many efforts have been put into developing new models to study ASD, both in vitro and in vivo. These models have a lot of potential to help to validate some of the previously associated risk factors to the development of the disorder, and to test new potential therapies that help to alleviate ASD symptoms. The present review is focused on the recent advances towards the generation of models for the study of ASD, which would be a useful tool to decipher the bases of the disorder, as well as to conduct drug screenings that hopefully lead to the identification of useful compounds to help patients deal with the symptoms of ASD.
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35
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Matos MR, Ho SM, Schrode N, Brennand KJ. Integration of CRISPR-engineering and hiPSC-based models of psychiatric genomics. Mol Cell Neurosci 2020; 107:103532. [PMID: 32712198 PMCID: PMC7484226 DOI: 10.1016/j.mcn.2020.103532] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Neuropsychiatric disorders are highly heritable polygenic disorders arising from the complex interplay of highly penetrant rare variants and common variants of small effect. There is a large index of comorbidity and shared genetic risk between disorders, reflecting the pleiotropy of individual variants as well as predicted downstream pathway-level convergence. Importantly, the mechanism(s) through which psychiatric disease-associated variants interact to contribute to disease risk remains unknown. Human induced pluripotent stem cell (hiPSC)-based models are increasingly useful for the systematic study of the complex genetics associated with brain diseases, particularly when combined with CRISPR-mediated genomic engineering, which together facilitate isogenic comparisons of defined neuronal cell types. In this review, we discuss the latest CRISPR technologies and consider how they can be successfully applied to the functional characterization of the growing list genetic variants linked to psychiatric disease.
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Affiliation(s)
- Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Seok-Man Ho
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Nadine Schrode
- Department of Genetics and Genomics, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America.
| | - Kristen J Brennand
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Genetics and Genomics, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America.
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36
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Eintracht J, Toms M, Moosajee M. The Use of Induced Pluripotent Stem Cells as a Model for Developmental Eye Disorders. Front Cell Neurosci 2020; 14:265. [PMID: 32973457 PMCID: PMC7468397 DOI: 10.3389/fncel.2020.00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Approximately one-third of childhood blindness is attributed to developmental eye disorders, of which 80% have a genetic cause. Eye morphogenesis is tightly regulated by a highly conserved network of transcription factors when disrupted by genetic mutations can result in severe ocular malformation. Human-induced pluripotent stem cells (hiPSCs) are an attractive tool to study early eye development as they are more physiologically relevant than animal models, can be patient-specific and their use does not elicit the ethical concerns associated with human embryonic stem cells. The generation of self-organizing hiPSC-derived optic cups is a major advancement to understanding mechanisms of ocular development and disease. Their development in vitro has been found to mirror that of the human eye and these early organoids have been used to effectively model microphthalmia caused by a VSX2 variant. hiPSC-derived optic cups, retina, and cornea organoids are powerful tools for future modeling of disease phenotypes and will enable a greater understanding of the pathophysiology of many other developmental eye disorders. These models will also provide an effective platform for identifying molecular therapeutic targets and for future clinical applications.
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Affiliation(s)
| | - Maria Toms
- UCL Institute of Ophthalmology, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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37
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López-Tobón A, Trattaro S, Testa G. The sociability spectrum: evidence from reciprocal genetic copy number variations. Mol Autism 2020; 11:50. [PMID: 32546261 PMCID: PMC7298749 DOI: 10.1186/s13229-020-00347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/11/2020] [Indexed: 02/14/2023] Open
Abstract
Sociability entails some of the most complex behaviors processed by the central nervous system. It includes the detection, integration, and interpretation of social cues and elaboration of context-specific responses that are quintessentially species-specific. There is an ever-growing accumulation of molecular associations to autism spectrum disorders (ASD), from causative genes to endophenotypes across multiple functional layers; these however, have rarely been put in context with the opposite manifestation featured in hypersociability syndromes. Genetic copy number variations (CNVs) allow to investigate the relationships between gene dosage and its corresponding phenotypes. In particular, CNVs of the 7q11.23 locus, which manifest diametrically opposite social behaviors, offer a privileged window to look into the molecular substrates underlying the developmental trajectories of the social brain. As by definition sociability is studied in humans postnatally, the developmental fluctuations causing social impairments have thus far remained a black box. Here, we review key evidence of molecular players involved at both ends of the sociability spectrum, focusing on genetic and functional associations of neuroendocrine regulators and synaptic transmission pathways. We then proceed to propose the existence of a molecular axis centered around the paradigmatic dosage imbalances at the 7q11.23 locus, regulating networks responsible for the development of social behavior in humans and highlight the key role that neurodevelopmental models from reprogrammed pluripotent cells will play for its understanding.
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Affiliation(s)
- Alejandro López-Tobón
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Sebastiano Trattaro
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
- Human Technopole, Via Cristina Belgioioso 171, Milan, Italy.
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Drakulic D, Djurovic S, Syed YA, Trattaro S, Caporale N, Falk A, Ofir R, Heine VM, Chawner SJRA, Rodriguez-Moreno A, van den Bree MBM, Testa G, Petrakis S, Harwood AJ. Copy number variants (CNVs): a powerful tool for iPSC-based modelling of ASD. Mol Autism 2020; 11:42. [PMID: 32487215 PMCID: PMC7268297 DOI: 10.1186/s13229-020-00343-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Patients diagnosed with chromosome microdeletions or duplications, known as copy number variants (CNVs), present a unique opportunity to investigate the relationship between patient genotype and cell phenotype. CNVs have high genetic penetrance and give a good correlation between gene locus and patient clinical phenotype. This is especially effective for the study of patients with neurodevelopmental disorders (NDD), including those falling within the autism spectrum disorders (ASD). A key question is whether this correlation between genetics and clinical presentation at the level of the patient can be translated to the cell phenotypes arising from the neurodevelopment of patient induced pluripotent stem cells (iPSCs).Here, we examine how iPSCs derived from ASD patients with an associated CNV inform our understanding of the genetic and biological mechanisms underlying the aetiology of ASD. We consider selection of genetically characterised patient iPSCs; use of appropriate control lines; aspects of human neurocellular biology that can capture in vitro the patient clinical phenotype; and current limitations of patient iPSC-based studies. Finally, we consider how future research may be enhanced to maximise the utility of CNV patients for research of pathological mechanisms or therapeutic targets.
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Affiliation(s)
- Danijela Drakulic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, 152, Serbia
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, 5007, Bergen, Norway
| | - Yasir Ahmed Syed
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Sebastiano Trattaro
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Nicolò Caporale
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Rivka Ofir
- BGU-iPSC Core Facility, The Regenerative Medicine & Stem Cell (RMSC) Research Center, Ben Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Vivi M Heine
- Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Child and Youth Psychiatry, Emma Children's Hospital, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Samuel J R A Chawner
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Antonio Rodriguez-Moreno
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Ctra. de Utrera, Km 1, 41013, Seville, Spain
| | - Marianne B M van den Bree
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, 20146, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece.
| | - Adrian J Harwood
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK.
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The early overgrowth theory of autism spectrum disorder: Insight into convergent mechanisms from valproic acid exposure and translational models. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020. [PMID: 32711813 DOI: 10.1016/bs.pmbts.2020.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The development of new approaches for the clinical management of autism spectrum disorder (ASD) can only be realized through a better understanding of the neurobiological changes associated with ASD. One strategy for gaining deeper insight into the neurobiological mechanisms associated with ASD is to identify converging pathogenic processes associated with human idiopathic clinicopathology that are conserved in translational models of ASD. In this chapter, we first present the early overgrowth theory of ASD. Second, we introduce valproic acid (VPA), one of the most robust and well-known environmental risk factors associated with ASD, and we summarize the rapidly growing body of animal research literature using VPA as an ASD translational model. Lastly, we will detail the mechanisms of action of VPA and its impact on functional neural systems, as well as discuss future research directions that could have a lasting impact on the field.
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Ross PJ, Mok RSF, Smith BS, Rodrigues DC, Mufteev M, Scherer SW, Ellis J. Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells. Mol Autism 2020; 11:33. [PMID: 32398033 PMCID: PMC7218542 DOI: 10.1186/s13229-020-00333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent stem cells (iPSCs) enable the production of personalized neurons that are genetically matched to people with ASD and can therefore be used to directly test the effects of genomic variation on neuronal gene expression, synapse function, and connectivity. The combined use of human pluripotent stem cells with genome editing to introduce or correct specific variants has proved to be a powerful approach for exploring the functional consequences of ASD-associated variants in protein-coding genes and, more recently, long non-coding RNAs (lncRNAs). Here, we review recent studies that implicate lncRNAs, other non-coding mutations, and regulatory variants in ASD susceptibility. We also discuss experimental design considerations for using iPSCs and genome editing to study the role of the non-protein-coding genome in ASD.
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Affiliation(s)
- P Joel Ross
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Rebecca S F Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brandon S Smith
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Culotta L, Penzes P. Exploring the mechanisms underlying excitation/inhibition imbalance in human iPSC-derived models of ASD. Mol Autism 2020; 11:32. [PMID: 32393347 PMCID: PMC7216514 DOI: 10.1186/s13229-020-00339-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorder (ASD) is a range of neurodevelopmental disorders characterized by impaired social interaction and communication, and repetitive or restricted behaviors. ASD subjects exhibit complex genetic and clinical heterogeneity, thus hindering the discovery of pathophysiological mechanisms. Considering that several ASD-risk genes encode proteins involved in the regulation of synaptic plasticity, neuronal excitability, and neuronal connectivity, one hypothesis that has emerged is that ASD arises from a disruption of the neuronal network activity due to perturbation of the synaptic excitation and inhibition (E/I) balance. The development of induced pluripotent stem cell (iPSC) technology and recent advances in neuronal differentiation techniques provide a unique opportunity to model complex neuronal connectivity and to test the E/I hypothesis of ASD in human-based models. Here, we aim to review the latest advances in studying the different cellular and molecular mechanisms contributing to E/I balance using iPSC-based in vitro models of ASD.
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Affiliation(s)
- Lorenza Culotta
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL, USA
| | - Peter Penzes
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL, USA.
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Rees E, Owen MJ. Translating insights from neuropsychiatric genetics and genomics for precision psychiatry. Genome Med 2020; 12:43. [PMID: 32349784 PMCID: PMC7189552 DOI: 10.1186/s13073-020-00734-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/03/2020] [Indexed: 12/30/2022] Open
Abstract
The primary aim of precision medicine is to tailor healthcare more closely to the needs of individual patients. This requires progress in two areas: the development of more precise treatments and the ability to identify patients or groups of patients in the clinic for whom such treatments are likely to be the most effective. There is widespread optimism that advances in genomics will facilitate both of these endeavors. It can be argued that of all medical specialties psychiatry has most to gain in these respects, given its current reliance on syndromic diagnoses, the minimal foundation of existing mechanistic knowledge, and the substantial heritability of psychiatric phenotypes. Here, we review recent advances in psychiatric genomics and assess the likely impact of these findings on attempts to develop precision psychiatry. Emerging findings indicate a high degree of polygenicity and that genetic risk maps poorly onto the diagnostic categories used in the clinic. The highly polygenic and pleiotropic nature of psychiatric genetics will impact attempts to use genomic data for prediction and risk stratification, and also poses substantial challenges for conventional approaches to gaining biological insights from genetic findings. While there are many challenges to overcome, genomics is building an empirical platform upon which psychiatry can now progress towards better understanding of disease mechanisms, better treatments, and better ways of targeting treatments to the patients most likely to benefit, thus paving the way for precision psychiatry.
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Affiliation(s)
- Elliott Rees
- grid.5600.30000 0001 0807 5670MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute and Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
| | - Michael J. Owen
- grid.5600.30000 0001 0807 5670MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute and Division of Psychological Medicine and Clinical Neuroscience, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ UK
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Abstract
PURPOSE OF REVIEW We review the ways in which stem cells are used in psychiatric disease research, including the related advances in gene editing and directed cell differentiation. RECENT FINDINGS The recent development of induced pluripotent stem cell (iPSC) technologies has created new possibilities for the study of psychiatric disease. iPSCs can be derived from patients or controls and differentiated to an array of neuronal and non-neuronal cell types. Their genomes can be edited as desired, and they can be assessed for a variety of phenotypes. This makes them especially interesting for studying genetic variation, which is particularly useful today now that our knowledge on the genetics of psychiatric disease is quickly expanding. The recent advances in cell engineering have led to powerful new methods for studying psychiatric illness including schizophrenia, bipolar disorder, and autism. There is a wide array of possible applications as illustrated by the many examples from the literature, most of which are cited here.
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Affiliation(s)
- Debamitra Das
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyra Feuer
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marah Wahbeh
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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44
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Gordon A, Geschwind DH. Human in vitro models for understanding mechanisms of autism spectrum disorder. Mol Autism 2020; 11:26. [PMID: 32299488 PMCID: PMC7164291 DOI: 10.1186/s13229-020-00332-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.
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Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Kinnear C, Agrawal R, Loo C, Pahnke A, Rodrigues DC, Thompson T, Akinrinade O, Ahadian S, Keeley F, Radisic M, Mital S, Ellis J. Everolimus Rescues the Phenotype of Elastin Insufficiency in Patient Induced Pluripotent Stem Cell-Derived Vascular Smooth Muscle Cells. Arterioscler Thromb Vasc Biol 2020; 40:1325-1339. [PMID: 32212852 PMCID: PMC7176340 DOI: 10.1161/atvbaha.119.313936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Supplemental Digital Content is available in the text. Objective: Elastin gene deletion or mutation leads to arterial stenoses due to vascular smooth muscle cell (SMC) proliferation. Human induced pluripotent stem cells–derived SMCs can model the elastin insufficiency phenotype in vitro but show only partial rescue with rapamycin. Our objective was to identify drug candidates with superior efficacy in rescuing the SMC phenotype in elastin insufficiency patients. Approach and Results: SMCs generated from induced pluripotent stem cells from 5 elastin insufficiency patients with severe recurrent vascular stenoses (3 Williams syndrome and 2 elastin mutations) were phenotypically immature, hyperproliferative, poorly responsive to endothelin, and exerted reduced tension in 3-dimensional smooth muscle biowires. Elastin mRNA and protein were reduced in SMCs from patients compared to healthy control SMCs. Fourteen drug candidates were tested on patient SMCs. Of the mammalian target of rapamycin inhibitors studied, everolimus restored differentiation, rescued proliferation, and improved endothelin-induced calcium flux in all patient SMCs except one Williams syndrome. Of the calcium channel blockers, verapamil increased SMC differentiation and reduced proliferation in Williams syndrome patient cells but not in elastin mutation patients and had no effect on endothelin response. Combination treatment with everolimus and verapamil was not superior to everolimus alone. Other drug candidates had limited efficacy. Conclusions: Everolimus caused the most consistent improvement in SMC differentiation, proliferation and in SMC function in patients with both syndromic and nonsyndromic elastin insufficiency, and offers the best candidate for drug repurposing for treatment of elastin insufficiency associated vasculopathy.
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Affiliation(s)
- Caroline Kinnear
- From the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.K., R.A., O.A., S.M.)
| | - Rahul Agrawal
- From the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.K., R.A., O.A., S.M.)
| | - Caitlin Loo
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.L., D.C.R., T.T., J.E.).,Department of Molecular Genetics (C.L., J.E.), University of Toronto, Ontario, Canada
| | - Aric Pahnke
- Institute of Biomaterials and Biomedical Engineering (A.P., S.A., M.R.), University of Toronto, Ontario, Canada.,Department of Chemical Engineering and Applied Chemistry (A.P., S.A., M.R.), University of Toronto, Ontario, Canada
| | - Deivid Carvalho Rodrigues
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.L., D.C.R., T.T., J.E.)
| | - Tadeo Thompson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.L., D.C.R., T.T., J.E.)
| | - Oyediran Akinrinade
- From the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.K., R.A., O.A., S.M.)
| | - Samad Ahadian
- Institute of Biomaterials and Biomedical Engineering (A.P., S.A., M.R.), University of Toronto, Ontario, Canada.,Department of Chemical Engineering and Applied Chemistry (A.P., S.A., M.R.), University of Toronto, Ontario, Canada
| | - Fred Keeley
- Department of Biochemistry (F.K.), University of Toronto, Ontario, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada (F.K.)
| | - Milica Radisic
- Institute of Biomaterials and Biomedical Engineering (A.P., S.A., M.R.), University of Toronto, Ontario, Canada.,Department of Chemical Engineering and Applied Chemistry (A.P., S.A., M.R.), University of Toronto, Ontario, Canada
| | - Seema Mital
- From the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.K., R.A., O.A., S.M.).,Department of Pediatrics, The Hospital for Sick Children (S.M.), University of Toronto, Ontario, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada (C.L., D.C.R., T.T., J.E.).,Department of Molecular Genetics (C.L., J.E.), University of Toronto, Ontario, Canada
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Neurofibromatosis Type 1 Implicates Ras Pathways in the Genetic Architecture of Neurodevelopmental Disorders. Behav Genet 2020; 50:191-202. [DOI: 10.1007/s10519-020-09991-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 01/04/2020] [Indexed: 01/12/2023]
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Ross PJ, Zhang WB, Mok RS, Zaslavsky K, Deneault E, D’Abate L, Rodrigues DC, Yuen RK, Faheem M, Mufteev M, Piekna A, Wei W, Pasceri P, Landa RJ, Nagy A, Varga B, Salter MW, Scherer SW, Ellis J. Synaptic Dysfunction in Human Neurons With Autism-Associated Deletions in PTCHD1-AS. Biol Psychiatry 2020; 87:139-149. [PMID: 31540669 PMCID: PMC6948145 DOI: 10.1016/j.biopsych.2019.07.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 06/23/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The Xp22.11 locus that encompasses PTCHD1, DDX53, and the long noncoding RNA PTCHD1-AS is frequently disrupted in male subjects with autism spectrum disorder (ASD), but the functional consequences of these genetic risk factors for ASD are unknown. METHODS To evaluate the functional consequences of PTCHD1 locus deletions, we generated induced pluripotent stem cells (iPSCs) from unaffected control subjects and 3 subjects with ASD with microdeletions affecting PTCHD1-AS/PTCHD1, PTCHD1-AS/DDX53, or PTCHD1-AS alone. Function of iPSC-derived cortical neurons was assessed using molecular approaches and electrophysiology. We also compiled novel and known genetic variants of the PTCHD1 locus to explore the roles of PTCHD1 and PTCHD1-AS in genetic risk for ASD and other neurodevelopmental disorders. Finally, genome editing was used to explore the functional consequences of deleting a single conserved exon of PTCHD1-AS. RESULTS iPSC-derived neurons from subjects with ASD exhibited reduced miniature excitatory postsynaptic current frequency and N-methyl-D-aspartate receptor hypofunction. We found that 35 ASD-associated deletions mapping to the PTCHD1 locus disrupted exons of PTCHD1-AS. We also found a novel ASD-associated deletion of PTCHD1-AS exon 3 and showed that exon 3 loss altered PTCHD1-AS splicing without affecting expression of the neighboring PTCHD1 coding gene. Finally, targeted disruption of PTCHD1-AS exon 3 recapitulated diminished miniature excitatory postsynaptic current frequency, supporting a role for the long noncoding RNA in the etiology of ASD. CONCLUSIONS Our genetic findings provide strong evidence that PTCHD1-AS deletions are risk factors for ASD, and human iPSC-derived neurons implicate these deletions in the neurophysiology of excitatory synapses and in ASD-associated synaptic impairment.
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Affiliation(s)
- P. Joel Ross
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,These authors contributed equally to this work,Present address: Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Wen-Bo Zhang
- Neuroscience & Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada,These authors contributed equally to this work
| | - Rebecca S.F. Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kirill Zaslavsky
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric Deneault
- Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lia D’Abate
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Deivid C. Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K.C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Muhammad Faheem
- Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Pasceri
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebecca J. Landa
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andras Nagy
- Lunenfeld-Tenenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada,Institute of Medical Science and Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Balazs Varga
- Lunenfeld-Tenenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada,Present address: Wellcome Trust MRC Stem Cell Institute, University of Cambridge, Cambridge UK
| | - Michael W. Salter
- Neuroscience & Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Stephen W. Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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McDiarmid TA, Belmadani M, Liang J, Meili F, Mathews EA, Mullen GP, Hendi A, Wong WR, Rand JB, Mizumoto K, Haas K, Pavlidis P, Rankin CH. Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation. Proc Natl Acad Sci U S A 2020; 117:656-667. [PMID: 31754030 PMCID: PMC6968627 DOI: 10.1073/pnas.1912049116] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major challenge facing the genetics of autism spectrum disorders (ASDs) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system, we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 135 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8•chd-7 and NLGN3•nlg-1 that underlie mechanosensory hyperresponsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of conserved ASD-associated neuroligin variants revealed varied partial loss of function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin-inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers in vivo variant functional assays, and potential therapeutic targets for ASD.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel Belmadani
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Fabian Meili
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Eleanor A Mathews
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Gregory P Mullen
- Biology Program, Oklahoma City University, Oklahoma City, OK 73106
| | - Ardalan Hendi
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - James B Rand
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kurt Haas
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Paul Pavlidis
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada;
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Avazzadeh S, McDonagh K, Reilly J, Wang Y, Boomkamp SD, McInerney V, Krawczyk J, Fitzgerald J, Feerick N, O'Sullivan M, Jalali A, Forman EB, Lynch SA, Ennis S, Cosemans N, Peeters H, Dockery P, O'Brien T, Quinlan LR, Gallagher L, Shen S. Increased Ca 2+ signaling in NRXN1α +/- neurons derived from ASD induced pluripotent stem cells. Mol Autism 2019; 10:52. [PMID: 31893021 PMCID: PMC6937972 DOI: 10.1186/s13229-019-0303-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/05/2019] [Indexed: 12/28/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a high co-morbidity of epilepsy and associated with hundreds of rare risk factors. NRXN1 deletion is among the commonest rare genetic factors shared by ASD, schizophrenia, intellectual disability, epilepsy, and developmental delay. However, how NRXN1 deletions lead to different clinical symptoms is unknown. Patient-derived cells are essential to investigate the functional consequences of NRXN1 lesions to human neurons in different diseases. Methods Skin biopsies were donated by five healthy donors and three ASD patients carrying NRXN1α+/− deletions. Seven control and six NRXN1α+/− iPSC lines were derived and differentiated into day 100 cortical excitatory neurons using dual SMAD inhibition. Calcium (Ca2+) imaging was performed using Fluo4-AM, and the properties of Ca2+ transients were compared between two groups of neurons. Transcriptome analysis was carried out to undercover molecular pathways associated with NRXN1α+/− neurons. Results NRXN1α+/− neurons were found to display altered calcium dynamics, with significantly increased frequency, duration, and amplitude of Ca2+ transients. Whole genome RNA sequencing also revealed altered ion transport and transporter activity, with upregulated voltage-gated calcium channels as one of the most significant pathways in NRXN1α+/− neurons identified by STRING and GSEA analyses. Conclusions This is the first report to show that human NRXN1α+/− neurons derived from ASD patients’ iPSCs present novel phenotypes of upregulated VGCCs and increased Ca2+ transients, which may facilitate the development of drug screening assays for the treatment of ASD.
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Affiliation(s)
- Sahar Avazzadeh
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
| | - Katya McDonagh
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
| | - Jamie Reilly
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
| | - Yanqin Wang
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland.,2Department of Physiology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Stephanie D Boomkamp
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
| | - Veronica McInerney
- 3HRB Clinical Research Facility, National University of Ireland (NUI), Galway, Ireland
| | - Janusz Krawczyk
- 4Department of Haematology, Galway University Hospital, Galway, Ireland
| | | | - Niamh Feerick
- 5School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Amirhossein Jalali
- 6School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eva B Forman
- 7Children's University Hospital, Temple Street, Dublin, Ireland
| | - Sally A Lynch
- Department of Clinical Genetics, OLCHC, Dublin 12, Ireland.,9Children's University Hospital, Temple St, Dublin, Ireland.,10Academic Center on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Sean Ennis
- 11UCD Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Nele Cosemans
- 12Centre for Human Genetics, University Hospital Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Hilde Peeters
- 10Academic Center on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Peter Dockery
- 13Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | - Timothy O'Brien
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
| | - Leo R Quinlan
- 14Physiology and Human Movement Laboratory, CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | | | - Sanbing Shen
- 1Regenerative Medicine Institute, School of Medicine, Biomedical Science Building BMS-1021, National University of Ireland Galway, Dangan, Upper Newcastle, Galway, Ireland
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50
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Genova E, Cavion F, Lucafò M, Leo LD, Pelin M, Stocco G, Decorti G. Induced pluripotent stem cells for therapy personalization in pediatric patients: Focus on drug-induced adverse events. World J Stem Cells 2019; 11:1020-1044. [PMID: 31875867 PMCID: PMC6904863 DOI: 10.4252/wjsc.v11.i12.1020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 09/05/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023] Open
Abstract
Adverse drug reactions (ADRs) are major clinical problems, particularly in special populations such as pediatric patients. Indeed, ADRs may be caused by a plethora of different drugs leading, in some cases, to hospitalization, disability or even death. In addition, pediatric patients may respond differently to drugs with respect to adults and may be prone to developing different kinds of ADRs, leading, in some cases, to more severe consequences. To improve the comprehension, and thus the prevention, of ADRs, the set-up of sensitive and personalized assays is urgently needed. Important progress is represented by the possibility of setting up groundbreaking patient-specific assays. This goal has been powerfully achieved using induced pluripotent stem cells (iPSCs). Due to their genetic and physiological species-specific differences and their ability to be differentiated ideally into all tissues of the human body, this model may be accurate in predicting drug toxicity, especially when this toxicity is related to individual genetic differences. This review is an up-to-date summary of the employment of iPSCs as a model to study ADRs, with particular attention to drugs used in the pediatric field. We especially focused on the intestinal, hepatic, pancreatic, renal, cardiac, and neuronal levels, also discussing progress in organoids creation. The latter are three-dimensional in vitro culture systems derived from pluripotent or adult stem cells simulating the architecture and functionality of native organs such as the intestine, liver, pancreas, kidney, heart, and brain. Based on the existing knowledge, these models are powerful and promising tools in multiple clinical applications including toxicity screening, disease modeling, personalized and regenerative medicine.
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Affiliation(s)
- Elena Genova
- PhD School in Reproduction and Development Sciences, University of Trieste, Trieste 34127, Italy
| | - Federica Cavion
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Marianna Lucafò
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste 34137, Italy
| | - Luigina De Leo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste 34137, Italy
| | - Marco Pelin
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy.
| | - Giuliana Decorti
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste 34137, Italy
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