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Herrera ML, Paraíso-Luna J, Bustos-Martínez I, Barco Á. Targeting epigenetic dysregulation in autism spectrum disorders. Trends Mol Med 2024:S1471-4914(24)00162-X. [PMID: 38971705 DOI: 10.1016/j.molmed.2024.06.004] [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: 03/10/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
Autism spectrum disorders (ASD) comprise a range of neurodevelopmental pathologies characterized by deficits in social interaction and repetitive behaviors, collectively affecting almost 1% of the worldwide population. Deciphering the etiology of ASD has proven challenging due to the intricate interplay of genetic and environmental factors and the variety of molecular pathways affected. Epigenomic alterations have emerged as key players in ASD etiology. Their research has led to the identification of biomarkers for diagnosis and pinpointed specific gene targets for therapeutic interventions. This review examines the role of epigenetic alterations, resulting from both genetic and environmental influences, as a central causative factor in ASD, delving into its contribution to pathogenesis and treatment strategies.
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Affiliation(s)
- Macarena L Herrera
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Isabel Bustos-Martínez
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain.
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Mostafavi Abdolmaleky H, Alam R, Nohesara S, Deth RC, Zhou JR. iPSC-Derived Astrocytes and Neurons Replicate Brain Gene Expression, Epigenetic, Cell Morphology and Connectivity Alterations Found in Autism. Cells 2024; 13:1095. [PMID: 38994948 PMCID: PMC11240613 DOI: 10.3390/cells13131095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Excessive inflammatory reactions and oxidative stress are well-recognized molecular findings in autism and these processes can affect or be affected by the epigenetic landscape. Nonetheless, adequate therapeutics are unavailable, as patient-specific brain molecular markers for individualized therapies remain challenging. METHODS We used iPSC-derived neurons and astrocytes of patients with autism vs. controls (5/group) to examine whether they replicate the postmortem brain expression/epigenetic alterations of autism. Additionally, DNA methylation of 10 postmortem brain samples (5/group) was analyzed for genes affected in PSC-derived cells. RESULTS We found hyperexpression of TGFB1, TGFB2, IL6 and IFI16 and decreased expression of HAP1, SIRT1, NURR1, RELN, GPX1, EN2, SLC1A2 and SLC1A3 in the astrocytes of patients with autism, along with DNA hypomethylation of TGFB2, IL6, TNFA and EN2 gene promoters and a decrease in HAP1 promoter 5-hydroxymethylation in the astrocytes of patients with autism. In neurons, HAP1 and IL6 expression trended alike. While HAP1 promoter was hypermethylated in neurons, IFI16 and SLC1A3 promoters were hypomethylated and TGFB2 exhibited increased promoter 5-hydroxymethlation. We also found a reduction in neuronal arborization, spine size, growth rate, and migration, but increased astrocyte size and a reduced growth rate in autism. In postmortem brain samples, we found DNA hypomethylation of TGFB2 and IFI16 promoter regions, but DNA hypermethylation of HAP1 and SLC1A2 promoters in autism. CONCLUSION Autism-associated expression/epigenetic alterations in iPSC-derived cells replicated those reported in the literature, making them appropriate surrogates to study disease pathogenesis or patient-specific therapeutics.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Reza Alam
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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3
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Chandrasekaran V, Wellens S, Bourguignon A, Djidrovski I, Fransen L, Ghosh S, Mazidi Z, Murphy C, Nunes C, Singh P, Zana M, Armstrong L, Dinnyés A, Grillari J, Grillari-Voglauer R, Leonard MO, Verfaillie C, Wilmes A, Zurich MG, Exner T, Jennings P, Culot M. Evaluation of the impact of iPSC differentiation protocols on transcriptomic signatures. Toxicol In Vitro 2024; 98:105826. [PMID: 38615723 DOI: 10.1016/j.tiv.2024.105826] [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: 03/26/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Human induced pluripotent stem cells (iPSC) have the potential to produce desired target cell types in vitro and allow for the high-throughput screening of drugs/chemicals at population level thereby minimising the cost of drug discovery and drug withdrawals after clinical trials. There is a substantial need for the characterisation of the iPSC derived models to better understand and utilise them for toxicological relevant applications. In our study, iPSC (SBAD2 or SBAD3 lines obtained from StemBANCC project) were differentiated towards toxicologically relevant cell types: alveolar macrophages, brain capillary endothelial cells, brain cells, endothelial cells, hepatocytes, lung airway epithelium, monocytes, podocytes and renal proximal tubular cells. A targeted transcriptomic approach was employed to understand the effects of differentiation protocols on these cell types. Pearson correlation and principal component analysis (PCA) separated most of the intended target cell types and undifferentiated iPSC models as distinct groups with a high correlation among replicates from the same model. Based on PCA, the intended target cell types could also be separated into the three germ layer groups (ectoderm, endoderm and mesoderm). Differential expression analysis (DESeq2) presented the upregulated genes in each intended target cell types that allowed the evaluation of the differentiation to certain degree and the selection of key differentiation markers. In conclusion, these data confirm the versatile use of iPSC differentiated cell types as standardizable and relevant model systems for in vitro toxicology.
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Affiliation(s)
- Vidya Chandrasekaran
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Sara Wellens
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Aurore Bourguignon
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Ivo Djidrovski
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Leonie Fransen
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Sreya Ghosh
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Zahra Mazidi
- Evercyte GmbH, Vienna, Austria; Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cormac Murphy
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Carolina Nunes
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - Pranika Singh
- Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | | | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - András Dinnyés
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Johannes Grillari
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | | | - Martin O Leonard
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Marie-Gabrielle Zurich
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | | | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands.
| | - Maxime Culot
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France.
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Henis M, Rücker T, Scharrenberg R, Richter M, Baltussen L, Hong S, Meka DP, Schwanke B, Neelagandan N, Daaboul D, Murtaza N, Krisp C, Harder S, Schlüter H, Kneussel M, Hermans-Borgmeyer I, de Wit J, Singh KK, Duncan KE, de Anda FC. The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation. SCIENCE ADVANCES 2024; 10:eadf7001. [PMID: 38608030 PMCID: PMC11014455 DOI: 10.1126/sciadv.adf7001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, genetics, and translation assays in cultured cells and mouse brain to reveal altered translation mediated by loss of the kinase TAOK2 in 16p11.2 deletion models. We show that TAOK2 associates with the translational machinery and functions as a translational brake by phosphorylating eukaryotic elongation factor 2 (eEF2). Previously, all signal-mediated regulation of translation elongation via eEF2 phosphorylation was believed to be mediated by a single kinase, eEF2K. However, we show that TAOK2 can directly phosphorylate eEF2 on the same regulatory site, but functions independently of eEF2K signaling. Collectively, our results reveal an eEF2K-independent signaling pathway for control of translation elongation and suggest altered translation as a molecular component in the etiology of some forms of ASD.
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Affiliation(s)
- Melad Henis
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, New Valley University, 72511 El-Kharga, Egypt
| | - Tabitha Rücker
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Robin Scharrenberg
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Melanie Richter
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Lucas Baltussen
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Shuai Hong
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Durga Praveen Meka
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Birgit Schwanke
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Nagammal Neelagandan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Danie Daaboul
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Nadeem Murtaza
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario L8S 4A9, Canada
| | - Christoph Krisp
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Sönke Harder
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Matthias Kneussel
- Institute of Neurogenetics, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Transgenic Service Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Karun K. Singh
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Faculty of Medicine, University of Toronto, Medical Sciences Building, 1 King's College Cir, Toronto, Ontario M5S 1 A8, Canada
| | - Kent E. Duncan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Froylan Calderón de Anda
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
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Li H, Cui J, Hu C, Li H, Luo X, Hao Y. Identification and Analysis of ZIC-Related Genes in Cerebellum of Autism Spectrum Disorders. Neuropsychiatr Dis Treat 2024; 20:325-339. [PMID: 38410689 PMCID: PMC10895985 DOI: 10.2147/ndt.s444138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
Objective Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with significant genetic heterogeneity. The ZIC gene family can regulate neurodevelopment, especially in the cerebellum, and has been implicated in ASD-like behaviors in mice. We performed bioinformatic analysis to identify the ZIC gene family in the ASD cerebellum. Methods We explored the roles of ZIC family genes in ASD by investigating (i) the association of ZIC genes with ASD risk genes from the Simons Foundation Autism Research Initiative (SFARI) database and ZIC genes in the brain regions of the Human Protein Atlas (HPA) database; (ii) co-expressed gene networks of genes positively and negatively correlated with ZIC1, ZIC2, and ZIC3, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and receiver operating characteristic (ROC) curve analysis of genes in these networks; and (iii) the relationship between ZIC1, ZIC2, ZIC3, and their related genes with cerebellar immune cells and stromal cells in ASD patients. Results (i) ZIC1, ZIC2, and ZIC3 were associated with neurodevelopmental disorders and risk genes related to ASD in the human cerebellum and (ii) ZIC1, ZIC2, and ZIC3 were highly expressed in the cerebellum, which may play a pathogenic role by affecting neuronal development and the cerebellar internal environment in patients with ASD, including immune cells, astrocytes, and endothelial cells. (iii) OLFM3, SLC27A4, GRB2, TMED1, NR2F1, and STRBP are closely related to ZIC1, ZIC2, and ZIC3 in ASD cerebellum and have good diagnostic accuracy. (iv) ASD mice in the maternal immune activation model demonstrated that Zic3 and Nr2f1 levels were decreased in the immune-activated cerebellum. Conclusion Our study supports the role of ZIC1, ZIC2, and ZIC3 in ASD pathogenesis and provides potential targets for early and accurate prediction of ASD.
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Affiliation(s)
- Heli Li
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jinru Cui
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Cong Hu
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Hao Li
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Yan Hao
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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Vacharasin JM, Ward JA, McCord MM, Cox K, Imitola J, Lizarraga SB. Neuroimmune mechanisms in autism etiology - untangling a complex problem using human cellular models. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae003. [PMID: 38665176 PMCID: PMC11044813 DOI: 10.1093/oons/kvae003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 04/28/2024]
Abstract
Autism spectrum disorder (ASD) affects 1 in 36 people and is more often diagnosed in males than in females. Core features of ASD are impaired social interactions, repetitive behaviors and deficits in verbal communication. ASD is a highly heterogeneous and heritable disorder, yet its underlying genetic causes account only for up to 80% of the cases. Hence, a subset of ASD cases could be influenced by environmental risk factors. Maternal immune activation (MIA) is a response to inflammation during pregnancy, which can lead to increased inflammatory signals to the fetus. Inflammatory signals can cross the placenta and blood brain barriers affecting fetal brain development. Epidemiological and animal studies suggest that MIA could contribute to ASD etiology. However, human mechanistic studies have been hindered by a lack of experimental systems that could replicate the impact of MIA during fetal development. Therefore, mechanisms altered by inflammation during human pre-natal brain development, and that could underlie ASD pathogenesis have been largely understudied. The advent of human cellular models with induced pluripotent stem cell (iPSC) and organoid technology is closing this gap in knowledge by providing both access to molecular manipulations and culturing capability of tissue that would be otherwise inaccessible. We present an overview of multiple levels of evidence from clinical, epidemiological, and cellular studies that provide a potential link between higher ASD risk and inflammation. More importantly, we discuss how stem cell-derived models may constitute an ideal experimental system to mechanistically interrogate the effect of inflammation during the early stages of brain development.
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Affiliation(s)
- Janay M Vacharasin
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
- Department of Biological Sciences, Francis Marion University, 4822 East Palmetto Street, Florence, S.C. 29506, USA
| | - Joseph A Ward
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
| | - Mikayla M McCord
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Kaitlin Cox
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Jaime Imitola
- Laboratory of Neural Stem Cells and Functional Neurogenetics, UConn Health, Departments of Neuroscience, Neurology, Genetics and Genome Sciences, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-5357, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
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7
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Bu Q, Dai Y, Zhang H, Li M, Liu H, Huang Y, Zeng A, Qin F, Jiang L, Wang L, Chen Y, Li H, Wang X, Zhao Y, Qin M, Zhao Y, Zhang N, Kuang W, Zhao Y, Cen X. Neurodevelopmental defects in human cortical organoids with N-acetylneuraminic acid synthase mutation. SCIENCE ADVANCES 2023; 9:eadf2772. [PMID: 38000033 PMCID: PMC10672180 DOI: 10.1126/sciadv.adf2772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Biallelic genetic variants in N-acetylneuraminic acid synthase (NANS), a critical enzyme in endogenous sialic acid biosynthesis, are clinically associated with neurodevelopmental disorders. However, the mechanism underlying the neuropathological consequences has remained elusive. Here, we found that NANS mutation resulted in the absence of both sialic acid and protein polysialylation in the cortical organoids and notably reduced the proliferation and expansion of neural progenitors. NANS mutation dysregulated neural migration and differentiation, disturbed synapse formation, and weakened neuronal activity. Single-cell RNA sequencing revealed that NANS loss of function markedly altered transcriptional programs involved in neuronal differentiation and ribosomal biogenesis in various neuronal cell types. Similarly, Nans heterozygous mice exhibited impaired cortical neurogenesis and neurobehavioral deficits. Collectively, our findings reveal a crucial role of NANS-mediated endogenous sialic acid biosynthesis in regulating multiple features of human cortical development, thus linking NANS mutation with its clinically relevant neurodevelopmental disorders.
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Affiliation(s)
- Qian Bu
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Molecular Toxicology Laboratory of Sichuan Provincial Education office, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yanping Dai
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Huaqin Zhang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Min Li
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haxiaoyu Liu
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yan Huang
- Molecular Toxicology Laboratory of Sichuan Provincial Education office, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Ailing Zeng
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Linhong Jiang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Liang Wang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yaxing Chen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongchun Li
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaojie Wang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yue Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Meng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ying Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ni Zhang
- Mental Health Center of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weihong Kuang
- Mental Health Center of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yinglan Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaobo Cen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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8
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Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. Conclusions We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
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Affiliation(s)
- Madison R Glass
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alvaro Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC
| | - Kazue Hashimoto-Torii
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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9
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Koesterich J, An JY, Inoue F, Sohota A, Ahituv N, Sanders SJ, Kreimer A. Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. Int J Mol Sci 2023; 24:3509. [PMID: 36834916 PMCID: PMC9959321 DOI: 10.3390/ijms24043509] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/13/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of autistic probands and neurotypical siblings to test the hypothesis that mutations in cases have a greater functional impact than those in controls. We leveraged massively parallel reporter assays (MPRAs) to detect transcriptional consequences of these variants in neural progenitor cells and identified 165 functionally high confidence de novo variants (HcDNVs). While these HcDNVs are enriched for markers of active transcription, disruption to transcription factor binding sites, and open chromatin, we did not identify differences in functional impact based on ASD diagnostic status.
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Affiliation(s)
- Justin Koesterich
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
- Department of Cell and Developmental Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Joon-Yong An
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neuroscience, University of California, San Francisco, CA 94143, USA
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul 02841, Republic of Korea
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Ajuni Sohota
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
| | - Stephan J. Sanders
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neuroscience, University of California, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94158, USA
- Institute for Developmental and Regenerative Medicine, Old Road Campus, Roosevelt Dr, Headington, Oxford OX3 7TY, UK
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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10
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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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11
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Karagyaur M, Primak A, Efimenko A, Skryabina M, Tkachuk V. The Power of Gene Technologies: 1001 Ways to Create a Cell Model. Cells 2022; 11:cells11203235. [PMID: 36291103 PMCID: PMC9599997 DOI: 10.3390/cells11203235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 12/04/2022] Open
Abstract
Modern society faces many biomedical challenges that require urgent solutions. Two of the most important include the elucidation of mechanisms of socially significant diseases and the development of prospective drug treatments for these diseases. Experimental cell models are a convenient tool for addressing many of these problems. The power of cell models is further enhanced when combined with gene technologies, which allows the examination of even more subtle changes within the structure of the genome and permits testing of proteins in a native environment. The list and possibilities of these recently emerging technologies are truly colossal, which requires a rethink of a number of approaches for obtaining experimental cell models. In this review, we analyze the possibilities and limitations of promising gene technologies for obtaining cell models, and also give recommendations on the development and creation of relevant models. In our opinion, this review will be useful for novice cell biologists, as it provides some reference points in the rapidly growing universe of gene and cell technologies.
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Affiliation(s)
- Maxim Karagyaur
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
- Correspondence:
| | - Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Mariya Skryabina
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Vsevolod Tkachuk
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
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12
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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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13
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Recent Developments in Autism Genetic Research: A Scientometric Review from 2018 to 2022. Genes (Basel) 2022; 13:genes13091646. [PMID: 36140813 PMCID: PMC9498399 DOI: 10.3390/genes13091646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Genetic research in Autism Spectrum Disorder (ASD) has progressed tremendously in recent decades. Dozens of genetic loci and hundreds of alterations in the genetic sequence, expression, epigenetic transformation, and interactions with other physiological and environmental systems have been found to increase the likelihood of developing ASD. There is therefore a need to represent this wide-ranging yet voluminous body of literature in a systematic manner so that this information can be synthesised and understood at a macro level. Therefore, this study made use of scientometric methods, particularly document co-citation analysis (DCA), to systematically review literature on ASD genetic research from 2018 to 2022. A total of 14,818 articles were extracted from Scopus and analyzed with CiteSpace. An optimized DCA analysis revealed that recent literature on ASD genetic research can be broadly organised into 12 major clusters representing various sub-topics. These clusters are briefly described in the manuscript and potential applications of this study are discussed.
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14
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Legault EM, Bouquety J, Drouin-Ouellet J. Disease Modeling of Neurodegenerative Disorders Using Direct Neural Reprogramming. Cell Reprogram 2022; 24:228-251. [PMID: 35749150 DOI: 10.1089/cell.2021.0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding the pathophysiology of CNS-associated neurological diseases has been hampered by the inaccessibility of patient brain tissue to perform live analyses at the molecular level. To this end, neural cells obtained by differentiation of patient-derived induced pluripotent stem cells (iPSCs) are considerably helpful, especially in the context of monogenic-based disorders. More recently, the use of direct reprogramming to convert somatic cells to neural cells has emerged as an alternative to iPSCs to generate neurons, astrocytes, and oligodendrocytes. This review focuses on the different studies that used direct neural reprogramming to study disease-associated phenotypes in the context of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis.
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Affiliation(s)
| | - Julie Bouquety
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada
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15
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Rare CACNA1H and RELN variants interact through mTORC1 pathway in oligogenic autism spectrum disorder. Transl Psychiatry 2022; 12:234. [PMID: 35668055 PMCID: PMC9170683 DOI: 10.1038/s41398-022-01997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Oligogenic inheritance of autism spectrum disorder (ASD) has been supported by several studies. However, little is known about how the risk variants interact and converge on causative neurobiological pathways. We identified in an ASD proband deleterious compound heterozygous missense variants in the Reelin (RELN) gene, and a de novo splicing variant in the Cav3.2 calcium channel (CACNA1H) gene. Here, by using iPSC-derived neural progenitor cells (NPCs) and a heterologous expression system, we show that the variant in Cav3.2 leads to increased calcium influx into cells, which overactivates mTORC1 pathway and, consequently, further exacerbates the impairment of Reelin signaling. Also, we show that Cav3.2/mTORC1 overactivation induces proliferation of NPCs and that both mutant Cav3.2 and Reelin cause abnormal migration of these cells. Finally, analysis of the sequencing data from two ASD cohorts-a Brazilian cohort of 861 samples, 291 with ASD; the MSSNG cohort of 11,181 samples, 5,102 with ASD-revealed that the co-occurrence of risk variants in both alleles of Reelin pathway genes and in one allele of calcium channel genes confer significant liability for ASD. Our results support the notion that genes with co-occurring deleterious variants tend to have interconnected pathways underlying oligogenic forms of ASD.
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16
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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Zhuang W, Liu H, He Z, Ju J, Gao Q, Shan Z, Lei L. miR-92a-2-5p Regulates the Proliferation and Differentiation of ASD-Derived Neural Progenitor Cells. Curr Issues Mol Biol 2022; 44:2431-2442. [PMID: 35735607 PMCID: PMC9222067 DOI: 10.3390/cimb44060166] [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: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with abnormal behavior. However, the pathogenesis of ASD remains to be clarified. It has been demonstrated that miRNAs are essential regulators of ASD. However, it is still unclear how miR-92a-2-5p acts on the developing brain and the cell types directly. In this study, we used neural progenitor cells (NPCs) derived from ASD-hiPSCs as well as from neurotypical controls to examine the effects of miR-92a-2-5p on ASD-NPCs proliferation and neuronal differentiation, and whether miR-92a-2-5p could interact with genetic risk factor, DLG3 for ASD. We observed that miR-92a-2-5p upregulated in ASD-NPCs results in decreased proliferation and neuronal differentiation. Inhibition of miR-92a-2-5p could promote proliferation and neuronal differentiation of ASD-NPCs. DLG3 was negatively regulated by miR-92a-2-5p in NPCs. Our results suggest that miR-92a-2-5p is a strong risk factor for ASD and potentially contributes to neuropsychiatric disorders.
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Affiliation(s)
| | | | | | | | | | | | - Lei Lei
- Correspondence: (Z.S.); (L.L.)
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18
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Neuroligins in neurodevelopmental conditions: how mouse models of de novo mutations can help us link synaptic function to social behavior. Neuronal Signal 2022; 6:NS20210030. [PMID: 35601025 PMCID: PMC9093077 DOI: 10.1042/ns20210030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Neurodevelopmental conditions (or neurodevelopmental disorders, NDDs) are highly heterogeneous with overlapping characteristics and shared genetic etiology. The large symptom variability and etiological heterogeneity have made it challenging to understand the biological mechanisms underpinning NDDs. To accommodate this individual variability, one approach is to move away from diagnostic criteria and focus on distinct dimensions with relevance to multiple NDDs. This domain approach is well suited to preclinical research, where genetically modified animal models can be used to link genetic variability to neurobiological mechanisms and behavioral traits. Genetic factors associated with NDDs can be grouped functionally into common biological pathways, with one prominent functional group being genes associated with the synapse. These include the neuroligins (Nlgns), a family of postsynaptic transmembrane proteins that are key modulators of synaptic function. Here, we review how research using Nlgn mouse models has provided insight into how synaptic proteins contribute to behavioral traits associated with NDDs. We focus on how mutations in different Nlgns affect social behaviors, as differences in social interaction and communication are a common feature of most NDDs. Importantly, mice carrying distinct mutations in Nlgns share some neurobiological and behavioral phenotypes with other synaptic gene mutations. Comparing the functional implications of mutations in multiple synaptic proteins is a first step towards identifying convergent neurobiological pathways in multiple brain regions and circuits.
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19
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Gomes AKS, Dantas RM, Yokota BY, Silva ALTE, Griesi-Oliveira K, Passos-Bueno MR, Sertié AL. Interleukin-17a Induces Neuronal Differentiation of Induced-Pluripotent Stem Cell-Derived Neural Progenitors From Autistic and Control Subjects. Front Neurosci 2022; 16:828646. [PMID: 35360153 PMCID: PMC8964130 DOI: 10.3389/fnins.2022.828646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Prenatal exposure to maternal immune activation (MIA) has been suggested to increase the probability of autism spectrum disorder (ASD). Recent evidence from animal studies indicates a key role for interleukin-17a (IL-17a) in promoting MIA-induced behavioral and brain abnormalities reminiscent of ASD. However, it is still unclear how IL-17a acts on the human developing brain and the cell types directly affected by IL-17a signaling. In this study, we used iPSC-derived neural progenitor cells (NPCs) from individuals with ASD of known and unknown genetic cause as well as from neurotypical controls to examine the effects of exogenous IL-17a on NPC proliferation, migration and neuronal differentiation, and whether IL-17a and genetic risk factors for ASD interact exacerbating alterations in NPC function. We observed that ASD and control NPCs endogenously express IL-17a receptor (IL17RA), and that IL-17a/IL17RA activation modulates downstream ERK1/2 and mTORC1 signaling pathways. Exogenous IL-17a did not induce abnormal proliferation and migration of ASD and control NPCs but, on the other hand, it significantly increased the expression of synaptic (Synaptophysin-1, Synapsin-1) and neuronal polarity (MAP2) proteins in these cells. Also, as we observed that ASD and control NPCs exhibited similar responses to exogenous IL-17a, it is possible that a more inflammatory environment containing other immune molecules besides IL-17a may be needed to trigger gene-environment interactions during neurodevelopment. In conclusion, our results suggest that exogenous IL-17a positively regulates the neuronal differentiation of human NPCs, which may disturb normal neuronal and synaptic development and contribute to MIA-related changes in brain function and behavior.
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Affiliation(s)
| | | | - Bruno Yukio Yokota
- Hospital Israelita Albert Einstein, Centro de Pesquisa Experimental, São Paulo, Brazil
| | | | | | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Células Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Andréa Laurato Sertié
- Hospital Israelita Albert Einstein, Centro de Pesquisa Experimental, São Paulo, Brazil
- *Correspondence: Andréa Laurato Sertié,
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Girardi ACDS, van Opstal Takahashi VN, Vadasz E, Costa CIS, Zachi EC, Vianna-Morgante AM, Passos-Bueno MR. FMR1 premutation in children with autism spectrum disorders: Should additional diagnostic tests be performed? Am J Med Genet A 2022; 188:1334-1337. [PMID: 34981645 DOI: 10.1002/ajmg.a.62624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/15/2021] [Accepted: 12/05/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Cristina De Sanctis Girardi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Vanessa Naomi van Opstal Takahashi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Estevão Vadasz
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Claudia Ismania Samogi Costa
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Cristina Zachi
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Psicologia Universidade de São Paulo, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Células-tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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21
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Mutations in trpγ, the homologue of TRPC6 autism candidate gene, causes autism-like behavioral deficits in Drosophila. Mol Psychiatry 2022; 27:3328-3342. [PMID: 35501408 PMCID: PMC9708601 DOI: 10.1038/s41380-022-01555-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 11/09/2022]
Abstract
Autism Spectrum Disorder (ASD) is characterized by impaired social communication, restricted interests, and repetitive and stereotyped behaviors. The TRPC6 (transient receptor potential channel 6) represents an ASD candidate gene under an oligogenic/multifactorial model based on the initial description and cellular characterization of an individual with ASD bearing a de novo heterozygous mutation disrupting TRPC6, together with the enrichment of disruptive TRPC6 variants in ASD cases as compared to controls. Here, we perform a clinical re-evaluation of the initial non-verbal patient, and also present eight newly reported individuals ascertained for ASD and bearing predicted loss-of-function mutations in TRPC6. In order to understand the consequences of mutations in TRPC6 on nervous system function, we used the fruit fly, Drosophila melanogaster, to show that null mutations in transient receptor gamma (trpγ; the fly gene most similar to TRPC6), cause a number of behavioral defects that mirror features seen in ASD patients, including deficits in social interactions (based on courtship behavior), impaired sleep homeostasis (without affecting the circadian control of sleep), hyperactivity in both young and old flies, and defects in learning and memory. Some defects, most notably in sleep, differed in severity between males and females and became normal with age. Interestingly, hyperforin, a TRPC6 agonist and the primary active component of the St. John's wort antidepressant, attenuated many of the deficits expressed by trpγ mutant flies. In summary, our results provide further evidence that the TRPC6 gene is a risk factor for ASD. In addition, they show that the behavioral defects caused by mutations in TRPC6 can be modeled in Drosophila, thereby establishing a paradigm to examine the impact of mutations in other candidate genes.
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22
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Knowles R, Dehorter N, Ellender T. From Progenitors to Progeny: Shaping Striatal Circuit Development and Function. J Neurosci 2021; 41:9483-9502. [PMID: 34789560 PMCID: PMC8612473 DOI: 10.1523/jneurosci.0620-21.2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding how neurons of the striatum are formed and integrate into complex synaptic circuits is essential to provide insight into striatal function in health and disease. In this review, we summarize our current understanding of the development of striatal neurons and associated circuits with a focus on their embryonic origin. Specifically, we address the role of distinct types of embryonic progenitors, found in the proliferative zones of the ganglionic eminences in the ventral telencephalon, in the generation of diverse striatal interneurons and projection neurons. Indeed, recent evidence would suggest that embryonic progenitor origin dictates key characteristics of postnatal cells, including their neurochemical content, their location within striatum, and their long-range synaptic inputs. We also integrate recent observations regarding embryonic progenitors in cortical and other regions and discuss how this might inform future research on the ganglionic eminences. Last, we examine how embryonic progenitor dysfunction can alter striatal formation, as exemplified in Huntington's disease and autism spectrum disorder, and how increased understanding of embryonic progenitors can have significant implications for future research directions and the development of improved therapeutic options.SIGNIFICANCE STATEMENT This review highlights recently defined novel roles for embryonic progenitor cells in shaping the functional properties of both projection neurons and interneurons of the striatum. It outlines the developmental mechanisms that guide neuronal development from progenitors in the embryonic ganglionic eminences to progeny in the striatum. Where questions remain open, we integrate observations from cortex and other regions to present possible avenues for future research. Last, we provide a progenitor-centric perspective onto both Huntington's disease and autism spectrum disorder. We suggest that future investigations and manipulations of embryonic progenitor cells in both research and clinical settings will likely require careful consideration of their great intrinsic diversity and neurogenic potential.
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Affiliation(s)
- Rhys Knowles
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Nathalie Dehorter
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Tommas Ellender
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
- Department of Biomedical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
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23
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Caracci MO, Avila ME, Espinoza-Cavieres FA, López HR, Ugarte GD, De Ferrari GV. Wnt/β-Catenin-Dependent Transcription in Autism Spectrum Disorders. Front Mol Neurosci 2021; 14:764756. [PMID: 34858139 PMCID: PMC8632544 DOI: 10.3389/fnmol.2021.764756] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) is a heterogeneous group of neurodevelopmental disorders characterized by synaptic dysfunction and defects in dendritic spine morphology. In the past decade, an extensive list of genes associated with ASD has been identified by genome-wide sequencing initiatives. Several of these genes functionally converge in the regulation of the Wnt/β-catenin signaling pathway, a conserved cascade essential for stem cell pluripotency and cell fate decisions during development. Here, we review current information regarding the transcriptional program of Wnt/β-catenin signaling in ASD. First, we discuss that Wnt/β-catenin gain and loss of function studies recapitulate brain developmental abnormalities associated with ASD. Second, transcriptomic approaches using patient-derived induced pluripotent stem cells (iPSC) cells, featuring mutations in high confidence ASD genes, reveal a significant dysregulation in the expression of Wnt signaling components. Finally, we focus on the activity of chromatin-remodeling proteins and transcription factors considered high confidence ASD genes, including CHD8, ARID1B, ADNP, and TBR1, that regulate Wnt/β-catenin-dependent transcriptional activity in multiple cell types, including pyramidal neurons, interneurons and oligodendrocytes, cells which are becoming increasingly relevant in the study of ASD. We conclude that the level of Wnt/β-catenin signaling activation could explain the high phenotypical heterogeneity of ASD and be instrumental in the development of new diagnostics tools and therapies.
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Affiliation(s)
- Mario O. Caracci
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Miguel E. Avila
- Faculty of Veterinary Medicine and Agronomy, Nucleus of Applied Research in Veterinary and Agronomic Sciences (NIAVA), Institute of Natural Sciences, Universidad de Las Américas, Santiago, Chile
| | - Francisca A. Espinoza-Cavieres
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Héctor R. López
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giorgia D. Ugarte
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giancarlo V. De Ferrari
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
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24
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Watanabe S, Kurotani T, Oga T, Noguchi J, Isoda R, Nakagami A, Sakai K, Nakagaki K, Sumida K, Hoshino K, Saito K, Miyawaki I, Sekiguchi M, Wada K, Minamimoto T, Ichinohe N. Functional and molecular characterization of a non-human primate model of autism spectrum disorder shows similarity with the human disease. Nat Commun 2021; 12:5388. [PMID: 34526497 PMCID: PMC8443557 DOI: 10.1038/s41467-021-25487-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is a multifactorial disorder with characteristic synaptic and gene expression changes. Early intervention during childhood is thought to benefit prognosis. Here, we examined the changes in cortical synaptogenesis, synaptic function, and gene expression from birth to the juvenile stage in a marmoset model of ASD induced by valproic acid (VPA) treatment. Early postnatally, synaptogenesis was reduced in this model, while juvenile-age VPA-treated marmosets showed increased synaptogenesis, similar to observations in human tissue. During infancy, synaptic plasticity transiently increased and was associated with altered vocalization. Synaptogenesis-related genes were downregulated early postnatally. At three months of age, the differentially expressed genes were associated with circuit remodeling, similar to the expression changes observed in humans. In summary, we provide a functional and molecular characterization of a non-human primate model of ASD, highlighting its similarity to features observed in human ASD.
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Affiliation(s)
- Satoshi Watanabe
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Tohru Kurotani
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Tomofumi Oga
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Jun Noguchi
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Risa Isoda
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Akiko Nakagami
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan ,grid.411827.90000 0001 2230 656XDepartment of Psychology, Japan Women’s University, Kawasaki, Kanagawa Japan
| | - Kazuhisa Sakai
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Keiko Nakagaki
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Kayo Sumida
- grid.459996.e0000 0004 0376 2692Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Konohana-ku, Osaka, Japan
| | - Kohei Hoshino
- grid.417741.00000 0004 1797 168XPreclinical Research Laboratories, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Koichi Saito
- grid.459996.e0000 0004 0376 2692Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Konohana-ku, Osaka, Japan
| | - Izuru Miyawaki
- grid.417741.00000 0004 1797 168XPreclinical Research Laboratories, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Masayuki Sekiguchi
- grid.419280.60000 0004 1763 8916Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Keiji Wada
- grid.419280.60000 0004 1763 8916Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
| | - Takafumi Minamimoto
- grid.482503.80000 0004 5900 003XDepartment of Functional Brain Imaging, National Institutes for Quantum and Radiological Science and Technology, Chiba, Chiba, Japan
| | - Noritaka Ichinohe
- grid.419280.60000 0004 1763 8916Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo Japan
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25
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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26
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Complement C4 Is Reduced in iPSC-Derived Astrocytes of Autism Spectrum Disorder Subjects. Int J Mol Sci 2021; 22:ijms22147579. [PMID: 34299197 PMCID: PMC8305914 DOI: 10.3390/ijms22147579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/17/2022] Open
Abstract
In recent years, accumulating evidence has shown that the innate immune complement system is involved in several aspects of normal brain development and in neurodevelopmental disorders, including autism spectrum disorder (ASD). Although abnormal expression of complement components was observed in post-mortem brain samples from individuals with ASD, little is known about the expression patterns of complement molecules in distinct cell types in the developing autistic brain. In the present study, we characterized the mRNA and protein expression profiles of a wide range of complement system components, receptors and regulators in induced pluripotent stem cell (iPSC)-derived neural progenitor cells, neurons and astrocytes of individuals with ASD and neurotypical controls, which constitute in vitro cellular models that recapitulate certain features of both human brain development and ASD pathophysiology. We observed that all the analyzed cell lines constitutively express several key complement molecules. Interestingly, using different quantification strategies, we found that complement C4 mRNA and protein are expressed in significantly lower levels by astrocytes derived from ASD individuals compared to control astrocytes. As astrocytes participate in synapse elimination, and diminished C4 levels have been linked to defective synaptic pruning, our findings may contribute to an increased understanding of the atypically enhanced brain connectivity in ASD.
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27
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Gao H, Ni Y, Mo X, Li D, Teng S, Huang Q, Huang S, Liu G, Zhang S, Tang Y, Lu L, Liang H. Drug repositioning based on network-specific core genes identifies potential drugs for the treatment of autism spectrum disorder in children. Comput Struct Biotechnol J 2021; 19:3908-3921. [PMID: 34306572 PMCID: PMC8280514 DOI: 10.1016/j.csbj.2021.06.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Identification of exact causative genes is important for in silico drug repositioning based on drug-gene-disease relationships. However, the complex polygenic etiology of the autism spectrum disorder (ASD) is a challenge in the identification of etiological genes. The network-based core gene identification method can effectively use the interactions between genes and accurately identify the pathogenic genes of ASD. We developed a novel network-based drug repositioning framework that contains three steps: network-specific core gene (NCG) identification, potential therapeutic drug repositioning, and candidate drug validation. First, through the analysis of transcriptome data for 178 brain tissues, gene network analysis identified 365 NCGs in 18 coexpression modules that were significantly correlated with ASD. Second, we evaluated two proposed drug repositioning methods. In one novel approach (dtGSEA), we used the NCGs to probe drug-gene interaction data and identified 35 candidate drugs. In another approach, we compared NCG expression patterns with drug-induced transcriptome data from the Connectivity Map database and found 46 candidate drugs. Third, we validated the candidate drugs using an in-house mental diseases and compounds knowledge graph (MCKG) that contained 7509 compounds, 505 mental diseases, and 123,890 edges. We found a total of 42 candidate drugs that were associated with mental illness, among which 10 drugs (baclofen, sulpiride, estradiol, entinostat, everolimus, fluvoxamine, curcumin, calcitriol, metronidazole, and zinc) were postulated to be associated with ASD. This study proposes a powerful network-based drug repositioning framework and also provides candidate drugs as well as potential drug targets for the subsequent development of ASD therapeutic drugs.
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Affiliation(s)
- Huan Gao
- Clinical Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, Guangdong, China
| | - Yuan Ni
- Ping An Technology, No. 20 Keji South 12 Road, Shen Zhen 518063, Guangdong, China
| | - Xueying Mo
- School of Information Management, Wuhan University, Wuhan 430072, Hubei, China
| | - Dantong Li
- Clinical Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, Guangdong, China
| | - Shan Teng
- Department of Psychology, School of Public Health, Southern Medical University, Guangzhou,510515, China
| | - Qingsheng Huang
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou 510623, Guangdong, China
| | - Shuai Huang
- Clinical Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, Guangdong, China
| | - Guangjian Liu
- Clinical Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, Guangdong, China
| | - Sheng Zhang
- Ping An Technology, No. 20 Keji South 12 Road, Shen Zhen 518063, Guangdong, China
| | - Yaping Tang
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou 510623, Guangdong, China
| | - Long Lu
- School of Information Management, Wuhan University, Wuhan 430072, Hubei, China
- Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou 510623, Guangdong, China
| | - Huiying Liang
- Clinical Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, Guangdong, China
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28
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Human Pluripotent Stem-Cell-Derived Models as a Missing Link in Drug Discovery and Development. Pharmaceuticals (Basel) 2021; 14:ph14060525. [PMID: 34070895 PMCID: PMC8230131 DOI: 10.3390/ph14060525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), have the potential to accelerate the drug discovery and development process. In this review, by analyzing each stage of the drug discovery and development process, we identified the active role of hPSC-derived in vitro models in phenotypic screening, target-based screening, target validation, toxicology evaluation, precision medicine, clinical trial in a dish, and post-clinical studies. Patient-derived or genome-edited PSCs can generate valid in vitro models for dissecting disease mechanisms, discovering novel drug targets, screening drug candidates, and preclinically and post-clinically evaluating drug safety and efficacy. With the advances in modern biotechnologies and developmental biology, hPSC-derived in vitro models will hopefully improve the cost-effectiveness and the success rate of drug discovery and development.
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29
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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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30
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Advances in autism research, 2021: continuing to decipher the secrets of autism. Mol Psychiatry 2021; 26:1426-1428. [PMID: 34045682 DOI: 10.1038/s41380-021-01168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/09/2022]
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31
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Schafer ST, Gage FH. The When and Where: Molecular and Cellular Convergence in Autism. Biol Psychiatry 2021; 89:419-420. [PMID: 33541523 DOI: 10.1016/j.biopsych.2020.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California.
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32
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Patient-Derived Induced Pluripotent Stem Cells (iPSCs) and Cerebral Organoids for Drug Screening and Development in Autism Spectrum Disorder: Opportunities and Challenges. Pharmaceutics 2021; 13:pharmaceutics13020280. [PMID: 33669772 PMCID: PMC7922555 DOI: 10.3390/pharmaceutics13020280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorder (ASD) represents a group of neurodevelopmental diseases characterized by persistent deficits in social communication, interaction, and repetitive patterns of behaviors, interests, and activities. The etiopathogenesis is multifactorial with complex interactions between genetic and environmental factors. The clinical heterogeneity and complex etiology of this pediatric disorder have limited the development of pharmacological therapies. The major limit to ASD research remains a lack of relevant human disease models which can faithfully recapitulate key features of the human pathology and represent its genetic heterogeneity. Recent advances in induced pluripotent stem cells (iPSCs), reprogrammed from somatic cells of patients into all types of patient-specific neural cells, have provided a promising cellular tool for disease modeling and development of novel drug treatments. The iPSCs technology allowed not only a better investigation of the disease etiopathogenesis but also opened up the potential for personalized therapies and offered new opportunities for drug discovery, pharmacological screening, and toxicity assessment. Moreover, iPSCs can be differentiated and organized into three-dimensional (3D) organoids, providing a model which mimics the complexity of the brain’s architecture and more accurately recapitulates tissue- and organ-level disease pathophysiology. The aims of this review were to describe the current state of the art of the use of human patient-derived iPSCs and brain organoids in modeling ASD and developing novel therapeutic strategies and to discuss the opportunities and major challenges in this rapidly moving field.
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33
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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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Griesi-Oliveira K, Passos-Bueno MR. Reply to Lombardo, 2020: An additional route of investigation: what are the mechanisms controlling ribosomal protein genes dysregulation in autistic neuronal cells? Mol Psychiatry 2021; 26:1436-1437. [PMID: 32467646 PMCID: PMC8159728 DOI: 10.1038/s41380-020-0792-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 02/04/2023]
Affiliation(s)
| | - Maria Rita Passos-Bueno
- grid.11899.380000 0004 1937 0722Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Ribosomal protein genes in post-mortem cortical tissue and iPSC-derived neural progenitor cells are commonly upregulated in expression in autism. Mol Psychiatry 2021; 26:1432-1435. [PMID: 32404943 PMCID: PMC8159733 DOI: 10.1038/s41380-020-0773-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/21/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
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Šimić G, Vukić V, Kopić J, Krsnik Ž, Hof PR. Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective. Biomolecules 2020; 11:E2. [PMID: 33375093 PMCID: PMC7822183 DOI: 10.3390/biom11010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.
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Affiliation(s)
- Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Vana Vukić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Janja Kopić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Željka Krsnik
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Reilly J, Gallagher L, Leader G, Shen S. Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation. PLoS One 2020; 15:e0242773. [PMID: 33338084 PMCID: PMC7748153 DOI: 10.1371/journal.pone.0242773] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous disorder that is often accompanied with many co-morbidities. Recent genetic studies have identified various pathways from hundreds of candidate risk genes with varying levels of association to ASD. However, it is unknown which pathways are specific to the core symptoms or which are shared by the co-morbidities. We hypothesised that critical ASD candidates should appear widely across different scoring systems, and that comorbidity pathways should be constituted by genes expressed in the relevant tissues. We analysed the Simons Foundation for Autism Research Initiative (SFARI) database and four independently published scoring systems and identified 292 overlapping genes. We examined their mRNA expression using the Genotype-Tissue Expression (GTEx) database and validated protein expression levels using the human protein atlas (HPA) dataset. This led to clustering of the overlapping ASD genes into 2 groups; one with 91 genes primarily expressed in the central nervous system (CNS geneset) and another with 201 genes expressed in both CNS and peripheral tissues (CNS+PT geneset). Bioinformatic analyses showed a high enrichment of CNS development and synaptic transmission in the CNS geneset, and an enrichment of synapse, chromatin remodelling, gene regulation and endocrine signalling in the CNS+PT geneset. Calcium signalling and the glutamatergic synapse were found to be highly interconnected among pathways in the combined geneset. Our analyses demonstrate that 2/3 of ASD genes are expressed beyond the brain, which may impact peripheral function and involve in ASD co-morbidities, and relevant pathways may be explored for the treatment of ASD co-morbidities.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- * E-mail: (JR); (SS)
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity Centre for Health Sciences—Trinity College Dublin, St. James’s Hospital, Dublin, Ireland
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland (NUI) Galway, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
- * E-mail: (JR); (SS)
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Walsh K, Voineagu MA, Vafaee F, Voineagu I. TDAview: an online visualization tool for topological data analysis. Bioinformatics 2020; 36:4805-4809. [PMID: 32614445 DOI: 10.1093/bioinformatics/btaa600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/13/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022] Open
Abstract
SUMMARY TDAview is an online tool for topological data analysis (TDA) and visualization. It implements the Mapper algorithm for TDA and provides extensive graph visualization options. TDAview is a user-friendly tool that allows biologists and clinicians without programming knowledge to harness the power of TDA. TDAview supports an analysis and visualization mode in which a Mapper graph is constructed based on user-specified parameters, followed by graph visualization. It can also be used in a visualization only mode in which TDAview is used for visualizing the data properties of a Mapper graph generated using other open-source software. The graph visualization options allow data exploration by graphical display of metadata variable values for nodes and edges, as well as the generation of publishable figures. TDAview can handle large datasets, with tens of thousands of data points, and thus has a wide range of applications for high-dimensional data, including the construction of topology-based gene co-expression networks. AVAILABILITY AND IMPLEMENTATION TDAview is a free online tool available at https://voineagulab.github.io/TDAview/. The source code, usage documentation and example data are available at TDAview GitHub repository: https://github.com/Voineagulab/TDAview.
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Affiliation(s)
- Kieran Walsh
- Department of Biotechnology and Biomolecular Sciences
| | - Mircea A Voineagu
- Department of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
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Hohmann SS, Ilieva M, Michel TM. In vitro models for ASD-patient-derived iPSCs and cerebral organoids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 173:355-375. [PMID: 32711817 DOI: 10.1016/bs.pmbts.2020.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Autism spectrum disorder (ASD) is a set of pervasive neurodevelopmental disorders. The causation is multigenic in most cases, which makes it difficult to model the condition in vitro. Advances in pluripotent stem cell technology has made it possible to generate in vitro models of human brain development. Induced pluripotent stem cells (iPSCs) can be generated from somatic cells and have the ability to differentiate to all of the body's cells. This chapter aims to give an overview of the iPSC technology for generating neural cells and cerebral organoids as models for neurodevelopment and how these models are utilized in the study of ASD. The combination of iPSC technology and the genetic modification tool CRISPR/Cas9 is described, and current limitations and future perspectives of iPSC technology is discussed.
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Affiliation(s)
- Sonja Simone Hohmann
- Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark.
| | - Mirolyuba Ilieva
- Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark; Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark; BRIDGE-Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tanja Maria Michel
- Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark; Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark; BRIDGE-Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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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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