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Li M, Yuan Y, Hou Z, Hao S, Jin L, Wang B. Human brain organoid: trends, evolution, and remaining challenges. Neural Regen Res 2024; 19:2387-2399. [PMID: 38526275 PMCID: PMC11090441 DOI: 10.4103/1673-5374.390972] [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: 06/19/2023] [Revised: 09/26/2023] [Accepted: 10/28/2023] [Indexed: 03/26/2024] Open
Abstract
Advanced brain organoids provide promising platforms for deciphering the cellular and molecular processes of human neural development and diseases. Although various studies and reviews have described developments and advancements in brain organoids, few studies have comprehensively summarized and analyzed the global trends in this area of neuroscience. To identify and further facilitate the development of cerebral organoids, we utilized bibliometrics and visualization methods to analyze the global trends and evolution of brain organoids in the last 10 years. First, annual publications, countries/regions, organizations, journals, authors, co-citations, and keywords relating to brain organoids were identified. The hotspots in this field were also systematically identified. Subsequently, current applications for brain organoids in neuroscience, including human neural development, neural disorders, infectious diseases, regenerative medicine, drug discovery, and toxicity assessment studies, are comprehensively discussed. Towards that end, several considerations regarding the current challenges in brain organoid research and future strategies to advance neuroscience will be presented to further promote their application in neurological research.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Zongkun Hou
- School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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2
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Dennys CN, Vermudez SAD, Deacon RJM, Sierra-Delgado JA, Rich K, Zhang X, Buch A, Weiss K, Moxley Y, Rajpal H, Espinoza FD, Powers S, Ávila AS, Gogliotti RG, Cogram P, Niswender CM, Meyer KC. MeCP2 gene therapy ameliorates disease phenotype in mouse model for Pitt Hopkins syndrome. Neurotherapeutics 2024:e00376. [PMID: 38876822 DOI: 10.1016/j.neurot.2024.e00376] [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: 10/17/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/16/2024] Open
Abstract
The neurodevelopmental disorder Pitt Hopkins syndrome (PTHS) causes clinical symptoms similar to Rett syndrome (RTT) patients. However, RTT is caused by MECP2 mutations whereas mutations in the TCF4 gene lead to PTHS. The mechanistic commonalities underling these two disorders are unknown, but their shared symptomology suggest that convergent pathway-level disruption likely exists. We reprogrammed patient skin derived fibroblasts into induced neuronal progenitor cells. Interestingly, we discovered that MeCP2 levels were decreased in PTHS patient iNPCs relative to healthy controls and that both iNPCs and iAstrocytes displayed defects in function and differentiation in a mutation-specific manner. When Tcf4+/- mice were genetically crossed with mice overexpressing MeCP2, molecular and phenotypic defects were significantly ameliorated, underlining and important role of MeCP2 in PTHS pathology. Importantly, post-natal intracerebroventricular gene replacement therapy with adeno-associated viral vector serotype 9 (AAV9)-expressing MeCP2 (AAV9.P546.MeCP2) significantly improved iNPC and iAstrocyte function and effectively ameliorated histological and behavioral defects in Tcf4+/- mice. Combined, our data suggest a previously unknown role of MeCP2 in PTHS pathology and common pathways that might be affected in multiple neurodevelopmental disorders. Our work highlights potential novel therapeutic targets for PTHS, including upregulation of MeCP2 expression or its downstream targets or, potentially, MeCP2-based gene therapy.
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Affiliation(s)
- Cassandra N Dennys
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sheryl Anne D Vermudez
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert J M Deacon
- Department of Genetics, Institute of Ecology and Biodiversity, Faculty of Science, University of Chile, Chile
| | - J Andrea Sierra-Delgado
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Kelly Rich
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Xiaojin Zhang
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Aditi Buch
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Kelly Weiss
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Yuta Moxley
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Hemangi Rajpal
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Francisca D Espinoza
- Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, 4090541, Chile
| | - Samantha Powers
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Ariel S Ávila
- Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, 4090541, Chile
| | - Rocco G Gogliotti
- Department of Molecular Pharmacology and Neuroscience, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patricia Cogram
- Department of Genetics, Institute of Ecology and Biodiversity, Faculty of Science, University of Chile, Chile
| | - Colleen M Niswender
- Department of Pharmacology and Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathrin C Meyer
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Medical Center, Columbus, OH, USA; Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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3
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Espinoza F, Carrazana R, Retamal-Fredes E, Ávila D, Papes F, Muotri AR, Ávila A. Tcf4 dysfunction alters dorsal and ventral cortical neurogenesis in Pitt-Hopkins syndrome mouse model showing sexual dimorphism. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167178. [PMID: 38636614 DOI: 10.1016/j.bbadis.2024.167178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by haploinsufficiency of transcription factor 4 (TCF4). In this work, we focused on the cerebral cortex and investigated in detail the progenitor cell dynamics and the outcome of neurogenesis in a PTHS mouse model. Labeling and quantification of progenitors and newly generated neurons at various time points during embryonic development revealed alterations affecting the dynamic of cortical progenitors since the earliest stages of cortex formation in PTHS mice. Consequently, establishment of neuronal populations and layering of the cortex were found to be altered in heterozygotes subjects at birth. Interestingly, defective layering process of pyramidal neurons was partially rescued by reintroducing TCF4 expression using focal in utero electroporation in the cerebral cortex. Coincidentally with a defective dorsal neurogenesis, we found that ventral generation of interneurons was also defective in this model, which may lead to an excitation/inhibition imbalance in PTHS. Overall, sex-dependent differences were detected with more marked effects evidenced in males compared with females. All of this contributes to expand our understanding of PTHS, paralleling the advances of research in autism spectrum disorder and further validating the PTHS mouse model as an important tool to advance preclinical studies.
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Affiliation(s)
- Francisca Espinoza
- Neurodevelopmental Biology Unit, Biomedical Sciences Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción (UCSC), Concepción, Chile
| | - Ramón Carrazana
- Neurodevelopmental Biology Unit, Biomedical Sciences Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción (UCSC), Concepción, Chile
| | - Eduardo Retamal-Fredes
- Neurodevelopmental Biology Unit, Biomedical Sciences Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción (UCSC), Concepción, Chile
| | - Denisse Ávila
- Department of Biochemical Engineering, University College of London (UCL), London, UK
| | - Fabio Papes
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariel Ávila
- Neurodevelopmental Biology Unit, Biomedical Sciences Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción (UCSC), Concepción, Chile.
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4
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Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR. Generation of 'semi-guided' cortical organoids with complex neural oscillations. Nat Protoc 2024:10.1038/s41596-024-00994-0. [PMID: 38702386 DOI: 10.1038/s41596-024-00994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/22/2024] [Indexed: 05/06/2024]
Abstract
Temporal development of neural electrophysiology follows genetic programming, similar to cellular maturation and organization during development. The emergent properties of this electrophysiological development, namely neural oscillations, can be used to characterize brain development. Recently, we utilized the innate programming encoded in the human genome to generate functionally mature cortical organoids. In brief, stem cells are suspended in culture via continuous shaking and naturally aggregate into embryoid bodies before being exposed to media formulations for neural induction, differentiation and maturation. The specific culture format, media composition and duration of exposure to these media distinguish organoid protocols and determine whether a protocol is guided or unguided toward specific neural fate. The 'semi-guided' protocol presented here has shorter induction and differentiation steps with less-specific patterning molecules than most guided protocols but maintains the use of neurotrophic factors such as brain-derived growth factor and neurotrophin-3, unlike unguided approaches. This approach yields the cell type diversity of unguided approaches while maintaining reproducibility for disease modeling. Importantly, we characterized the electrophysiology of these organoids and found that they recapitulate the maturation of neural oscillations observed in the developing human brain, a feature not shown with other approaches. This protocol represents the potential first steps toward bridging molecular and cellular biology to human cognition, and it has already been used to discover underlying features of human brain development, evolution and neurological conditions. Experienced cell culture technicians can expect the protocol to take 1 month, with extended maturation, electrophysiology recording, and adeno-associated virus transduction procedure options.
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Affiliation(s)
- Michael Q Fitzgerald
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Tiffany Chu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Francesca Puppo
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Rebeca Blanch
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel Chillón
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
- Center for Academic Research and Training in Anthropogeny and Archealization, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Education and Integrated Space Stem Cell Orbital Research Center, Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA.
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Phalnikar K, Srividya M, Mythri SV, Vasavi NS, Ganguly A, Kumar A, S P, Kalia K, Mishra SS, Dhanya SK, Paul P, Holla B, Ganesh S, Reddy PC, Sud R, Viswanath B, Muralidharan B. Altered neuroepithelial morphogenesis and migration defects in iPSC-derived cerebral organoids and 2D neural stem cells in familial bipolar disorder. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae007. [PMID: 38638145 PMCID: PMC11024480 DOI: 10.1093/oons/kvae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 04/20/2024]
Abstract
Bipolar disorder (BD) is a severe mental illness that can result from neurodevelopmental aberrations, particularly in familial BD, which may include causative genetic variants. In the present study, we derived cortical organoids from BD patients and healthy (control) individuals from a clinically dense family in the Indian population. Our data reveal that the patient organoids show neurodevelopmental anomalies, including organisational, proliferation and migration defects. The BD organoids show a reduction in both the number of neuroepithelial buds/cortical rosettes and the ventricular zone size. Additionally, patient organoids show a lower number of SOX2-positive and EdU-positive cycling progenitors, suggesting a progenitor proliferation defect. Further, the patient neurons show abnormal positioning in the ventricular/intermediate zone of the neuroepithelial bud. Transcriptomic analysis of control and patient organoids supports our cellular topology data and reveals dysregulation of genes crucial for progenitor proliferation and neuronal migration. Lastly, time-lapse imaging of neural stem cells in 2D in vitro cultures reveals abnormal cellular migration in BD samples. Overall, our study pinpoints a cellular and molecular deficit in BD patient-derived organoids and neural stem cell cultures.
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Affiliation(s)
- Kruttika Phalnikar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - M Srividya
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - S V Mythri
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - N S Vasavi
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Archisha Ganguly
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Aparajita Kumar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Padmaja S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Kishan Kalia
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Srishti S Mishra
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Sreeja Kumari Dhanya
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Pradip Paul
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Bharath Holla
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Suhas Ganesh
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India-201314
| | - Reeteka Sud
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Biju Viswanath
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Bhavana Muralidharan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
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6
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Davis BA, Chen HY, Ye Z, Ostlund I, Tippani M, Das D, Sripathy SR, Wang Y, Martin JM, Shim G, Panchwagh NM, Moses RL, Farinelli F, Bohlen JF, Li M, Luikart BW, Jaffe AE, Maher BJ. TCF4 Mutations Disrupt Synaptic Function Through Dysregulation of RIMBP2 in Patient-Derived Cortical Neurons. Biol Psychiatry 2024; 95:662-675. [PMID: 37573005 PMCID: PMC10858293 DOI: 10.1016/j.biopsych.2023.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Genetic variation in the TCF4 (transcription factor 4) gene is associated with risk for a variety of developmental and psychiatric conditions, which includes a syndromic form of autism spectrum disorder called Pitt-Hopkins syndrome (PTHS). TCF4 encodes an activity-dependent transcription factor that is highly expressed during cortical development and in animal models has been shown to regulate various aspects of neuronal development and function. However, our understanding of how disease-causing mutations in TCF4 confer pathophysiology in a human context is lacking. METHODS To model PTHS, we differentiated human cortical neurons from human induced pluripotent stem cells that were derived from patients with PTHS and neurotypical individuals. To identify pathophysiology and disease mechanisms, we assayed cortical neurons with whole-cell electrophysiology, Ca2+ imaging, multielectrode arrays, immunocytochemistry, and RNA sequencing. RESULTS Cortical neurons derived from patients with TCF4 mutations showed deficits in spontaneous synaptic transmission, network excitability, and homeostatic plasticity. Transcriptomic analysis indicated that these phenotypes resulted in part from altered expression of genes involved in presynaptic neurotransmission and identified the presynaptic binding protein RIMBP2 as the most differentially expressed gene in PTHS neurons. Remarkably, TCF4-dependent deficits in spontaneous synaptic transmission and network excitability were rescued by increasing RIMBP2 expression in presynaptic neurons. CONCLUSIONS Taken together, these results identify TCF4 as a critical transcriptional regulator of human synaptic development and plasticity and specifically identifies dysregulation of presynaptic function as an early pathophysiology in PTHS.
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Affiliation(s)
- Brittany A Davis
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Huei-Ying Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Zengyou Ye
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Isaac Ostlund
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Debamitra Das
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Srinidhi Rao Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Yanhong Wang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Jacqueline M Martin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Gina Shim
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Neel M Panchwagh
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Rebecca L Moses
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Federica Farinelli
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Joseph F Bohlen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Meijie Li
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Bryan W Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Brady J Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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7
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Zhao T, Wu S, Shen Y, Leng J, Genchev GZ, Lu H, Feng J. Clinical and genetic characterization of 47 Chinese pediatric patients with Pitt-Hopkins syndrome: a retrospective study. Orphanet J Rare Dis 2024; 19:51. [PMID: 38331897 PMCID: PMC10851572 DOI: 10.1186/s13023-024-03055-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder that remains underdiagnosed and its clinical presentations and mutation profiles in a diverse population are yet to be evaluated. This retrospective study aims to investigate the clinical and genetic characteristics of Chinese patients with PTHS. METHODS The clinical, biochemical, genetic, therapeutic, and follow-up data of 47 pediatric patients diagnosed with PTHS between 2018 and 2021 were retrospectively analyzed. RESULTS The Chinese PTHS patients presented with specific facial features and exhibited global developmental delay of wide severity range. The locus heterogeneity of the TCF4 gene in the patients was highlighted, emphasizing the significance of genetic studies for accurate diagnosis, albeit no significant correlations between genotype and phenotype were observed in this cohort. The study also reports the outcomes of patients who underwent therapeutic interventions, such as ketogenic diets and biomedical interventions. CONCLUSIONS The findings of this retrospective analysis expand the phenotypic and molecular spectra of PTHS patients. The study underscores the need for a long-term prospective follow-up study to assess potential therapeutic interventions.
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Affiliation(s)
- Tingting Zhao
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengnan Wu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, USA
| | - Jing Leng
- Wellness Center, 16 Philadelphia Ave, Shillington, PA, 19607, USA
| | - Georgi Z Genchev
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hui Lu
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jincai Feng
- Department of Rehabilitation, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Diagnosis and Treatment Center of Pitt-Hopkins Syndrome, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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8
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Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
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Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Gao Z, Lu C, Zhu Y, Liu Y, Lin Y, Gao W, Tian L, Wu L. Merazin hydrate produces rapid antidepressant effects by activating CaMKII to promote neuronal activities and proliferation in hippocampus. Brain Res 2024; 1822:148665. [PMID: 37924927 DOI: 10.1016/j.brainres.2023.148665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
In our previous studies, we demonstrated that merazin hydrate (MH) had rapid antidepressant effects, but the deep mechanism needed to be further investigated. In this study, we used depressive-like model, behavioral tests, molecular biology and pharmacological interventions to reveal the underlying mechanisms of MH's rapid antidepressants. We found that a single administration of MH was able to produce rapid antidepressant effects in chronic unpredictable mild stress (CUMS) exposed mice at 1 day later, similar to ketamine. Moreover, MH could not only significantly up-regulated the expressions of cFOS, but also obviously increased the number of Ki67 positive cells in hippocampal dentate gyrus (DG). Furthermore, we also found that the phosphorylated expression of calcium/calmodulin-dependent protein kinase II (CaMKII) was significantly reduced by CUMS in hippocampus, which was also reversed by MH. In addition, pharmacological inhibition of CaMKII by using KN-93 (a CaMKII antagonist) blocked the MH's up-regulation of cFOS and Ki67 in hippocampal DG. To sum up, this study demonstrated that MH produced rapid antidepressant effects by activating CaMKII to promote neuronal activities and proliferation in hippocampus.
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Affiliation(s)
- Ziwei Gao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China
| | - Chao Lu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China
| | - Yaping Zhu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China
| | - Yuxin Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China
| | - Yuesong Lin
- Nanjing Luhe District Hospital of Traditional Chinese Medicine, Nanjing 211500, China
| | - Wenming Gao
- Nanjing Luhe District Hospital of Traditional Chinese Medicine, Nanjing 211500, China
| | - Liyuan Tian
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China.
| | - Lei Wu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Department of Pharmacy, Nanjing 210029, China.
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10
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Jia M, Guo X, Liu R, Sun L, Wang Q, Wu J. Overexpress miR-132 in the Brain Parenchyma by a Non-invasive Way Improves Tissue Repairment and Releases Memory Impairment After Traumatic Brain Injury. Cell Mol Neurobiol 2023; 44:5. [PMID: 38104297 DOI: 10.1007/s10571-023-01435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023]
Abstract
Traumatic brain injury (TBI) is a serious public health problem worldwide, which could lead to an extremely high percentage of mortality and disability. Current treatment strategies mainly concentrate on neuronal protection and reconstruction, among them, exogenous neural stem cell (NSC) transplantation has long been regarded as the most effective curative treatment. However, due to secondary trauma, transplant rejection, and increased incidence of brain malignant tumor, a non-invasive therapy that enhanced endogenous neurogenesis was more suitable for TBI treatment. Our previous work has shown that miR-132 overexpression could improve neuronal differentiation of NSCs in vitro and in vivo. So, we engineered a new kind of AAV vector named AAV-PHP.eB which can transfect brain parenchyma through intravenous injection to overexpress miR-132 in brain after TBI. We found that miR-132 overexpression could reduce impact volume, promote neurogenesis in the dentate gyrus (DG), accelerate neuroblast migrating into the impact cortex, ameliorate microglia-mediated inflammatory reaction, and ultimately restore learning memory function. Our results revealed that AAV-PHP.eB-based miR-132 overexpression could improve endogenous tissue repairment and release clinical symptoms after traumatic brain injury. This work would provide a new therapeutic strategy for TBI treatment and other neurological disorders characterized by markable neuronal loss and memory impairment. miR-132 overexpression accelerates endogenous neurogenesis and releases TBI-induced tissue repairment and memory impairment. Controlled cortical impact onto the cortex would induce serious cortical injury and microglia accumulation in both cortex and hippocampus. Moreover, endogenous neuroblast could migrate around the injury core. miR-132 overexpression could accelerate neuroblast migration toward the injury core and decreased microglia accumulation in the ipsilateral cortex and hippocampus. miR-132 could be a suitable target on neuroprotective therapy after TBI.
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Affiliation(s)
- Meng Jia
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China
| | - Xi Guo
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China
| | - Ru Liu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China
| | - Lei Sun
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China
| | - Qun Wang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Jianping Wu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100070, China.
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070, China.
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11
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Lim Y. Transcription factors in microcephaly. Front Neurosci 2023; 17:1302033. [PMID: 38094004 PMCID: PMC10716367 DOI: 10.3389/fnins.2023.1302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Higher cognition in humans, compared to other primates, is often attributed to an increased brain size, especially forebrain cortical surface area. Brain size is determined through highly orchestrated developmental processes, including neural stem cell proliferation, differentiation, migration, lamination, arborization, and apoptosis. Disruption in these processes often results in either a small (microcephaly) or large (megalencephaly) brain. One of the key mechanisms controlling these developmental processes is the spatial and temporal transcriptional regulation of critical genes. In humans, microcephaly is defined as a condition with a significantly smaller head circumference compared to the average head size of a given age and sex group. A growing number of genes are identified as associated with microcephaly, and among them are those involved in transcriptional regulation. In this review, a subset of genes encoding transcription factors (e.g., homeobox-, basic helix-loop-helix-, forkhead box-, high mobility group box-, and zinc finger domain-containing transcription factors), whose functions are important for cortical development and implicated in microcephaly, are discussed.
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Affiliation(s)
- Youngshin Lim
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Science Education, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
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12
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Bhogale S, Seward C, Stubbs L, Sinha S. SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.565900. [PMID: 38014229 PMCID: PMC10680628 DOI: 10.1101/2023.11.09.565900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A common way to investigate gene regulatory mechanisms is to identify differentially expressed genes using transcriptomics, find their candidate enhancers using epigenomics, and search for over-represented transcription factor (TF) motifs in these enhancers using bioinformatics tools. A related follow-up task is to model gene expression as a function of enhancer sequences and rank TF motifs by their contribution to such models, thus prioritizing among regulators. We present a new computational tool called SEAMoD that performs the above tasks of motif finding and sequence-to-expression modeling simultaneously. It trains a convolutional neural network model to relate enhancer sequences to differential expression in one or more biological conditions. The model uses TF motifs to interpret the sequences, learning these motifs and their relative importance to each biological condition from data. It also utilizes epigenomic information in the form of activity scores of putative enhancers and automatically searches for the most promising enhancer for each gene. Compared to existing neural network models of non-coding sequences, SEAMoD uses far fewer parameters, requires far less training data, and emphasizes biological interpretability. We used SEAMoD to understand regulatory mechanisms underlying the differentiation of neural stem cell (NSC) derived from mouse forebrain. We profiled gene expression and histone modifications in NSC and three differentiated cell types and used SEAMoD to model differential expression of nearly 12,000 genes with an accuracy of 81%, in the process identifying the Olig2, E2f family TFs, Foxo3, and Tcf4 as key transcriptional regulators of the differentiation process.
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13
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Chen HY, Phan BN, Shim G, Hamersky GR, Sadowski N, O'Donnell TS, Sripathy SR, Bohlen JF, Pfenning AR, Maher BJ. Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes. Mol Psychiatry 2023; 28:4679-4692. [PMID: 37770578 PMCID: PMC11144438 DOI: 10.1038/s41380-023-02248-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Transcription factor 4 (TCF4) is a basic helix-loop-helix transcription factor that is implicated in a variety of psychiatric disorders including autism spectrum disorder (ASD), major depression, and schizophrenia. Autosomal dominant mutations in TCF4 are causal for a specific ASD called Pitt-Hopkins Syndrome (PTHS). However, our understanding of etiological and pathophysiological mechanisms downstream of TCF4 mutations is incomplete. Single cell sequencing indicates TCF4 is highly expressed in GABAergic interneurons (INs). Here, we performed cell-type specific expression analysis (CSEA) and cellular deconvolution (CD) on bulk RNA sequencing data from 5 different PTHS mouse models. Using CSEA we observed differentially expressed genes (DEGs) were enriched in parvalbumin expressing (PV+) INs and CD predicted a reduction in the PV+ INs population. Therefore, we investigated the role of TCF4 in regulating the development and function of INs in the Tcf4+/tr mouse model of PTHS. In Tcf4+/tr mice, immunohistochemical (IHC) analysis of subtype-specific IN markers and reporter mice identified reductions in PV+, vasoactive intestinal peptide (VIP+), and cortistatin (CST+) expressing INs in the cortex and cholinergic (ChAT+) INs in the striatum, with the somatostatin (SST+) IN population being spared. The reduction of these specific IN populations led to cell-type specific alterations in the balance of excitatory and inhibitory inputs onto PV+ and VIP+ INs and excitatory pyramidal neurons within the cortex. These data indicate TCF4 is a critical regulator of the development of specific subsets of INs and highlight the inhibitory network as an important source of pathophysiology in PTHS.
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Affiliation(s)
- Huei-Ying Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - BaDoi N Phan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Gina Shim
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Gregory R Hamersky
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Norah Sadowski
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Thomas S O'Donnell
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Srinidhi Rao Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joseph F Bohlen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Andreas R Pfenning
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Brady J Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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14
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Yazarlou F, Tabibian M, Azarnezhad A, Sadeghi Rad H, Lipovich L, Sanati G, Mostafavi Abdolmaleky H, Alizadeh F. Evaluating Gene Expression and Methylation Profiles of TCF4, MBP, and EGR1 in Peripheral Blood of Drug-Free Patients with Schizophrenia: Correlations with Psychopathology, Intelligence, and Cognitive Impairment. J Mol Neurosci 2023; 73:738-750. [PMID: 37668894 DOI: 10.1007/s12031-023-02150-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
Discovery and validation of new, reliable diagnostic and predictive biomarkers for schizophrenia (SCZ) are an ongoing effort. Here, we assessed the mRNA expression and DNA methylation of the TCF4, MBP, and EGR1 genes in the blood of patients with SCZ and evaluated their relationships to psychopathology and cognitive impairments. Quantitative real-time PCR and quantitative methylation-specific PCR methods were used to assess the expression level and promoter DNA methylation status of these genes in 70 drug-free SCZ patients and 72 healthy controls. The correlation of molecular changes with psychopathology and cognitive performance of participants was evaluated. We observed downregulation of TCF4 and upregulation of MBP mRNA levels in SCZ cases, relative to controls in our study. DNA methylation status at the promoter region of TCF4 demonstrated an altered pattern in SCZ as well. Additionally, TCF4 mRNA levels were inversely correlated with PANSS and Stroop total errors and positively correlated with WAIS total score and working memory, consistent with previous studies by our group. In contrast, MBP mRNA level was significantly positively correlated with PANSS and Stroop total errors and inversely correlated with WAIS total score and working memory. These epigenetic and expression signatures can help to assemble a peripheral biomarker-based diagnostic panel for SCZ.
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Affiliation(s)
- Fatemeh Yazarlou
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai, United Arab Emirates
| | - Mobina Tabibian
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnologies, Shahid Beheshti University, Tehran, Iran
| | - Asaad Azarnezhad
- Liver and Digestive Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Habib Sadeghi Rad
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People's Republic of China
- Center for Molecular Medicine and Genetics, Wayne State University, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Golshid Sanati
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | - Fatemeh Alizadeh
- Department of Genomic Psychiatry and Behavioral Genomics (DGPBG), Roozbeh Hospital, School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
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15
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Alula KM, Theiss AL. Autophagy in Crohn's Disease: Converging on Dysfunctional Innate Immunity. Cells 2023; 12:1779. [PMID: 37443813 PMCID: PMC10341259 DOI: 10.3390/cells12131779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease marked by relapsing, transmural intestinal inflammation driven by innate and adaptive immune responses. Autophagy is a multi-step process that plays a critical role in maintaining cellular homeostasis by degrading intracellular components, such as damaged organelles and invading bacteria. Dysregulation of autophagy in CD is revealed by the identification of several susceptibility genes, including ATG16L1, IRGM, NOD2, LRRK2, ULK1, ATG4, and TCF4, that are involved in autophagy. In this review, the role of altered autophagy in the mucosal innate immune response in the context of CD is discussed, with a specific focus on dendritic cells, macrophages, Paneth cells, and goblet cells. Selective autophagy, such as xenophagy, ERphagy, and mitophagy, that play crucial roles in maintaining intestinal homeostasis in these innate immune cells, are discussed. As our understanding of autophagy in CD pathogenesis evolves, the development of autophagy-targeted therapeutics may benefit subsets of patients harboring impaired autophagy.
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Affiliation(s)
| | - Arianne L. Theiss
- Division of Gastroenterology & Hepatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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16
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Kilpatrick S, Irwin C, Singh KK. Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations. Transl Psychiatry 2023; 13:217. [PMID: 37344450 DOI: 10.1038/s41398-023-02510-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder caused by genetic or environmental perturbations during early development. Diagnoses are dependent on the identification of behavioral abnormalities that likely emerge well after the disorder is established, leaving critical developmental windows uncharacterized. This is further complicated by the incredible clinical and genetic heterogeneity of the disorder that is not captured in most mammalian models. In recent years, advancements in stem cell technology have created the opportunity to model ASD in a human context through the use of pluripotent stem cells (hPSCs), which can be used to generate 2D cellular models as well as 3D unguided- and region-specific neural organoids. These models produce profoundly intricate systems, capable of modeling the developing brain spatiotemporally to reproduce key developmental milestones throughout early development. When complemented with multi-omics, genome editing, and electrophysiology analysis, they can be used as a powerful tool to profile the neurobiological mechanisms underlying this complex disorder. In this review, we will explore the recent advancements in hPSC-based modeling, discuss present and future applications of the model to ASD research, and finally consider the limitations and future directions within the field to make this system more robust and broadly applicable.
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Affiliation(s)
- Savannah Kilpatrick
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada
| | - Courtney Irwin
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karun K Singh
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
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17
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Yde Ohki CM, Walter NM, Rickli M, Salazar Campos JM, Werling AM, Döring C, Walitza S, Grünblatt E. Protocol for a Wnt reporter assay to measure its activity in human neural stem cells derived from induced pluripotent stem cells. CURRENT RESEARCH IN NEUROBIOLOGY 2023; 5:100095. [PMID: 37426743 PMCID: PMC10329100 DOI: 10.1016/j.crneur.2023.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
The canonical Wnt signaling is an essential pathway that regulates cellular proliferation, maturation, and differentiation during neurodevelopment and maintenance of adult tissue homeostasis. This pathway has been implicated with the pathophysiology of neuropsychiatric disorders and was associated with cognitive processes, such as learning and memory. However, the molecular investigation of the Wnt signaling in functional human neural cell lines might be challenging since brain biopsies are not possible and animal models may not represent the polygenic profile of some neurological and neurodevelopmental disorders. In this context, using induced pluripotent stem cells (iPSCs) has become a powerful tool to model disorders that affect the Central Nervous System (CNS) in vitro, by maintaining patients' genetic backgrounds. In this method paper, we report the development of a virus-free Wnt reporter assay in neural stem cells (NSCs) derived from human iPSCs from two healthy individuals, by using a vector containing a reporter gene (luc2P) under the control of a TCF/LEF (T-cell factor/lymphoid enhancer factor) responsive element. Dose-response curve analysis from this luciferase-based method might be useful when testing the activity of the Wnt signaling pathway after agonists (e.g. Wnt3a) or antagonists (e.g. DKK1) administration, comparing activity between cases and controls in distinct disorders. Using such a reporter assay method may help to elucidate whether neurological or neurodevelopmental mental disorders show alterations in this pathway, and testing whether targeted treatment may reverse these. Therefore, our established assay aims to help researchers on the functional and molecular investigation of the Wnt pathway in patient-specific cell types comprising several neuropsychiatric disorders.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Biomedicine PhD Program, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
| | - Natalie Monet Walter
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Michelle Rickli
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - José Maria Salazar Campos
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Anna Maria Werling
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Christian Döring
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
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18
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Sekine K, Onoguchi M, Hamada M. Transposons contribute to the acquisition of cell type-specific cis-elements in the brain. Commun Biol 2023; 6:631. [PMID: 37301950 PMCID: PMC10257727 DOI: 10.1038/s42003-023-04989-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mammalian brains have evolved in stages over a long history to acquire higher functions. Recently, several transposable element (TE) families have been shown to evolve into cis-regulatory elements of brain-specific genes. However, it is not fully understood how TEs are important for gene regulatory networks. Here, we performed a single-cell level analysis using public data of scATAC-seq to discover TE-derived cis-elements that are important for specific cell types. Our results suggest that DNA elements derived from TEs, MER130 and MamRep434, can function as transcription factor-binding sites based on their internal motifs for Neurod2 and Lhx2, respectively, especially in glutamatergic neuronal progenitors. Furthermore, MER130- and MamRep434-derived cis-elements were amplified in the ancestors of Amniota and Eutheria, respectively. These results suggest that the acquisition of cis-elements with TEs occurred in different stages during evolution and may contribute to the acquisition of different functions or morphologies in the brain.
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Affiliation(s)
- Kotaro Sekine
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Masahiro Onoguchi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
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19
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Abrams Z. How Brain Organoids Are Revolutionizing Neuroscience. IEEE Pulse 2023; 14:2-6. [PMID: 37607158 DOI: 10.1109/mpuls.2023.3294102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Measuring just a millimeter or two in diameter, brain organoids are a far cry from a fully functioning human brain. But these miniature tissues, typically derived from stem cells, are increasingly able to mimic the structure and function of our most complex organ, unlocking exciting possibilities for neuroscience, artificial intelligence, and beyond.
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20
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Wang L, Owusu-Hammond C, Sievert D, Gleeson JG. Stem Cell-Based Organoid Models of Neurodevelopmental Disorders. Biol Psychiatry 2023; 93:622-631. [PMID: 36759260 PMCID: PMC10022535 DOI: 10.1016/j.biopsych.2023.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The past decade has seen an explosion in the identification of genetic causes of neurodevelopmental disorders, including Mendelian, de novo, and somatic factors. These discoveries provide opportunities to understand cellular and molecular mechanisms as well as potential gene-gene and gene-environment interactions to support novel therapies. Stem cell-based models, particularly human brain organoids, can capture disease-associated alleles in the context of the human genome, engineered to mirror disease-relevant aspects of cellular complexity and developmental timing. These models have brought key insights into neurodevelopmental disorders as diverse as microcephaly, autism, and focal epilepsy. However, intrinsic organoid-to-organoid variability, low levels of certain brain-resident cell types, and long culture times required to reach maturity can impede progress. Several recent advances incorporate specific morphogen gradients, mixtures of diverse brain cell types, and organoid engraftment into animal models. Together with nonhuman primate organoid comparisons, mechanisms of human neurodevelopmental disorders are emerging.
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Affiliation(s)
- Lu Wang
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Charlotte Owusu-Hammond
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - David Sievert
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Joseph G Gleeson
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California.
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21
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Aldeeri AA, Abu-El-Haija A. A typical variant in TCF4 exon 18 is not associated with Pitt-Hopkins syndrome but with a familial case of mild and nonspecific neurodevelopmental disorder. Am J Med Genet A 2023; 191:1070-1076. [PMID: 36574749 DOI: 10.1002/ajmg.a.63098] [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: 08/30/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/28/2022]
Abstract
TCF4 gene encodes a class I helix-loop-helix transcription factor critical for the developing brain. Common polymorphisms in TCF4 and disruptive variants in the proximal region of the gene have been linked to relatively mild neuropsychiatric or neurodevelopmental disorders. In contrast, variants impacting distal exons are associated with Pitt-Hopkins syndrome (PTHS), a severe autosomal dominant condition characterized by profound intellectual disability, developmental delay, limited or absent speech, distinctive facies, and disordered breathing. Although phenotypic variability has been observed in PTHS, intellectual impairment and significant speech and motor delays are invariably present. In contrast to the typical de novo variants causing TCF4-related disorder and PTHS, we report a familial form of TCF4-related disorder where the missense variant arose de novo in the father and was inherited by two of his children. Although this family's variant's position in exon 18 predicted a typical PTHS phenotype, none of the affected individuals met the clinical diagnostic criteria for PTHS suggested by Zollino et al. in the first international consensus statement (as in the study by Zollino et al. in 2019). Rather, the three affected family members exhibited remarkably variable and milder phenotypes than would have been predicted from the position of their TCF4 variant. Thus, the clinical spectrum of PTHS-associated TCF4 variants may be broader than previously reported.
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Affiliation(s)
- Abdulrahman A Aldeeri
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Internal Medicine, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Aya Abu-El-Haija
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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22
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Yde Ohki CM, Walter NM, Bender A, Rickli M, Ruhstaller S, Walitza S, Grünblatt E. Growth rates of human induced pluripotent stem cells and neural stem cells from attention-deficit hyperactivity disorder patients: a preliminary study. J Neural Transm (Vienna) 2023; 130:243-252. [PMID: 36800023 PMCID: PMC10033475 DOI: 10.1007/s00702-023-02600-1] [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: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental polygenic disorder that affects more than 5% of children and adolescents around the world. Genetic and environmental factors play important roles in ADHD etiology, which leads to a wide range of clinical outcomes and biological phenotypes across the population. Brain maturation delays of a 4-year lag are commonly found in patients, when compared to controls of the same age. Possible differences in cellular growth rates might reflect the clinical observations in ADHD patients. However, the cellular mechanisms are still not elucidated. To test this hypothesis, we analysed the proliferation of induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) derived from male children and adolescents diagnosed with ADHD and with genetic predisposition to it (assessed using polygenic risk scores), as well as their respective matched controls. In the current pilot study, it was noticeable that NSCs from the ADHD group proliferate less than controls, while no differences were seen at the iPSC developmental stage. Our results from two distinct proliferation methods indicate that the functional and structural delays found in patients might be associated with these in vitro phenotypic differences, but start at a distinct neurodevelopmental stage. These findings are the first ones in the field of disease modelling of ADHD and might be crucial to better understand the pathophysiology of this disorder.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Biomedicine PhD Program, University of Zurich, Zurich, Switzerland
| | - Natalie Monet Walter
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Audrey Bender
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michelle Rickli
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sina Ruhstaller
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
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23
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Merhi M, Ahmad F, Taib N, Inchakalody V, Uddin S, Shablak A, Dermime S. The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update. Semin Cancer Biol 2023; 89:1-17. [PMID: 36621515 DOI: 10.1016/j.semcancer.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Cancer immunity is regulated by several mechanisms that include co-stimulatory and/or co-inhibitory molecules known as immune checkpoints expressed by the immune cells. In colorectal cancer (CRC), CTLA-4, LAG3, TIM-3 and PD-1 are the major co-inhibitory checkpoints involved in tumor development and progression. On the other hand, the deregulation of transcription factors and cancer stem cells activity plays a major role in the development of drug resistance and in the spread of metastatic disease in CRC. In this review, we describe how the modulation of such transcription factors affects the response of CRC to therapies. We also focus on the role of cancer stem cells in tumor metastasis and chemoresistance and discuss both preclinical and clinical approaches for targeting stem cells to prevent their tumorigenic effect. Finally, we provide an update on the clinical applications of immune checkpoint inhibitors in CRC and discuss the regulatory effects of transcription factors on the expression of the immune inhibitory checkpoints with specific focus on the PD-1 and PD-L1 molecules.
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Affiliation(s)
- Maysaloun Merhi
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Fareed Ahmad
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Alaaeldin Shablak
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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24
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Ghosh A, Nadella N, Monaghan-Nichols AP, Chu XP. Gene Therapy as an Emerging Treatment for Scn2a Mutation-Induced Autism Spectrum Disorders. FUNDAMENTAL RESEARCH 2023. [DOI: 10.1016/j.fmre.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
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25
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Davis BA, Chen HY, Ye Z, Ostlund I, Tippani M, Das D, Sripathy SR, Wang Y, Martin JM, Shim G, Panchwagh NM, Moses RL, Farinelli F, Bohlen JF, Li M, Luikart BW, Jaffe AE, Maher BJ. TCF4 mutations disrupt synaptic function through dysregulation of RIMBP2 in patient-derived cortical neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524788. [PMID: 36712024 PMCID: PMC9882330 DOI: 10.1101/2023.01.19.524788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genetic variation in the transcription factor 4 ( TCF4) gene is associated with risk for a variety of developmental and psychiatric conditions, which includes a syndromic form of ASD called Pitt Hopkins Syndrome (PTHS). TCF4 encodes an activity-dependent transcription factor that is highly expressed during cortical development and in animal models is shown to regulate various aspects of neuronal development and function. However, our understanding of how disease-causing mutations in TCF4 confer pathophysiology in a human context is lacking. Here we show that cortical neurons derived from patients with TCF4 mutations have deficits in spontaneous synaptic transmission, network excitability and homeostatic plasticity. Transcriptomic analysis indicates these phenotypes result from altered expression of genes involved in presynaptic neurotransmission and identifies the presynaptic binding protein, RIMBP2 as the most differentially expressed gene in PTHS neurons. Remarkably, TCF4-dependent deficits in spontaneous synaptic transmission and network excitability were rescued by increasing RIMBP2 expression in presynaptic neurons. Together, these results identify TCF4 as a critical transcriptional regulator of human synaptic development and plasticity and specifically identifies dysregulation of presynaptic function as an early pathophysiology in PTHS.
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Affiliation(s)
- Brittany A. Davis
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Huei-Ying Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Zengyou Ye
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Isaac Ostlund
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Debamitra Das
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Srinidhi Rao Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Jacqueline M. Martin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Gina Shim
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Neel M. Panchwagh
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Rebecca L. Moses
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Federica Farinelli
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Joseph F. Bohlen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Meijie Li
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Bryan W. Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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26
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Kurishev AO, Karpov DS, Nadolinskaia NI, Goncharenko AV, Golimbet VE. CRISPR/Cas-Based Approaches to Study Schizophrenia and Other Neurodevelopmental Disorders. Int J Mol Sci 2022; 24:ijms24010241. [PMID: 36613684 PMCID: PMC9820593 DOI: 10.3390/ijms24010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The study of diseases of the central nervous system (CNS) at the molecular level is challenging because of the complexity of neural circuits and the huge number of specialized cell types. Moreover, genomic association studies have revealed the complex genetic architecture of schizophrenia and other genetically determined mental disorders. Investigating such complex genetic architecture to decipher the molecular basis of CNS pathologies requires the use of high-throughput models such as cells and their derivatives. The time is coming for high-throughput genetic technologies based on CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/Cas systems to manipulate multiple genomic targets. CRISPR/Cas systems provide the desired complexity, versatility, and flexibility to create novel genetic tools capable of both altering the DNA sequence and affecting its function at higher levels of genetic information flow. CRISPR/Cas tools make it possible to find and investigate the intricate relationship between the genotype and phenotype of neuronal cells. The purpose of this review is to discuss innovative CRISPR-based approaches for studying the molecular mechanisms of CNS pathologies using cellular models.
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Affiliation(s)
| | - Dmitry S. Karpov
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Nonna I. Nadolinskaia
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vera E. Golimbet
- Mental Health Research Center, Kashirskoe sh. 34, 115522 Moscow, Russia
- Correspondence:
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Abstract
The current understanding of neurological diseases is derived mostly from direct analysis of patients and from animal models of disease. However, most patient studies do not capture the earliest stages of disease development and offer limited opportunities for experimental intervention, so rarely yield complete mechanistic insights. The use of animal models relies on evolutionary conservation of pathways involved in disease and is limited by an inability to recreate human-specific processes. In vitro models that are derived from human pluripotent stem cells cultured in 3D have emerged as a new model system that could bridge the gap between patient studies and animal models. In this Review, we summarize how such organoid models can complement classical approaches to accelerate neurological research. We describe our current understanding of neurodevelopment and how this process differs between humans and other animals, making human-derived models of disease essential. We discuss different methodologies for producing organoids and how organoids can be and have been used to model neurological disorders, including microcephaly, Zika virus infection, Alzheimer disease and other neurodegenerative disorders, and neurodevelopmental diseases, such as Timothy syndrome, Angelman syndrome and tuberous sclerosis. We also discuss the current limitations of organoid models and outline how organoids can be used to revolutionize research into the human brain and neurological diseases. In this Review, Eichmüller and Knoblich discuss how human brain organoids can recapitulate the unique processes that occur in human brain development and how they can complement classical approaches to revolutionize research into neurological diseases. Development of the human brain involves unique processes that are relevant to neurological disease but cannot be studied in animal models, so alternative model systems are required. Organoids are 3D human cell culture models that originate from pluripotent stem cells and recapitulate the hallmarks of human neurodevelopment, enabling studies of human brain development in vitro. Specific mutations can be introduced into organoids to study their effects on neurodevelopment; combined with high-throughput screening methods, this approach can determine the disease relevance of mutations in human tissue. To study specific diseases, brain organoids can be generated from induced pluripotent stem cells from individual patients, thereby preserving the specific genetic background of the individual and generating an insightful model. Through recapitulation of previously inaccessible periods of human brain development, brain organoids have enabled identification of novel mechanisms that underlie neurodevelopmental, neurodegenerative and infectious diseases. Combining organoids, patient research and animal models enables us to take full advantage of each of these systems and will provide unprecedented insights into neurodevelopment and neurological diseases.
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28
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Cell landscape of larval and adult Xenopus laevis at single-cell resolution. Nat Commun 2022; 13:4306. [PMID: 35879314 PMCID: PMC9314398 DOI: 10.1038/s41467-022-31949-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell atlases have been constructed for vertebrates such as Homo sapiens, Macaca fascicularis, Mus musculus and Danio rerio. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the first Xenopus cell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research on Xenopus metamorphosis and adult organs.
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