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Cai Y, Zhang X, Li C, Ghashghaei HT, Greenbaum A. COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains. CELL REPORTS METHODS 2023; 3:100454. [PMID: 37159668 PMCID: PMC10163164 DOI: 10.1016/j.crmeth.2023.100454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/28/2023] [Accepted: 03/23/2023] [Indexed: 05/11/2023]
Abstract
Tissue clearing renders entire organs transparent to accelerate whole-tissue imaging; for example, with light-sheet fluorescence microscopy. Yet, challenges remain in analyzing the large resulting 3D datasets that consist of terabytes of images and information on millions of labeled cells. Previous work has established pipelines for automated analysis of tissue-cleared mouse brains, but the focus there was on single-color channels and/or detection of nuclear localized signals in relatively low-resolution images. Here, we present an automated workflow (COMBINe, Cell detectiOn in Mouse BraIN) to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM). COMBINe blends modules from multiple pipelines with RetinaNet at its core. We quantitatively analyzed the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) on neuronal and astrocyte populations in the mouse forebrain.
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Affiliation(s)
- Yuheng Cai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Xuying Zhang
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - H. Troy Ghashghaei
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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2
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Xu H, Jia J, Jeong HH, Zhao Z. Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome. PATTERNS (NEW YORK, N.Y.) 2023; 4:100674. [PMID: 36873907 PMCID: PMC9982299 DOI: 10.1016/j.patter.2022.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/02/2022] [Accepted: 12/13/2022] [Indexed: 02/12/2023]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), a retrovirus, is the causative agent for adult T cell leukemia/lymphoma and many other human diseases. Accurate and high throughput detection of HTLV-1 virus integration sites (VISs) across the host genomes plays a crucial role in the prevention and treatment of HTLV-1-associated diseases. Here, we developed DeepHTLV, the first deep learning framework for VIS prediction de novo from genome sequence, motif discovery, and cis-regulatory factor identification. We demonstrated the high accuracy of DeepHTLV with more efficient and interpretive feature representations. Decoding the informative features captured by DeepHTLV resulted in eight representative clusters with consensus motifs for potential HTLV-1 integration. Furthermore, DeepHTLV revealed interesting cis-regulatory elements in regulation of VISs that have significant association with the detected motifs. Literature evidence demonstrated nearly half (34) of the predicted transcription factors enriched with VISs were involved in HTLV-1-associated diseases. DeepHTLV is freely available at https://github.com/bsml320/DeepHTLV.
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Affiliation(s)
- Haodong Xu
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA
| | - Johnathan Jia
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Hyun-Hwan Jeong
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, UTHealth Science Center at Houston, Houston, TX 77030, USA.,MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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3
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Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, McDonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L, Lister R. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell 2022; 185:4428-4447.e28. [PMID: 36318921 DOI: 10.1016/j.cell.2022.09.039] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 07/19/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Human brain development is underpinned by cellular and molecular reconfigurations continuing into the third decade of life. To reveal cell dynamics orchestrating neural maturation, we profiled human prefrontal cortex gene expression and chromatin accessibility at single-cell resolution from gestation to adulthood. Integrative analyses define the dynamic trajectories of each cell type, revealing major gene expression reconfiguration at the prenatal-to-postnatal transition in all cell types followed by continuous reconfiguration into adulthood and identifying regulatory networks guiding cellular developmental programs, states, and functions. We uncover links between expression dynamics and developmental milestones, characterize the diverse timing of when cells acquire adult-like states, and identify molecular convergence from distinct developmental origins. We further reveal cellular dynamics and their regulators implicated in neurological disorders. Finally, using this reference, we benchmark cell identities and maturation states in organoid models. Together, this captures the dynamic regulatory landscape of human cortical development.
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Affiliation(s)
- Charles A Herring
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Rebecca K Simmons
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Saskia Freytag
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Joel J D Moffet
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Dulce B Vargas-Landin
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Olivier Clément
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Enrique Goñi Echeverría
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, Cellular Genomics Futures Institute, and the RNA Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alba Alvarez-Franco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Kerrie McDonald
- Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jose M Polo
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3000, Australia
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia
| | - Anna K Nowak
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, Cellular Genomics Futures Institute, and the RNA Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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Wen Q, Verheijen M, Wittens MMJ, Czuryło J, Engelborghs S, Hauser D, van Herwijnen MHM, Lundh T, Bergdahl IA, Kyrtopoulos SA, de Kok TM, Smeets HJM, Briedé JJ, Krauskopf J. Lead-exposure associated miRNAs in humans and Alzheimer’s disease as potential biomarkers of the disease and disease processes. Sci Rep 2022; 12:15966. [PMID: 36153426 PMCID: PMC9509380 DOI: 10.1038/s41598-022-20305-5] [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: 02/25/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease that eventually affects memory and behavior. The identification of biomarkers based on risk factors for AD provides insight into the disease since the exact cause of AD remains unknown. Several studies have proposed microRNAs (miRNAs) in blood as potential biomarkers for AD. Exposure to heavy metals is a potential risk factor for onset and development of AD. Blood cells of subjects that are exposed to lead detected in the circulatory system, potentially reflect molecular responses to this exposure that are similar to the response of neurons. In this study we analyzed blood cell-derived miRNAs derived from a general population as proxies of potentially AD-related mechanisms triggered by lead exposure. Subsequently, we analyzed these mechanisms in the brain tissue of AD subjects and controls. A total of four miRNAs were identified as lead exposure-associated with hsa-miR-3651, hsa-miR-150-5p and hsa-miR-664b-3p being negatively and hsa-miR-627 positively associated. In human brain derived from AD and AD control subjects all four miRNAs were detected. Moreover, two miRNAs (miR-3651, miR-664b-3p) showed significant differential expression in AD brains versus controls, in accordance with the change direction of lead exposure. The miRNAs’ gene targets were validated for expression in the human brain and were found enriched in AD-relevant pathways such as axon guidance. Moreover, we identified several AD relevant transcription factors such as CREB1 associated with the identified miRNAs. These findings suggest that the identified miRNAs are involved in the development of AD and might be useful in the development of new, less invasive biomarkers for monitoring of novel therapies or of processes involved in AD development.
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Reis L, Raciti M, Rodriguez PG, Joseph B, Al Rayyes I, Uhlén P, Falk A, da Cunha Lima ST, Ceccatelli S. Glyphosate-based herbicide induces long-lasting impairment in neuronal and glial differentiation. ENVIRONMENTAL TOXICOLOGY 2022; 37:2044-2057. [PMID: 35485992 PMCID: PMC9541419 DOI: 10.1002/tox.23549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 05/09/2023]
Abstract
Glyphosate-based herbicides (GBH) are among the most sold pesticides in the world. There are several formulations based on the active ingredient glyphosate (GLY) used along with other chemicals to improve the absorption and penetration in plants. The final composition of commercial GBH may modify GLY toxicological profile, potentially enhancing its neurotoxic properties. The developing nervous system is particularly susceptible to insults occurring during the early phases of development, and exposure to chemicals in this period may lead to persistent impairments on neurogenesis and differentiation. The aim of this study was to evaluate the long-lasting effects of a sub-cytotoxic concentration, 2.5 parts per million of GBH and GLY, on the differentiation of human neuroepithelial stem cells (NES) derived from induced pluripotent stem cells (iPSC). We treated NES cells with each compound and evaluated the effects on key cellular processes, such as proliferation and differentiation in daughter cells never directly exposed to the toxicants. We found that GBH induced a more immature neuronal profile associated to increased PAX6, NESTIN and DCX expression, and a shift in the differentiation process toward glial cell fate at the expense of mature neurons, as shown by an increase in the glial markers GFAP, GLT1, GLAST and a decrease in MAP2. Such alterations were associated to dysregulation of key genes critically involved in neurogenesis, including PAX6, HES1, HES5, and DDK1. Altogether, the data indicate that subtoxic concentrations of GBH, but not of GLY, induce long-lasting impairments on the differentiation potential of NES cells.
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Affiliation(s)
- Luã Reis
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Marilena Raciti
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | | | - Bertrand Joseph
- Institute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | - Ibrahim Al Rayyes
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Per Uhlén
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Anna Falk
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Suzana Telles da Cunha Lima
- Laboratório de Bioprospecção e Biotecnologia, Instituto de BiologiaUniversidade Federal da Bahia (UFBA)SalvadorBrazil
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6
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Gupta C, Xu J, Jin T, Khullar S, Liu X, Alatkar S, Cheng F, Wang D. Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease. PLoS Comput Biol 2022; 18:e1010287. [PMID: 35849618 PMCID: PMC9333448 DOI: 10.1371/journal.pcbi.1010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/28/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, AD-induced regulatory changes across brain cell types remains uncharted. To address this, we integrated single-cell multi-omics datasets to predict the gene regulatory networks of four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes, in control and AD brains. Importantly, we analyzed and compared the structural and topological features of networks across cell types and examined changes in AD. Our analysis shows that hub TFs are largely common across cell types and AD-related changes are relatively more prominent in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are also highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes. The further disease-module-drug association analysis suggests cell-type candidate drugs and their potential target genes. Finally, our network-based machine learning analysis systematically prioritized cell type risk genes likely involved in AD. Our strategy is validated using an independent dataset which showed that top ranked genes can predict clinical phenotypes (e.g., cognitive impairment) of AD with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals cell-type gene dysregulation in AD. Alzheimer’s Disease (AD) is the leading cause of dementia. It affects parts of the brain that control language, behavior, and memory. The human brain is comprised of tens of billions of cells, such as neuronal cells that transmit information via electrical and chemical signals, and glial cells that maintain the brain’s immune system. Researchers have found that AD causes changes in the expression of genes within the brain cells. Gene expression is a tightly regulated process involving interconnected networks of multiple genes. Understanding how these gene networks change in AD is critical to identifying genetic biomarkers and potential drug targets. Using genomic data of post-mortem brains diagnosed with AD and healthy individuals, we identified gene networks that play a crucial role in regulating biological processes within neuronal and glial cells. We utilized these gene networks to make predictions on existing FDA approved drugs that could potentially be repurposed for AD. Furthermore, we used a machine learning strategy to identify novel genes that are more likely to be involved in AD pathology. The systems-level approach lends itself to analysis of single-cell genomics data of other human diseases.
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Affiliation(s)
- Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ting Jin
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiaoyu Liu
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sayali Alatkar
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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7
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Multicolor strategies for investigating clonal expansion and tissue plasticity. Cell Mol Life Sci 2022; 79:141. [PMID: 35187598 PMCID: PMC8858928 DOI: 10.1007/s00018-021-04077-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Understanding the generation of complexity in living organisms requires the use of lineage tracing tools at a multicellular scale. In this review, we describe the different multicolor strategies focusing on mouse models expressing several fluorescent reporter proteins, generated by classical (MADM, Brainbow and its multiple derivatives) or acute (StarTrack, CLoNe, MAGIC Markers, iOn, viral vectors) transgenesis. After detailing the multi-reporter genetic strategies that serve as a basis for the establishment of these multicolor mouse models, we briefly mention other animal and cellular models (zebrafish, chicken, drosophila, iPSC) that also rely on these constructs. Then, we highlight practical applications of multicolor mouse models to better understand organogenesis at single progenitor scale (clonal analyses) in the brain and briefly in several other tissues (intestine, skin, vascular, hematopoietic and immune systems). In addition, we detail the critical contribution of multicolor fate mapping strategies in apprehending the fine cellular choreography underlying tissue morphogenesis in several models with a particular focus on brain cytoarchitecture in health and diseases. Finally, we present the latest technological advances in multichannel and in-depth imaging, and automated analyses that enable to better exploit the large amount of data generated from multicolored tissues.
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Da CM, Liao HY, Deng YS, Zhao GH, Ma L, Zhang HH. Transcription Factor SP2 Regulates Ski-mediated Astrocyte Proliferation In Vitro. Neuroscience 2021; 479:22-34. [PMID: 34687796 DOI: 10.1016/j.neuroscience.2021.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors bind specific sequences upstream of the 5' end of their target genes to ensure proper spatiotemporal expression of the target gene. This study aims to demonstrate that the transcription factor SP2 regulates expression of the Ski gene, which has specific binding sites for SP2, and thus enables Ski to regulate astrocyte proliferation. The upstream regulation mechanism of astrocyte proliferation was explored to further regulate the formation of glial scar in specific time and space after spinal cord injury. JASPAR and UCSC databases were used to predict transcription factor binding and the threshold was gradually reduced to screen transcription factors upstream of Ski, leading to the identification of SP2. Next, we analyzed the correlation between the expression of SP2 and Ski in normal astrocytes and reactive astrocytes, as well as the changes in astrocyte proliferation. To confirm that SP2 regulates Ski during astrocyte proliferation, astrocytes were transfected siRNA targeting SP2 and then astrocyte proliferation were analyzed. Finally, a dual luciferase reporter assay and Chromatin immunoprecipitation (ChIP) assay confirmed that the promoter region of Ski contained a specific SP2 binding site. This is the first that SP2 has been identified and confirmed to play an important role in astrocyte proliferation by regulating Ski expression. These results may help identify novel targets for the treatment of spinal cord injury.
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Affiliation(s)
- Chao-Ming Da
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Hai-Yang Liao
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China
| | - Yin-Shuan Deng
- Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Guang-Hai Zhao
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Lin Ma
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Gansu Provincial Maternal and Child Health Hospital, 143Qilihe North Street, Lanzhou 730050, PR China
| | - Hai-Hong Zhang
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China.
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Cai Y, Zhang X, Kovalsky SZ, Ghashghaei HT, Greenbaum A. Detection and classification of neurons and glial cells in the MADM mouse brain using RetinaNet. PLoS One 2021; 16:e0257426. [PMID: 34559842 PMCID: PMC8462685 DOI: 10.1371/journal.pone.0257426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
The ability to automatically detect and classify populations of cells in tissue sections is paramount in a wide variety of applications ranging from developmental biology to pathology. Although deep learning algorithms are widely applied to microscopy data, they typically focus on segmentation which requires extensive training and labor-intensive annotation. Here, we utilized object detection networks (neural networks) to detect and classify targets in complex microscopy images, while simplifying data annotation. To this end, we used a RetinaNet model to classify genetically labeled neurons and glia in the brains of Mosaic Analysis with Double Markers (MADM) mice. Our initial RetinaNet-based model achieved an average precision of 0.90 across six classes of cells differentiated by MADM reporter expression and their phenotype (neuron or glia). However, we found that a single RetinaNet model often failed when encountering dense and saturated glial clusters, which show high variability in their shape and fluorophore densities compared to neurons. To overcome this, we introduced a second RetinaNet model dedicated to the detection of glia clusters. Merging the predictions of the two computational models significantly improved the automated cell counting of glial clusters. The proposed cell detection workflow will be instrumental in quantitative analysis of the spatial organization of cellular populations, which is applicable not only to preparations in neuroscience studies, but also to any tissue preparation containing labeled populations of cells.
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Affiliation(s)
- Yuheng Cai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Xuying Zhang
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Shahar Z. Kovalsky
- Department of Mathematics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - H. Troy Ghashghaei
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: ,
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10
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Li C, Moatti A, Zhang X, Troy Ghashghaei H, Greenabum A. Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:5214-5226. [PMID: 34513252 PMCID: PMC8407817 DOI: 10.1364/boe.427099] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/12/2021] [Accepted: 07/07/2021] [Indexed: 05/23/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) is a minimally invasive and high throughput imaging technique ideal for capturing large volumes of tissue with sub-cellular resolution. A fundamental requirement for LSFM is a seamless overlap of the light-sheet that excites a selective plane in the specimen, with the focal plane of the objective lens. However, spatial heterogeneity in the refractive index of the specimen often results in violation of this requirement when imaging deep in the tissue. To address this issue, autofocus methods are commonly used to refocus the focal plane of the objective-lens on the light-sheet. Yet, autofocus techniques are slow since they require capturing a stack of images and tend to fail in the presence of spherical aberrations that dominate volume imaging. To address these issues, we present a deep learning-based autofocus framework that can estimate the position of the objective-lens focal plane relative to the light-sheet, based on two defocused images. This approach outperforms or provides comparable results with the best traditional autofocus method on small and large image patches respectively. When the trained network is integrated with a custom-built LSFM, a certainty measure is used to further refine the network's prediction. The network performance is demonstrated in real-time on cleared genetically labeled mouse forebrain and pig cochleae samples. Our study provides a framework that could improve light-sheet microscopy and its application toward imaging large 3D specimens with high spatial resolution.
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Affiliation(s)
- Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Adele Moatti
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Xuying Zhang
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - H. Troy Ghashghaei
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Alon Greenabum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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11
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Liang D, Elwell AL, Aygün N, Krupa O, Wolter JM, Kyere FA, Lafferty MJ, Cheek KE, Courtney KP, Yusupova M, Garrett ME, Ashley-Koch A, Crawford GE, Love MI, de la Torre-Ubieta L, Geschwind DH, Stein JL. Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. Nat Neurosci 2021; 24:941-953. [PMID: 34017130 PMCID: PMC8254789 DOI: 10.1038/s41593-021-00858-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Common genetic risk for neuropsychiatric disorders is enriched in regulatory elements active during cortical neurogenesis. However, it remains poorly understood as to how these variants influence gene regulation. To model the functional impact of common genetic variation on the noncoding genome during human cortical development, we performed the assay for transposase accessible chromatin using sequencing (ATAC-seq) and analyzed chromatin accessibility quantitative trait loci (QTL) in cultured human neural progenitor cells and their differentiated neuronal progeny from 87 donors. We identified significant genetic effects on 988/1,839 neuron/progenitor regulatory elements, with highly cell-type and temporally specific effects. A subset (roughly 30%) of chromatin accessibility-QTL were also associated with changes in gene expression. Motif-disrupting alleles of transcriptional activators generally led to decreases in chromatin accessibility, whereas motif-disrupting alleles of repressors led to increases in chromatin accessibility. By integrating cell-type-specific chromatin accessibility-QTL and brain-relevant genome-wide association data, we were able to fine-map and identify regulatory mechanisms underlying noncoding neuropsychiatric disorder risk loci.
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Affiliation(s)
- Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angela L Elwell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Justin M Wolter
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Felix A Kyere
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Lafferty
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry E Cheek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenan P Courtney
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marianna Yusupova
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Rep 2021; 35:109274. [PMID: 34161767 PMCID: PMC8317686 DOI: 10.1016/j.celrep.2021.109274] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/14/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022] Open
Abstract
Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.
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Affiliation(s)
- Ximena Contreras
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Johanna Sonntag
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Lill Andersen
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Tina Bernthaler
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Anna Heger
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Randy L Johnson
- Department of Biochemistry and Molecular Biology, University of Texas, Houston, TX 77030, USA
| | - Lindsay A Schwarz
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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13
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Yu S, Ruan X, Liu X, Zhang F, Wang D, Liu Y, Yang C, Shao L, Liu Q, Zhu L, Lin Y, Xue Y. HNRNPD interacts with ZHX2 regulating the vasculogenic mimicry formation of glioma cells via linc00707/miR-651-3p/SP2 axis. Cell Death Dis 2021; 12:153. [PMID: 33542193 PMCID: PMC7862279 DOI: 10.1038/s41419-021-03432-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/15/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
Studies have found that RNA-binding proteins (RBPs) are dysfunctional and play a significant regulatory role in the development of glioma. Based on The Cancer Genome Atlas database and the previous studies, we selected heterogeneous nuclear ribonucleoprotein (HNRNPD) as the research candidate and sought its downstream targeted genes. In the present study, HNRNPD, linc00707, and specific protein 2 (SP2) were highly expressed, while zinc fingers and homeboxes 2 (ZHX2) and miR-651-3p were remarkedly downregulated in glioma tissues and cells. HNRNPD, linc00707, and SP2 knockdown or ZHX2 and miR-651-3p overexpression suppressed glioma cells proliferation, migration, and invasion and vasculogenic mimicry (VM) formation. Knockdown of HNRNPD increased the stability of ZHX2 mRNA. ZHX2 bound to the promoter region of linc00707 and negatively regulate its expression. Linc00707 could bind with miR-651-3p, while miR-651-3p bound to the 3' untranslated region (3'UTR) of SP2 mRNA to negatively regulate its expression. The transcription factor SP2 directly bound to the promoter regions of the VM formation-related proteins MMP2, MMP9, and VE-cadherin, playing a role in promoting transcription in order to regulate the VM formation ability of glioma cells.
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Affiliation(s)
- Sifei Yu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Fangfang Zhang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Lianqi Shao
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Qianshuo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Lu Zhu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China.
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14
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Shin J, Ma S, Hofer E, Patel Y, Vosberg DE, Tilley S, Roshchupkin GV, Sousa AMM, Jian X, Gottesman R, Mosley TH, Fornage M, Saba Y, Pirpamer L, Schmidt R, Schmidt H, Carrion-Castillo A, Crivello F, Mazoyer B, Bis JC, Li S, Yang Q, Luciano M, Karama S, Lewis L, Bastin ME, Harris MA, Wardlaw JM, Deary IE, Scholz M, Loeffler M, Witte AV, Beyer F, Villringer A, Armstrong NJ, Mather KA, Ames D, Jiang J, Kwok JB, Schofield PR, Thalamuthu A, Trollor JN, Wright MJ, Brodaty H, Wen W, Sachdev PS, Terzikhan N, Evans TE, Adams HHHH, Ikram MA, Frenzel S, Auwera-Palitschka SVD, Wittfeld K, Bülow R, Grabe HJ, Tzourio C, Mishra A, Maingault S, Debette S, Gillespie NA, Franz CE, Kremen WS, Ding L, Jahanshad N, Sestan N, Pausova Z, Seshadri S, Paus T. Global and Regional Development of the Human Cerebral Cortex: Molecular Architecture and Occupational Aptitudes. Cereb Cortex 2020; 30:4121-4139. [PMID: 32198502 DOI: 10.1093/cercor/bhaa035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have carried out meta-analyses of genome-wide association studies (GWAS) (n = 23 784) of the first two principal components (PCs) that group together cortical regions with shared variance in their surface area. PC1 (global) captured variations of most regions, whereas PC2 (visual) was specific to the primary and secondary visual cortices. We identified a total of 18 (PC1) and 17 (PC2) independent loci, which were replicated in another 25 746 individuals. The loci of the global PC1 included those associated previously with intracranial volume and/or general cognitive function, such as MAPT and IGF2BP1. The loci of the visual PC2 included DAAM1, a key player in the planar-cell-polarity pathway. We then tested associations with occupational aptitudes and, as predicted, found that the global PC1 was associated with General Learning Ability, and the visual PC2 was associated with the Form Perception aptitude. These results suggest that interindividual variations in global and regional development of the human cerebral cortex (and its molecular architecture) cascade-albeit in a very limited manner-to behaviors as complex as the choice of one's occupation.
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Affiliation(s)
- Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, M5G 0A4 ON, M5G 0A4, Canada.,Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Shaojie Ma
- Department of Genetics, Yale University School of Medicine, New Haven, 06510 CT, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, 06510 CT, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria.,Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, 8036 Graz, Austria
| | - Yash Patel
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Daniel E Vosberg
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Steven Tilley
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Gennady V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus MC, 3015 Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - André M M Sousa
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, 06510 CT, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, 77030 Houston, 77030 TX, USA
| | | | - Thomas H Mosley
- University of Mississippi Medical Center, Jackson, 39216 MS, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, 77030 Houston, 77030 TX, USA
| | - Yasaman Saba
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8036 Graz, Austria
| | - Lukas Pirpamer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
| | - Helena Schmidt
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8036 Graz, Austria
| | - Amaia Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 Nijmegen, The Netherlands
| | - Fabrice Crivello
- Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, et Université de Bordeaux, F-33000 Bordeaux, France
| | - Bernard Mazoyer
- Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, et Université de Bordeaux, F-33000 Bordeaux, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, 98101 WA, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK.,Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Sherif Karama
- Montreal Neurological Institute, McGill University, H3A 2B4 Montreal, QC, Canada
| | - Lindsay Lewis
- Montreal Neurological Institute, McGill University, H3A 2B4 Montreal, QC, Canada
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Mathew A Harris
- Centre for Clinical Brain Sciences, University of Edinburgh, EH8 9YL Edinburgh, UK.,Division of Psychiatry, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK.,UK Dementia Research Institute, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Ian E Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK.,Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04109 Leipzig, Germany.,LIFE Research Center for Civilization Diseases, 04103 Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04109 Leipzig, Germany.,LIFE Research Center for Civilization Diseases, 04103 Leipzig, Germany
| | - A Veronica Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany.,Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany.,Day Clinic for Cognitive Neurology, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Frauke Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany.,Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany
| | - Arno Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany.,Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany.,Day Clinic for Cognitive Neurology, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, 6150 Perth, WA, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia.,Neuroscience Research Australia, 2031 Sydney, NSW, Australia
| | - David Ames
- National Ageing Research Institute, Royal Melbourne Hospital, 3052 Melbourne, VIC, Australia.,Academic Unit for Psychiatry of Old Age, St. Vincent's Health, The University of Melbourne, 3010 Melbourne, VIC, Australia
| | - Jiyang Jiang
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, 2050 Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, 2031 Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Julian N Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia.,Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, 2031 Sydney, NSW, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, 4072 St Lucia, QLD, Australia.,Centre for Advanced Imaging, The University of Queensland, 4072 St Lucia, QLD, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia.,Dementia Centre for Research Collaboration, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Wei Wen
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia.,Neuropsychiatric Institute, Prince of Wales Hospital, 2031 Sydney, NSW, Australia
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Tavia E Evans
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Hieab H H H Adams
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands.,Department of Neurology, Erasmus MC University Medical Centre, 3015 Rotterdam, The Netherlands
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Sandra van der Auwera-Palitschka
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany.,44German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany.,44German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany.,44German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Christophe Tzourio
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France.,Department of Neurology, CHU de Bordeaux, F-33000 Bordeaux, France
| | - Aniket Mishra
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Sophie Maingault
- Institut des Maladies Neurodégénratives, UMR 5293, CEA, CNRS, University of Bordeaux, Ubordeaux, F-33000 Bordeaux, France
| | - Stephanie Debette
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France.,Department of Neurology, CHU de Bordeaux, F-33000 Bordeaux, France.,Department of Neurology, Boston University School of Medicine, Boston, 02118 MA, USA
| | - Nathan A Gillespie
- Virginia Institute for Psychiatric and Behavioural Genetics, Virginia Commonwealth University, Richmond, 23284 VA, USA
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, 92093 CA, USA.,Center for Behavior Genetics of Aging, University of California, San Diego, 92093 CA, USA
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, 92093 CA, USA.,Center for Behavior Genetics of Aging, University of California, San Diego, 92093 CA, USA.,VA San Diego Center of Excellence for Stress and Mental Health, San Diego, 92161 CA, USA
| | - Linda Ding
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, 90033 CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, 90033 CA, USA
| | | | - Nenad Sestan
- Department of Genetics, Yale University School of Medicine, New Haven, 06510 CT, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, 06510 CT, USA
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, M5G 0A4 ON, M5G 0A4, Canada.,Department of Physiology, University of Toronto, Toronto, M5S 1A8 ON, Canada.,Department of Nutritional Sciences, University of Toronto, Toronto, M5S 1A8 ON, Canada
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, 02118 MA, USA.,55Department of Epidemiology and Biostatistics, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, 78229 TX, USA
| | - Tomas Paus
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada.,Department of Psychology, University of Toronto, Toronto, M5S 3G3 ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, M5T 1R8 ON, Canada
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15
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Johnson CA, Ghashghaei HT. Sp2 regulates late neurogenic but not early expansive divisions of neural stem cells underlying population growth in the mouse cortex. Development 2020; 147:dev186056. [PMID: 32001437 PMCID: PMC7044455 DOI: 10.1242/dev.186056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/23/2020] [Indexed: 12/18/2022]
Abstract
Cellular and molecular mechanisms underlying the switch from self-amplification of cortical stem cells to neuronal and glial generation are incompletely understood, despite their importance for neural development. Here, we have investigated the role of the transcription factor specificity protein 2 (Sp2) in expansive and neurogenic divisions of the developing cerebral cortex by combining conditional genetic deletion with the mosaic analysis with double markers (MADM) system in mice. We find that loss of Sp2 in progenitors undergoing neurogenic divisions results in prolonged mitosis due to extension of early mitotic stages. This disruption is correlated with depletion of the populations of upper layer neurons in the cortex. In contrast, early cortical neural stem cells proliferate and expand normally in the absence of Sp2. These results indicate a stage-specific requirement for Sp2 in neural stem and progenitor cells, and reveal mechanistic differences between the early expansive and later neurogenic periods of cortical development.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Caroline A Johnson
- Department of Molecular Biomedical Sciences College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - H Troy Ghashghaei
- Department of Molecular Biomedical Sciences College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
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16
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Li L, Jin J, Yang XJ. Histone Deacetylase 3 Governs Perinatal Cerebral Development via Neural Stem and Progenitor Cells. iScience 2019; 20:148-167. [PMID: 31569049 PMCID: PMC6823663 DOI: 10.1016/j.isci.2019.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/01/2019] [Accepted: 09/11/2019] [Indexed: 12/13/2022] Open
Abstract
We report that cerebrum-specific inactivation of the histone deacetylase 3 (HDAC3) gene causes striking developmental defects in the neocortex, hippocampus, and corpus callosum; post-weaning lethality; and abnormal behaviors, including hyperactivity and anxiety. The defects are due to rapid loss of embryonic neural stem and progenitor cells (NSPCs). Premature neurogenesis and abnormal neuronal migration in the mutant brain alter NSPC homeostasis. Mutant cerebral cortices also display augmented DNA damage responses, apoptosis, and histone hyperacetylation. Moreover, mutant NSPCs are impaired in forming neurospheres in vitro, and treatment with the HDAC3-specific inhibitor RGFP966 abolishes neurosphere formation. Transcriptomic analyses of neonatal cerebral cortices and cultured neurospheres support that HDAC3 regulates transcriptional programs through interaction with different transcription factors, including NFIB. These findings establish HDAC3 as a major deacetylase critical for perinatal development of the mouse cerebrum and NSPCs, thereby suggesting a direct link of this enzymatic epigenetic regulator to human cerebral and intellectual development. HDAC3 inactivation causes developmental defects in the neocortex and hippocampus HDAC3 loss leads to depletion of embryonic neural stem and progenitor cells HDAC3 inhibition abolishes neurosphere formation in vitro HDAC3 interacts with NFIB and other transcription factors in cerebral development
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Affiliation(s)
- Lin Li
- The Rosalind & Morris Goodman Cancer Research Center, Montreal, QC H3A 1A3, Canada; Department of Medicine and McGill University, Montreal, QC H3A 1A3, Canada
| | - Jianliang Jin
- The Rosalind & Morris Goodman Cancer Research Center, Montreal, QC H3A 1A3, Canada; Research Center for Bone and Stem Cells, Department of Human Anatomy, Key Laboratory of Aging & Disease, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, Montreal, QC H3A 1A3, Canada; Department of Medicine and McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Department of Medicine, McGill University Health Center, Montreal, QC H3A 1A3, Canada.
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17
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Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
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18
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Bryois J, Garrett ME, Song L, Safi A, Giusti-Rodriguez P, Johnson GD, Shieh AW, Buil A, Fullard JF, Roussos P, Sklar P, Akbarian S, Haroutunian V, Stockmeier CA, Wray GA, White KP, Liu C, Reddy TE, Ashley-Koch A, Sullivan PF, Crawford GE. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nat Commun 2018; 9:3121. [PMID: 30087329 PMCID: PMC6081462 DOI: 10.1038/s41467-018-05379-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/28/2018] [Indexed: 01/19/2023] Open
Abstract
Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants.
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Affiliation(s)
- Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | | | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | | | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Annie W Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Alfonso Buil
- Research Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, 4000, Denmark
| | - John F Fullard
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Pamela Sklar
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- MIRECC, JJ Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Craig A Stockmeier
- Department of Psychiatry and Human Behavior, Center for Psychiatric Neuroscience, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Kevin P White
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Timothy E Reddy
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Durham, NC, 27701, USA
- Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-7264, USA.
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, 27599-7264, USA.
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, 27708, USA.
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19
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Liu BH, Wang J, Li CM, Qi L, Song YH, Pan H, Li TY, Wang BB. Novel mutation in SP2 in a Chinese pedigree with Neural tube defects. CNS Neurosci Ther 2018; 24:978-980. [PMID: 29855149 DOI: 10.1111/cns.12988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Bei-Hong Liu
- Graduate School of Peking Union Medical College, Beijing, China.,Center for Genetics, National Research Institute of Family Planning, Beijing, China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Cong-Min Li
- Zhengzhou First People's Hospital, Henan, China
| | - Lin Qi
- Children's Hospital Affiliated to Zhengzhou University, Henan, China
| | - Yan-Hong Song
- Children's Hospital Affiliated to Zhengzhou University, Henan, China
| | - Hong Pan
- Center for Genetics, National Research Institute of Family Planning, Beijing, China
| | - Teng-Yan Li
- Center for Genetics, National Research Institute of Family Planning, Beijing, China
| | - Bin-Bin Wang
- Graduate School of Peking Union Medical College, Beijing, China.,Center for Genetics, National Research Institute of Family Planning, Beijing, China
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20
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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21
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de la Torre-Ubieta L, Stein JL, Won H, Opland CK, Liang D, Lu D, Geschwind DH. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 2018; 172:289-304.e18. [PMID: 29307494 PMCID: PMC5924568 DOI: 10.1016/j.cell.2017.12.014] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 09/14/2017] [Accepted: 12/07/2017] [Indexed: 01/19/2023]
Abstract
Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. We link distal regulatory elements (DREs) to their cognate gene(s) together with chromatin interaction data and show that target genes of human-gained enhancers (HGEs) regulate cortical neurogenesis and are enriched in outer radial glia, a cell type linked to human cortical evolution. We experimentally validate the regulatory effects of predicted enhancers for FGFR2 and EOMES. We observe that common genetic variants associated with educational attainment, risk for neuropsychiatric disease, and intracranial volume are enriched within regulatory elements involved in cortical neurogenesis, demonstrating the importance of this early developmental process for adult human cognitive function.
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Affiliation(s)
- Luis de la Torre-Ubieta
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carli K Opland
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daning Lu
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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22
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Beattie R, Hippenmeyer S. Mechanisms of radial glia progenitor cell lineage progression. FEBS Lett 2017; 591:3993-4008. [PMID: 29121403 PMCID: PMC5765500 DOI: 10.1002/1873-3468.12906] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 12/11/2022]
Abstract
The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non‐cell‐autonomous or community effects in regulating RGP proliferation behavior and lineage progression.
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Affiliation(s)
- Robert Beattie
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity. J Neurosci 2017; 36:11394-11401. [PMID: 27911741 DOI: 10.1523/jneurosci.2359-16.2016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 12/16/2022] Open
Abstract
This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.
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24
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Wegener A, Küspert M, Sock E, Philipsen S, Suske G, Wegner M. Sp2 is the only glutamine-rich specificity protein with minor impact on development and differentiation in myelinating glia. J Neurochem 2016; 140:245-256. [PMID: 27889927 DOI: 10.1111/jnc.13908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 02/04/2023]
Abstract
Oligodendrocytes and Schwann cells are the myelinating glia of the vertebrate nervous system and by generation of myelin sheaths allow rapid saltatory conduction. Previous in vitro work had pointed to a role of the zinc finger containing specificity proteins Sp1 and Sp3 as major regulators of glial differentiation and myelination. Here, we asked whether such a role is also evident in vivo using mice with specific deletions of Sp1 or Sp3 in myelinating glia. We also studied glia-specific conditional Sp2- and constitutive Sp4-deficient mice to include all related glutamine-rich Sp factors into our analysis. Surprisingly, we did not detect developmental Schwann cell abnormalities in any of the mutant mice. Oligodendrocyte development and differentiation was also not fundamentally affected as oligodendrocytes were present in all mouse mutants and retained their ability to differentiate and initiate myelin gene expression. The most severe defect we observed was a 50% reduction in Mbp- and proteolipid protein 1 (Plp1)-positive differentiating oligodendrocytes in Sp2 mutants at birth. Unexpectedly, glial development appeared undisturbed even in the joint absence of Sp1 and Sp3. We conclude that Sp2 has a minor effect on the differentiation of myelinating glia, and that glutamine-rich Sp proteins are not essential regulators of the process.
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Affiliation(s)
- Amélie Wegener
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Melanie Küspert
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Guntram Suske
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
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25
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Cittaro D, Lampis V, Luchetti A, Coccurello R, Guffanti A, Felsani A, Moles A, Stupka E, D' Amato FR, Battaglia M. Histone Modifications in a Mouse Model of Early Adversities and Panic Disorder: Role for Asic1 and Neurodevelopmental Genes. Sci Rep 2016; 6:25131. [PMID: 27121911 PMCID: PMC4848503 DOI: 10.1038/srep25131] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Hyperventilation following transient, CO2-induced acidosis is ubiquitous in mammals and heritable. In humans, respiratory and emotional hypersensitivity to CO2 marks separation anxiety and panic disorders, and is enhanced by early-life adversities. Mice exposed to the repeated cross-fostering paradigm (RCF) of interference with maternal environment show heightened separation anxiety and hyperventilation to 6% CO2-enriched air. Gene-environment interactions affect CO2 hypersensitivity in both humans and mice. We therefore hypothesised that epigenetic modifications and increased expression of genes involved in pH-detection could explain these relationships. Medullae oblongata of RCF- and normally-reared female outbred mice were assessed by ChIP-seq for H3Ac, H3K4me3, H3K27me3 histone modifications, and by SAGE for differential gene expression. Integration of multiple experiments by network analysis revealed an active component of 148 genes pointing to the mTOR signalling pathway and nociception. Among these genes, Asic1 showed heightened mRNA expression, coherent with RCF-mice’s respiratory hypersensitivity to CO2 and altered nociception. Functional enrichment and mRNA transcript analyses yielded a consistent picture of enhancement for several genes affecting chemoception, neurodevelopment, and emotionality. Particularly, results with Asic1 support recent human findings with panic and CO2 responses, and provide new perspectives on how early adversities and genes interplay to affect key components of panic and related disorders.
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Affiliation(s)
- Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Lampis
- Developmental Psychopathology Unit, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Luchetti
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Roberto Coccurello
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Alessandro Guffanti
- Laboratory of Molecular Neuroscience, Department of Biological Chemistry, The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,Genomnia srl, Lainate, Italy
| | - Armando Felsani
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy.,Genomnia srl, Lainate, Italy
| | - Anna Moles
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy.,Genomnia srl, Lainate, Italy
| | - Elia Stupka
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Francesca R D' Amato
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Marco Battaglia
- Department of Psychiatry, University Of Toronto, Toronto, Canada.,Division of Child and Youth Mental Health, Centre for Addiction and Mental Health, Toronto, Canada
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TransOmic analysis of forebrain sections in Sp2 conditional knockout embryonic mice using IR-MALDESI imaging of lipids and LC-MS/MS label-free proteomics. Anal Bioanal Chem 2016; 408:3453-74. [PMID: 26942738 DOI: 10.1007/s00216-016-9421-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/08/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
Quantitative methods for detection of biological molecules are needed more than ever before in the emerging age of "omics" and "big data." Here, we provide an integrated approach for systematic analysis of the "lipidome" in tissue. To test our approach in a biological context, we utilized brain tissue selectively deficient for the transcription factor Specificity Protein 2 (Sp2). Conditional deletion of Sp2 in the mouse cerebral cortex results in developmental deficiencies including disruption of lipid metabolism. Silver (Ag) cationization was implemented for infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) to enhance the ion abundances for olefinic lipids, as these have been linked to regulation by Sp2. Combining Ag-doped and conventional IR-MALDESI imaging, this approach was extended to IR-MALDESI imaging of embryonic mouse brains. Further, our imaging technique was combined with bottom-up shotgun proteomic LC-MS/MS analysis and western blot for comparing Sp2 conditional knockout (Sp2-cKO) and wild-type (WT) cortices of tissue sections. This provided an integrated omics dataset which revealed many specific changes to fundamental cellular processes and biosynthetic pathways. In particular, step-specific altered abundances of nucleotides, lipids, and associated proteins were observed in the cerebral cortices of Sp2-cKO embryos.
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Zinc finger independent genome-wide binding of Sp2 potentiates recruitment of histone-fold protein Nf-y distinguishing it from Sp1 and Sp3. PLoS Genet 2015; 11:e1005102. [PMID: 25793500 PMCID: PMC4368557 DOI: 10.1371/journal.pgen.1005102] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are grouped into families based on sequence similarity within functional domains, particularly DNA-binding domains. The Specificity proteins Sp1, Sp2 and Sp3 are paradigmatic of closely related transcription factors. They share amino-terminal glutamine-rich regions and a conserved carboxy-terminal zinc finger domain that can bind to GC rich motifs in vitro. All three Sp proteins are ubiquitously expressed; yet they carry out unique functions in vivo raising the question of how specificity is achieved. Crucially, it is unknown whether they bind to distinct genomic sites and, if so, how binding site selection is accomplished. In this study, we have examined the genomic binding patterns of Sp1, Sp2 and Sp3 in mouse embryonic fibroblasts by ChIP-seq. Sp1 and Sp3 essentially occupy the same promoters and localize to GC boxes. The genomic binding pattern of Sp2 is different; Sp2 primarily localizes at CCAAT motifs. Consistently, re-expression of Sp2 and Sp3 mutants in corresponding knockout MEFs revealed strikingly different modes of genomic binding site selection. Most significantly, while the zinc fingers dictate genomic binding of Sp3, they are completely dispensable for binding of Sp2. Instead, the glutamine-rich amino-terminal region is sufficient for recruitment of Sp2 to its target promoters in vivo. We have identified the trimeric histone-fold CCAAT box binding transcription factor Nf-y as the major partner for Sp2-chromatin interaction. Nf-y is critical for recruitment of Sp2 to co-occupied regulatory elements. Equally, Sp2 potentiates binding of Nf-y to shared sites indicating the existence of an extensive Sp2-Nf-y interaction network. Our results unveil strikingly different recruitment mechanisms of Sp1/Sp2/Sp3 transcription factor members uncovering an unexpected layer of complexity in their binding to chromatin in vivo. A major question in eukaryotic gene regulation is how transcription factors with similar structural features elicit specific biological responses. We used the three transcription factors Sp1, Sp2 and Sp3 as a paradigm for investigating this question. All three proteins are ubiquitously expressed, and they share glutamine-rich domains as well as a conserved bona fide zinc finger DNA binding domain. Yet, each of the three proteins carries out unique functions in vivo, and each is absolutely essential for mouse development. By genome-wide binding analysis, we found that Sp1 and Sp3 on the one hand, and Sp2 on the other hand engage completely different protein domains for their genomic binding site selection. Most strikingly, the zinc finger domain of Sp2 is dispensable for recruitment to its target sites in vivo. Moreover, we provide strong evidence that the histone-fold protein Nf-y is necessary for recruitment of Sp2. Conversely, Sp2 potentiates Nf-y binding showing that binding of Sp2 and Nf-y to shared sites is mutually dependent. Our findings uncover an unexpected mechanistic diversity in promoter recognition by seemingly similar transcription factors. This work has broader implications for our understanding of how members of other multi-protein transcription factor families could achieve specificity.
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Li MD, Burns TC, Morgan AA, Khatri P. Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases. Acta Neuropathol Commun 2014; 2:93. [PMID: 25187168 PMCID: PMC4167139 DOI: 10.1186/s40478-014-0093-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 01/11/2023] Open
Abstract
Introduction Neurodegenerative diseases share common pathologic features including neuroinflammation, mitochondrial dysfunction and protein aggregation, suggesting common underlying mechanisms of neurodegeneration. We undertook a meta-analysis of public gene expression data for neurodegenerative diseases to identify a common transcriptional signature of neurodegeneration. Results Using 1,270 post-mortem central nervous system tissue samples from 13 patient cohorts covering four neurodegenerative diseases, we identified 243 differentially expressed genes, which were similarly dysregulated in 15 additional patient cohorts of 205 samples including seven neurodegenerative diseases. This gene signature correlated with histologic disease severity. Metallothioneins featured prominently among differentially expressed genes, and functional pathway analysis identified specific convergent themes of dysregulation. MetaCore network analyses revealed various novel candidate hub genes (e.g. STAU2). Genes associated with M1-polarized macrophages and reactive astrocytes were strongly enriched in the meta-analysis data. Evaluation of genes enriched in neurons revealed 70 down-regulated genes, over half not previously associated with neurodegeneration. Comparison with aging brain data (3 patient cohorts, 221 samples) revealed 53 of these to be unique to neurodegenerative disease, many of which are strong candidates to be important in neuropathogenesis (e.g. NDN, NAP1L2). ENCODE ChIP-seq analysis predicted common upstream transcriptional regulators not associated with normal aging (REST, RBBP5, SIN3A, SP2, YY1, ZNF143, IKZF1). Finally, we removed genes common to neurodegeneration from disease-specific gene signatures, revealing uniquely robust immune response and JAK-STAT signaling in amyotrophic lateral sclerosis. Conclusions Our results implicate pervasive bioenergetic deficits, M1-type microglial activation and gliosis as unifying themes of neurodegeneration, and identify numerous novel genes associated with neurodegenerative processes. Electronic supplementary material The online version of this article (doi:10.1186/s40478-014-0093-y) contains supplementary material, which is available to authorized users.
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29
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Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11515-013-1279-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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