1
|
Peter M, Shipman S, Heo J, Macklis JD. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized human neural progenitor cells. iScience 2024; 27:109911. [PMID: 38784012 PMCID: PMC11111830 DOI: 10.1016/j.isci.2024.109911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/04/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Differentiation of human pluripotent stem cells (hPSCs) into subtype-specific neurons holds substantial potential for disease modeling in vitro. For successful differentiation, a detailed understanding of the transcriptional networks regulating cell fate decisions is critical. The heterochronic nature of neurodevelopment, during which distinct cells in the brain and during in vitro differentiation acquire their fates in an unsynchronized manner, hinders pooled transcriptional comparisons. One approach is to "translate" chronologic time into linear developmental and maturational time. Simple binary promotor-driven fluorescent proteins (FPs) to pool similar cells are unable to achieve this goal, due to asynchronous promotor onset in individual cells. We tested five fluorescent timer (FT) molecules expressed from the endogenous paired box 6 (PAX6) promoter in 293T and human hPSCs. Each of these FT systems faithfully reported chronologic time in 293T cells, but none of the FT constructs followed the same fluorescence kinetics in human neural progenitor cells.
Collapse
Affiliation(s)
- Manuel Peter
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Seth Shipman
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jaewon Heo
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D. Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
2
|
Pottmeier P, Nikolantonaki D, Lanner F, Peuckert C, Jazin E. Sex-biased gene expression during neural differentiation of human embryonic stem cells. Front Cell Dev Biol 2024; 12:1341373. [PMID: 38764741 PMCID: PMC11101176 DOI: 10.3389/fcell.2024.1341373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Sex differences in the developing human brain are primarily attributed to hormonal influence. Recently however, genetic differences and their impact on the developing nervous system have attracted increased attention. To understand genetically driven sexual dimorphisms in neurodevelopment, we investigated genome-wide gene expression in an in vitro differentiation model of male and female human embryonic stem cell lines (hESC), independent of the effects of human sex hormones. Four male and four female-derived hESC lines were differentiated into a population of mixed neurons over 37 days. Differential gene expression and gene set enrichment analyses were conducted on bulk RNA sequencing data. While similar differentiation tendencies in all cell lines demonstrated the robustness and reproducibility of our differentiation protocol, we found sex-biased gene expression already in undifferentiated ESCs at day 0, but most profoundly after 37 days of differentiation. Male and female cell lines exhibited sex-biased expression of genes involved in neurodevelopment, suggesting that sex influences the differentiation trajectory. Interestingly, the highest contribution to sex differences was found to arise from the male transcriptome, involving both Y chromosome and autosomal genes. We propose 13 sex-biased candidate genes (10 upregulated in male cell lines and 3 in female lines) that are likely to affect neuronal development. Additionally, we confirmed gene dosage compensation of X/Y homologs escaping X chromosome inactivation through their Y homologs and identified a significant overexpression of the Y-linked demethylase UTY and KDM5D in male hESC during neuron development, confirming previous results in neural stem cells. Our results suggest that genetic sex differences affect neuronal differentiation trajectories, which could ultimately contribute to sex biases during human brain development.
Collapse
Affiliation(s)
- Philipp Pottmeier
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Danai Nikolantonaki
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fredrik Lanner
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| |
Collapse
|
3
|
Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
Collapse
Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
| |
Collapse
|
4
|
Khodosevich K, Dragicevic K, Howes O. Drug targeting in psychiatric disorders - how to overcome the loss in translation? Nat Rev Drug Discov 2024; 23:218-231. [PMID: 38114612 DOI: 10.1038/s41573-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
In spite of major efforts and investment in development of psychiatric drugs, many clinical trials have failed in recent decades, and clinicians still prescribe drugs that were discovered many years ago. Although multiple reasons have been discussed for the drug development deadlock, we focus here on one of the major possible biological reasons: differences between the characteristics of drug targets in preclinical models and the corresponding targets in patients. Importantly, based on technological advances in single-cell analysis, we propose here a framework for the use of available and newly emerging knowledge from single-cell and spatial omics studies to evaluate and potentially improve the translational predictivity of preclinical models before commencing preclinical and, in particular, clinical studies. We believe that these recommendations will improve preclinical models and the ability to assess drugs in clinical trials, reducing failure rates in expensive late-stage trials and ultimately benefitting psychiatric drug discovery and development.
Collapse
Affiliation(s)
- Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health, University of Copenhagen, Copenhagen, Denmark.
| | - Katarina Dragicevic
- Biotech Research and Innovation Centre, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Oliver Howes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
| |
Collapse
|
5
|
Bershteyn M, Bröer S, Parekh M, Maury Y, Havlicek S, Kriks S, Fuentealba L, Lee S, Zhou R, Subramanyam G, Sezan M, Sevilla ES, Blankenberger W, Spatazza J, Zhou L, Nethercott H, Traver D, Hampel P, Kim H, Watson M, Salter N, Nesterova A, Au W, Kriegstein A, Alvarez-Buylla A, Rubenstein J, Banik G, Bulfone A, Priest C, Nicholas CR. Human pallial MGE-type GABAergic interneuron cell therapy for chronic focal epilepsy. Cell Stem Cell 2023; 30:1331-1350.e11. [PMID: 37802038 PMCID: PMC10993865 DOI: 10.1016/j.stem.2023.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 03/17/2023] [Accepted: 08/25/2023] [Indexed: 10/08/2023]
Abstract
Mesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy. One-third of patients have drug-refractory seizures and are left with suboptimal therapeutic options such as brain tissue-destructive surgery. Here, we report the development and characterization of a cell therapy alternative for drug-resistant MTLE, which is derived from a human embryonic stem cell line and comprises cryopreserved, post-mitotic, medial ganglionic eminence (MGE) pallial-type GABAergic interneurons. Single-dose intrahippocampal delivery of the interneurons in a mouse model of chronic MTLE resulted in consistent mesiotemporal seizure suppression, with most animals becoming seizure-free and surviving longer. The grafted interneurons dispersed locally, functionally integrated, persisted long term, and significantly reduced dentate granule cell dispersion, a pathological hallmark of MTLE. These disease-modifying effects were dose-dependent, with a broad therapeutic range. No adverse effects were observed. These findings support an ongoing phase 1/2 clinical trial (NCT05135091) for drug-resistant MTLE.
Collapse
Affiliation(s)
| | - Sonja Bröer
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Mansi Parekh
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Yves Maury
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Steven Havlicek
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Sonja Kriks
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Luis Fuentealba
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Seonok Lee
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Robin Zhou
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | - Meliz Sezan
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | | | - Julien Spatazza
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Li Zhou
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - David Traver
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Philip Hampel
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Hannah Kim
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Michael Watson
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Naomi Salter
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | - Wai Au
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Arnold Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arturo Alvarez-Buylla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Rubenstein
- Department of Psychiatry, Weill Institute for Neurosciences, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gautam Banik
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | | | - Cory R Nicholas
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA.
| |
Collapse
|
6
|
Peter M, Shipman S, Macklis JD. Limitations of fluorescent timer protein maturation kinetics to isolate transcriptionally synchronized cortically differentiating human pluripotent stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552012. [PMID: 37609140 PMCID: PMC10441295 DOI: 10.1101/2023.08.04.552012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Differentiation of human pluripotent stem cells (hPSC) into distinct neuronal populations holds substantial potential for disease modeling in vitro, toward both elucidation of pathobiological mechanisms and screening of potential therapeutic agents. For successful differentiation of hPSCs into subtype-specific neurons using in vitro protocols, detailed understanding of the transcriptional networks and their dynamic programs regulating endogenous cell fate decisions is critical. One major roadblock is the heterochronic nature of neurodevelopment, during which distinct cells and cell types in the brain and during in vitro differentiation mature and acquire their fates in an unsynchronized manner, hindering pooled transcriptional comparisons. One potential approach is to "translate" chronologic time into linear developmental and maturational time. Attempts to partially achieve this using simple binary promotor-driven fluorescent proteins (FPs) to pool similar cells have not been able to achieve this goal, due to asynchrony of promotor onset in individual cells. Toward solving this, we generated and tested a range of knock-in hPSC lines that express five distinct dual FP timer systems or single time-resolved fluorescent timer (FT) molecules, either in 293T cells or in human hPSCs driving expression from the endogenous paired box 6 (PAX6) promoter of cerebral cortex progenitors. While each of these dual FP or FT systems faithfully reported chronologic time when expressed from a strong inducible promoter in 293T cells, none of the tested FP/FT constructs followed the same fluorescence kinetics in developing human neural progenitor cells, and were unsuccessful in identification and isolation of distinct, developmentally synchronized cortical progenitor populations based on ratiometric fluorescence. This work highlights unique and often surprising expression kinetics and regulation in specific cell types differentiating from hPSCs.
Collapse
Affiliation(s)
- Manuel Peter
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Seth Shipman
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Current Address: Gladstone Institute of Data Science and Biotechnology, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
| | - Jeffrey D. Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
7
|
Tian L, Wu W, Yu T. Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features. Biomolecules 2023; 13:1153. [PMID: 37509188 PMCID: PMC10377046 DOI: 10.3390/biom13071153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Random Forest (RF) is a widely used machine learning method with good performance on classification and regression tasks. It works well under low sample size situations, which benefits applications in the field of biology. For example, gene expression data often involve much larger numbers of features (p) compared to the size of samples (n). Though the predictive accuracy using RF is often high, there are some problems when selecting important genes using RF. The important genes selected by RF are usually scattered on the gene network, which conflicts with the biological assumption of functional consistency between effective features. To improve feature selection by incorporating external topological information between genes, we propose the Graph Random Forest (GRF) for identifying highly connected important features by involving the known biological network when constructing the forest. The algorithm can identify effective features that form highly connected sub-graphs and achieve equivalent classification accuracy to RF. To evaluate the capability of our proposed method, we conducted simulation experiments and applied the method to two real datasets-non-small cell lung cancer RNA-seq data from The Cancer Genome Atlas, and human embryonic stem cell RNA-seq dataset (GSE93593). The resulting high classification accuracy, connectivity of selected sub-graphs, and interpretable feature selection results suggest the method is a helpful addition to graph-based classification models and feature selection procedures.
Collapse
Affiliation(s)
- Leqi Tian
- School of Data Science, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Research Institute of Big Data, Shenzhen 518172, China
| | - Wenbin Wu
- School of Data Science, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Tianwei Yu
- School of Data Science, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Research Institute of Big Data, Shenzhen 518172, China
- Guangdong Provincial Key Laboratory of Big Data Computing, Shenzhen 518172, China
| |
Collapse
|
8
|
Frank JA, Singh M, Cullen HB, Kirou RA, Benkaddour-Boumzaouad M, Cortes JL, Garcia-Perez J, Coyne CB, Feschotte C. Evolution and antiviral activity of a human protein of retroviral origin. Science 2022; 378:422-428. [PMID: 36302021 PMCID: PMC10542854 DOI: 10.1126/science.abq7871] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endogenous retroviruses are abundant components of mammalian genomes descended from ancient germline infections. In several mammals, the envelope proteins encoded by these elements protect against exogenous viruses, but this activity has not been documented with endogenously expressed envelopes in humans. We report that the human genome harbors a large pool of envelope-derived sequences with the potential to restrict retroviral infection. To test this, we characterized an envelope-derived protein, Suppressyn. We found that Suppressyn is expressed in human preimplantation embryos and developing placenta using its ancestral retroviral promoter. Cell culture assays showed that Suppressyn, and its hominoid orthologs, could restrict infection by extant mammalian type D retroviruses. Our data support a generalizable model of retroviral envelope co-option for host immunity and genome defense.
Collapse
Affiliation(s)
- John A. Frank
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, NY, USA
| | - Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, NY, USA
| | - Harrison B. Cullen
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, NY, USA
| | - Raphael A. Kirou
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, NY, USA
| | - Meriem Benkaddour-Boumzaouad
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; PTS Granada, Spain
| | - Jose L. Cortes
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; PTS Granada, Spain
- Eppendorf; Iberica, Spain
| | - Jose Garcia-Perez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; PTS Granada, Spain
- MRC-Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital; Edinburgh, UK
| | - Carolyn B. Coyne
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, NY, USA
| |
Collapse
|
9
|
Schuster J, Klar J, Khalfallah A, Laan L, Hoeber J, Fatima A, Sequeira VM, Jin Z, Korol SV, Huss M, Nordgren A, Anderlid BM, Gallant C, Birnir B, Dahl N. ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function. Front Mol Neurosci 2022; 15:988993. [PMID: 36353360 PMCID: PMC9637781 DOI: 10.3389/fnmol.2022.988993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 07/30/2023] Open
Abstract
Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.
Collapse
Affiliation(s)
- Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ayda Khalfallah
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Loora Laan
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Velin Marita Sequeira
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Sergiy V. Korol
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Mikael Huss
- Wallenberg Long-Term Bioinformatics Support, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Bryndis Birnir
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| |
Collapse
|
10
|
Tasnim K, Liu J. Emerging Bioelectronics for Brain Organoid Electrophysiology. J Mol Biol 2022; 434:167165. [PMID: 34293341 PMCID: PMC8766612 DOI: 10.1016/j.jmb.2021.167165] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 01/17/2023]
Abstract
Human brain organoids are generated from three-dimensional (3D) cultures of human induced pluripotent stem cells and embryonic stem cells, which partially replicate the development and complexity of the human brain. Many methods have been used to characterize the structural and molecular phenotypes of human brain organoids. Further understanding the electrophysiological phenotypes of brain organoids requires advanced electrophysiological measurement technologies to achieve long-term stable 3D recording over the time course of the organoid development with single-cell, millisecond spatiotemporal resolution. In this review, first, we briefly introduce the development, generation, and applications of human brain organoids. We then discuss the conventional methods used for characterizing the morphological, genetic, and electrical properties of brain organoids. Next, we highlight the need for characterizing electrophysiological properties of brain organoids in a minimally invasive manner. In particular, we discuss recent advances in the multi-electrode array (MEA), 3D bioelectronics, and flexible bioelectronics and their applications in brain organoid electrophysiological measurement. In addition, we introduce the recently developed cyborg organoids platform as an emerging tool for the long-term stable 3D characterization of the brain organoids electrophysiology at high spatiotemporal resolution. Finally, we discuss the perspectives of new technologies that could achieve the high-throughput, multimodal characterizations from the same brain organoids.
Collapse
Affiliation(s)
- Kazi Tasnim
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA
| | - Jia Liu
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, 02134, USA.
| |
Collapse
|
11
|
Lam DD, Nikolic AA, Zhao C, Mirza-Schreiber N, Krężel W, Oexle K, Winkelmann J. Intronic elements associated with insomnia and restless legs syndrome exhibit cell type-specific epigenetic features contributing to MEIS1 regulation. Hum Mol Genet 2021; 31:1733-1746. [PMID: 34888668 DOI: 10.1093/hmg/ddab355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022] Open
Abstract
A highly evolutionarily conserved MEIS1 intronic region is strongly associated with restless legs syndrome (RLS) and insomnia. To understand its regulatory function, we dissected the region by analyzing chromatin accessibility, enhancer-promoter contacts, DNA methylation, and eQTLs in different human neural cell types and tissues. We observed specific activity with respect to cell type and developmental maturation, indicating a prominent role for distinct highly conserved intronic elements in forebrain inhibitory neuron differentiation. Two elements were hypomethylated in neural cells with higher MEIS1 expression, suggesting a role of enhancer demethylation in gene regulation. MEIS1 eQTLs showed a striking modular chromosomal distribution, with forebrain eQTLs clustering in intron 8/9. CRISPR interference targeting of individual elements in this region attenuated MEIS1 expression, revealing a complex regulatory interplay of distinct elements. In summary, we found that MEIS1 regulation is organized in a modular pattern. Disease-associated intronic regulatory elements control MEIS1 expression with cell type and maturation stage specificity, particularly in the inhibitory neuron lineage. The precise spatiotemporal activity of these elements likely contributes to the pathogenesis of insomnia and RLS.
Collapse
Affiliation(s)
- Daniel D Lam
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Ana Antic Nikolic
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Chen Zhao
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Nazanin Mirza-Schreiber
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wojciech Krężel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Centre National de la Recherche Scientifique, UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany.,Chair of Neurogenetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| |
Collapse
|
12
|
Yu Y, Zeng Z, Xie D, Chen R, Sha Y, Huang S, Cai W, Chen W, Li W, Ke R, Sun T. Interneuron origin and molecular diversity in the human fetal brain. Nat Neurosci 2021; 24:1745-1756. [PMID: 34737447 DOI: 10.1038/s41593-021-00940-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Precise generation of excitatory neurons and inhibitory interneurons is crucial for proper formation and function of neural circuits in the mammalian brain. Because of the size and complexity of the human brain, it is a challenge to reveal the rich diversity of interneurons. To decipher origin and diversity of interneurons in the human fetal subpallium, here we show molecular features of diverse subtypes of interneuron progenitors and precursors by conducting single-cell RNA sequencing and in situ sequencing. Interneuron precursors in the medial and lateral ganglionic eminence simultaneously procure temporal and spatial identity through expressing a combination of specific sets of RNA transcripts. Acquisition of various interneuron subtypes in adult human brains occurs even at fetal stages. Our study uncovers complex molecular signatures of interneuron progenitors and precursors in the human fetal subpallium and highlights the logic and programs in the origin and lineage specification of various interneurons.
Collapse
Affiliation(s)
- Yuan Yu
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Zhiwei Zeng
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Danlin Xie
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Renliang Chen
- Taokang Institute of Neuro Medicine, Xiamen, Fujian, China
| | - Yongqiang Sha
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China.,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Shiying Huang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wanhua Chen
- Department of Clinical Laboratory, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wenjun Li
- Fujian University of Traditional Chinese Medicine Jinjiang Affliated Hospital, Quanzhou, Fujian, China
| | - Rongqin Ke
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China.,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China. .,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.
| |
Collapse
|
13
|
Roth JG, Huang MS, Li TL, Feig VR, Jiang Y, Cui B, Greely HT, Bao Z, Paşca SP, Heilshorn SC. Advancing models of neural development with biomaterials. Nat Rev Neurosci 2021; 22:593-615. [PMID: 34376834 PMCID: PMC8612873 DOI: 10.1038/s41583-021-00496-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cells have emerged as a promising in vitro model system for studying the brain. Two-dimensional and three-dimensional cell culture paradigms have provided valuable insights into the pathogenesis of neuropsychiatric disorders, but they remain limited in their capacity to model certain features of human neural development. Specifically, current models do not efficiently incorporate extracellular matrix-derived biochemical and biophysical cues, facilitate multicellular spatio-temporal patterning, or achieve advanced functional maturation. Engineered biomaterials have the capacity to create increasingly biomimetic neural microenvironments, yet further refinement is needed before these approaches are widely implemented. This Review therefore highlights how continued progression and increased integration of engineered biomaterials may be well poised to address intractable challenges in recapitulating human neural development.
Collapse
Affiliation(s)
- Julien G Roth
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle S Huang
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Thomas L Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Vivian R Feig
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Yuanwen Jiang
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Sergiu P Paşca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Sarah C Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA.
| |
Collapse
|
14
|
Fitzgerald M, Sotuyo N, Tischfield DJ, Anderson SA. Generation of cerebral cortical GABAergic interneurons from pluripotent stem cells. Stem Cells 2020; 38:1375-1386. [PMID: 32638460 DOI: 10.1002/stem.3252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/18/2020] [Accepted: 06/11/2020] [Indexed: 11/11/2022]
Abstract
The cerebral cortex functions by the complex interactions of intrinsic and extrinsic neuronal activities, glial actions, and the effects of humoral factors. The intrinsic neuronal influences are mediated by two major subclasses: excitatory glutamatergic neurons that generally have axonal projections extending beyond the neuron's locality and inhibitory GABAergic neurons that generally project locally. These interneurons can be grouped based on morphological, neurochemical, electrophysiological, axonal targeting, and circuit influence characteristics. Cortical interneurons (CIns) can also be grouped based on their origins within the subcortical telencephalon. Interneuron subtypes, of which a dozen or more are thought to exist, are characterized by combinations of these subgrouping features. Due to their well-documented relevance to the causes of and treatments for neuropsychiatric disorders, and to their remarkable capacity to migrate extensively following transplantation, there has been tremendous interest in generating cortical GABAergic interneurons from human pluripotent stem cells. In this concise review, we discuss recent progress in understanding how interneuron subtypes are generated in vivo, and how that progress is being applied to the generation of rodent and human CIns in vitro. In addition, we will discuss approaches for the rigorous designation of interneuron subgroups or subtypes in transplantation studies, and challenges to this field, including the protracted maturation of human interneurons.
Collapse
Affiliation(s)
- Megan Fitzgerald
- The Children's Hospital of Philadelphia and the University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nathaniel Sotuyo
- The Children's Hospital of Philadelphia and the University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - David J Tischfield
- The Children's Hospital of Philadelphia and the University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Stewart A Anderson
- The Children's Hospital of Philadelphia and the University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
15
|
Kim T, Chen IR, Lin Y, Wang AYY, Yang JYH, Yang P. Impact of similarity metrics on single-cell RNA-seq data clustering. Brief Bioinform 2020; 20:2316-2326. [PMID: 30137247 DOI: 10.1093/bib/bby076] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Advances in high-throughput sequencing on single-cell gene expressions [single-cell RNA sequencing (scRNA-seq)] have enabled transcriptome profiling on individual cells from complex samples. A common goal in scRNA-seq data analysis is to discover and characterise cell types, typically through clustering methods. The quality of the clustering therefore plays a critical role in biological discovery. While numerous clustering algorithms have been proposed for scRNA-seq data, fundamentally they all rely on a similarity metric for categorising individual cells. Although several studies have compared the performance of various clustering algorithms for scRNA-seq data, currently there is no benchmark of different similarity metrics and their influence on scRNA-seq data clustering. Here, we compared a panel of similarity metrics on clustering a collection of annotated scRNA-seq datasets. Within each dataset, a stratified subsampling procedure was applied and an array of evaluation measures was employed to assess the similarity metrics. This produced a highly reliable and reproducible consensus on their performance assessment. Overall, we found that correlation-based metrics (e.g. Pearson's correlation) outperformed distance-based metrics (e.g. Euclidean distance). To test if the use of correlation-based metrics can benefit the recently published clustering techniques for scRNA-seq data, we modified a state-of-the-art kernel-based clustering algorithm (SIMLR) using Pearson's correlation as a similarity measure and found significant performance improvement over Euclidean distance on scRNA-seq data clustering. These findings demonstrate the importance of similarity metrics in clustering scRNA-seq data and highlight Pearson's correlation as a favourable choice. Further comparison on different scRNA-seq library preparation protocols suggests that they may also affect clustering performance. Finally, the benchmarking framework is available at http://www.maths.usyd.edu.au/u/SMS/bioinformatics/software.html.
Collapse
Affiliation(s)
- Taiyun Kim
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Irene Rui Chen
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yingxin Lin
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Andy Yi-Yang Wang
- Department of Anaesthesia, The University of Sydney Northern Clinical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
16
|
Inglis GAS, Zhou Y, Patterson DG, Scharer CD, Han Y, Boss JM, Wen Z, Escayg A. Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons. Hum Mol Genet 2020; 29:2579-2595. [PMID: 32794569 PMCID: PMC7471504 DOI: 10.1093/hmg/ddaa150] [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: 03/23/2020] [Revised: 06/09/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022] Open
Abstract
GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.
Collapse
Affiliation(s)
- George Andrew S Inglis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanfei Han
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
17
|
Analysis of pallial/cortical interneurons in key vertebrate models of Testudines, Anurans and Polypteriform fishes. Brain Struct Funct 2020; 225:2239-2269. [PMID: 32743670 DOI: 10.1007/s00429-020-02123-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/24/2020] [Indexed: 01/09/2023]
Abstract
The organization of the pallial derivatives across vertebrates follows a comparable elementary arrangement, although not all of them possess a layered cortical structure as sophisticated as the cerebral cortex of mammals. However, its expansion along evolution has only been possible by the development and coevolution of the cellular networks formed by excitatory neurons and inhibitory interneurons. Thus, the comparative analysis of interneuron types in vertebrate models of key evolutionary significance will provide important information, due to the extraordinary anatomical sophistication of their interneuron systems with simpler behavioral implications. Particularly in mammals, the main consensus for classifying interneuron types is based on non-overlapping markers, which do not form a single population, but consist of several distinct classes of inhibitory cells showing co-expression of other markers. In our study, we analyzed immunohistochemically the expression of the main markers like somatostatin (SOM), parvalbumin (PV), calretinin (CR), calbindin (CB), neuropeptide Y (NPY) and/or nitric oxide synthase (NOS) at the pallial regions of three different models of Osteichthyes. First, we selected two tetrapods, one amniote from the genus Pseudemys belonging to the order Testudine, at the base of the amniote diversification and with a three-layered simple cortex, and the Anuran Xenopus laevis, an anamniote tetrapod with a non-layered evaginated pallium, and finally the order Polypteriform, a small fish group at the base of the actinopterygian diversification with an everted telencephalon. SOM was the most conserved interneuron type in terms of its distribution and co-expression with other markers such as CR, in contrast to PV, which showed a different pattern between the models analyzed. In addition, the SOM expression supports a homological relationship between the medial pallial derivatives in all the models. CR and CB expressions in the tetrapods were observed, particularly, CR expressing cells were detected in the medial and the dorsal pallial derivatives, in contrast to CB, which appeared only in discrete scattered populations. However, the pallium of Polypteriforms fishes was almost devoid of CR cells, in contrast to the important number of CB cells observed in all the pallial regions. The NPY immunoreactivity was detected in all the pallial domains of all the models, as well as cells coexpressing CR. Finally, the pallial nitrergic expression was also conserved, which allows to postulate the homological relationships between the ventropallial and the amygdaloid derivatives. In summary, even in basal pallial models the neurochemically characterized interneurons indicate that their first appearance took place before the common ancestor of amniotes. Thus, our results suggest a shared pattern of interneuron types in the pallium of all Osteichthyes.
Collapse
|
18
|
Wylie DC, Hofmann HA, Zemelman BV. SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing. Bioinformatics 2020; 35:3944-3952. [PMID: 30903136 DOI: 10.1093/bioinformatics/btz198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/04/2019] [Accepted: 03/20/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION We set out to develop an algorithm that can mine differential gene expression data to identify candidate cell type-specific DNA regulatory sequences. Differential expression is usually quantified as a continuous score-fold-change, test-statistic, P-value-comparing biological classes. Unlike existing approaches, our de novo strategy, termed SArKS, applies non-parametric kernel smoothing to uncover promoter motif sites that correlate with elevated differential expression scores. SArKS detects motif k-mers by smoothing sequence scores over sequence similarity. A second round of smoothing over spatial proximity reveals multi-motif domains (MMDs). Discovered motif sites can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing. RESULTS We applied SArKS to published gene expression data representing distinct neocortical neuron classes in Mus musculus and interneuron developmental states in Homo sapiens. When benchmarked against several existing algorithms using a cross-validation procedure, SArKS identified larger motif sets that formed the basis for regression models with higher correlative power. AVAILABILITY AND IMPLEMENTATION https://github.com/denniscwylie/sarks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Dennis C Wylie
- Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA
| | - Hans A Hofmann
- Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, TX, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.,Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Boris V Zemelman
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA.,Department of Neuroscience, University of Texas at Austin, Austin, TX, USA.,Center for Learning and Memory, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
19
|
Mahadevan V, Peltekian A, McBain CJ. Translatome Analyses Using Conditional Ribosomal Tagging in GABAergic Interneurons and Other Sparse Cell Types. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 92:e93. [PMID: 32584517 PMCID: PMC7317066 DOI: 10.1002/cpns.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GABAergic interneurons comprise a small but diverse subset of neurons in the mammalian brain that tightly regulate neuronal circuit maturation and information flow and, ultimately, behavior. Because of their centrality in the etiology of numerous neurological disorders, examining the molecular architecture of these neurons under different physiological scenarios has piqued the interest of the broader neuroscience community. The last few years have seen an explosion in next-generation sequencing (NGS) approaches aimed at identifying genetic and state-dependent subtypes in neuronal diversity. Although several approaches are employed to address neuronal molecular diversity, ribosomal tagging has emerged at the forefront of identifying the translatomes of neuronal subtypes. This approach primarily relies on Cre recombinase-driven expression of hemagglutinin A (HA)-tagged RiboTag mice exclusively in the neuronal subtype of interest. This allows the immunoprecipitation of cell-type-specific, ribosome-engaged mRNA, expressed both in the soma and the neuronal processes, for targeted quantitative real-time PCR (qRT-PCR) or high-throughput RNA sequencing analyses. Here we detail the typical technical caveats associated with successful application of the RiboTag technique for analyzing GABAergic interneurons, and in theory other sparse cell types, in the central nervous system. Published 2020. U.S. Government. Basic Protocol 1: Breeding mice to obtain RiboTag homozygosity Support Protocol 1: Detection of ectopic Cre recombinase expression Basic Protocol 2: The RiboTag assay Support Protocol 2: Real-time quantitative PCR (qRT-PCR) assay of RiboTag-derived cell-type-specific RNA Support Protocol 3: Construction of cell-type-specific RNA-seq library Support Protocol 4: Secondary analyses of RiboTag-derived RNA-seq dataset.
Collapse
Affiliation(s)
- Vivek Mahadevan
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892
| | - Areg Peltekian
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892
| | - Chris J. McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892
| |
Collapse
|
20
|
Vinogradov AE, Anatskaya OV. Cell-cycle dependence of transcriptome gene modules: comparison of regression lines. FEBS J 2020; 287:4427-4439. [PMID: 32083797 DOI: 10.1111/febs.15257] [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] [Received: 09/12/2019] [Revised: 01/24/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
The transcriptome consists of various gene modules that can be mutually dependent, and ignoring these dependencies may lead to misinterpretation. The most important problem is module dependence on cell-cycle activity. Using meta-analysis of over 30 000 single-cell transcriptomes, we show gene module dependencies on cell-cycle signature, which can be consistently observed in various normal and cancer cells. Transcript levels of receptors, plasma membrane, and differentiation-related genes are negatively regressed on cell-cycle signature. Pluripotency, stress response, DNA repair, chromatin remodeling, proteasomal protein degradation, protein network connectivity, and unicellular evolutionary origin are regressed positively. These effects cannot be explained by partial overlap of corresponding gene sets because they remain if the overlapped genes were removed. We propose a visual analysis of gene module-specific regression lines as complement to an uncurated enrichment analysis. The different lines for a same gene module indicate different cell conditions. The approach is tested on several problems (polyploidy, pluripotency, cancer, phylostratigraphy). Intriguingly, we found variation in cell-cycle activity, which is independent of cell progression through the cycle. The upregulation of G2/M checkpoint genes with downregulation of G2/M transition and cytokinesis is revealed in polyploid cells. A temporal increase in cell-cycle activity at transition from pluripotent to more differentiated state is found in human embryonic stem cells. The upregulation of unicellular interactome cluster in human cancers is shown in single cells with control for cell-cycle activity. The greater scatter around regression line in cancer cells suggests greater heterogeneity caused by deviation from a line of normal cells.
Collapse
Affiliation(s)
| | - Olga V Anatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
21
|
Subramanian L, Calcagnotto ME, Paredes MF. Cortical Malformations: Lessons in Human Brain Development. Front Cell Neurosci 2020; 13:576. [PMID: 32038172 PMCID: PMC6993122 DOI: 10.3389/fncel.2019.00576] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Creating a functional cerebral cortex requires a series of complex and well-coordinated developmental steps. These steps have evolved across species with the emergence of cortical gyrification and coincided with more complex behaviors. The presence of diverse progenitor cells, a protracted timeline for neuronal migration and maturation, and diverse neuronal types are developmental features that have emerged in the gyrated cortex. These factors could explain how the human brain has expanded in size and complexity. However, their complex nature also renders new avenues of vulnerability by providing additional cell types that could contribute to disease and longer time windows that could impact the composition and organization of the cortical circuit. We aim to discuss the unique developmental steps observed in human corticogenesis and propose how disruption of these species-unique processes could lead to malformations of cortical development.
Collapse
Affiliation(s)
- Lakshmi Subramanian
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Maria Elisa Calcagnotto
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory, Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Graduate Program in Biological Sciences: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mercedes F Paredes
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States.,Neuroscience Graduate Division, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
22
|
Keefe F, Li M. Pluripotent stem cell derived inhibitory interneurons - principles and applications in health and disease. Neural Regen Res 2020; 15:251-252. [PMID: 31552890 PMCID: PMC6905328 DOI: 10.4103/1673-5374.265547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Francesca Keefe
- Neuroscience and Mental Health Research Institute, School of Medicine and School of Bioscience, Cardiff University, Cardiff, UK
| | - Meng Li
- Neuroscience and Mental Health Research Institute, School of Medicine and School of Bioscience, Cardiff University, Cardiff, UK
| |
Collapse
|
23
|
Xie Y, Ng NN, Safrina OS, Ramos CM, Ess KC, Schwartz PH, Smith MA, O'Dowd DK. Comparisons of dual isogenic human iPSC pairs identify functional alterations directly caused by an epilepsy associated SCN1A mutation. Neurobiol Dis 2019; 134:104627. [PMID: 31786370 DOI: 10.1016/j.nbd.2019.104627] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Over 1250 mutations in SCN1A, the Nav1.1 voltage-gated sodium channel gene, are associated with seizure disorders including GEFS+. To evaluate how a specific mutation, independent of genetic background, causes seizure activity we generated two pairs of isogenic human iPSC lines by CRISPR/Cas9 gene editing. One pair is a control line from an unaffected sibling, and the mutated control carrying the GEFS+ K1270T SCN1A mutation. The second pair is a GEFS+ patient line with the K1270T mutation, and the corrected patient line. By comparing the electrophysiological properties in inhibitory and excitatory iPSC-derived neurons from these pairs, we found the K1270T mutation causes cell type-specific alterations in sodium current density and evoked firing, resulting in hyperactive neural networks. We also identified differences associated with genetic background and interaction between the mutation and genetic background. Comparisons within and between dual pairs of isogenic iPSC-derived neuronal cultures provide a novel platform for evaluating cellular mechanisms underlying a disease phenotype and for developing patient-specific anti-seizure therapies.
Collapse
Affiliation(s)
- Yunyao Xie
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States of America
| | - Nathan N Ng
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States of America
| | - Olga S Safrina
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States of America
| | - Carmen M Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States of America
| | - Kevin C Ess
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Philip H Schwartz
- Children's Hospital of Orange County Research Institute, Orange, CA, United States of America
| | - Martin A Smith
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, United States of America
| | - Diane K O'Dowd
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States of America.
| |
Collapse
|
24
|
Tepe B, Hill MC, Pekarek BT, Hunt PJ, Martin TJ, Martin JF, Arenkiel BR. Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons. Cell Rep 2019; 25:2689-2703.e3. [PMID: 30517858 PMCID: PMC6342206 DOI: 10.1016/j.celrep.2018.11.034] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/18/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022] Open
Abstract
Cellular heterogeneity within the mammalian brain poses a challenge
toward understanding its complex functions. Within the olfactory bulb, odor
information is processed by subtypes of inhibitory interneurons whose
heterogeneity and functionality are influenced by ongoing adult neurogenesis. To
investigate this cellular heterogeneity and better understand adult-born neuron
development, we utilized single-cell RNA sequencing and computational modeling
to reveal diverse and transcriptionally distinct neuronal and nonneuronal cell
types. We also analyzed molecular changes during adult-born interneuron
maturation and uncovered developmental programs within their gene expression
profiles. Finally, we identified that distinct neuronal subtypes are
differentially affected by sensory experience. Together, these data provide a
transcriptome-based foundation for investigating subtype-specific neuronal
function in the olfactory bulb (OB), charting the molecular profiles that arise
during the maturation and integration of adult-born neurons and how they
dynamically change in an activity-dependent manner. Using single-cell sequencing, Tepe et al. describe cellular heterogeneity
in the mouse olfactory bulb, uncover markers for each cell type, and reveal
differentially regulated genes in adult-born neurons. These findings provide a
framework for studying cell-type-specific functions and circuit integration in
the mammalian brain.
Collapse
Affiliation(s)
- Burak Tepe
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brandon T Pekarek
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patrick J Hunt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas J Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; The Texas Heart Institute, 6770 Bertner Avenue, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Benjamin R Arenkiel
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; McNair Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
25
|
Scott AL, Pranckevicius NA, Nurse CA, Scott GR. Regulation of catecholamine release from the adrenal medulla is altered in deer mice ( Peromyscus maniculatus) native to high altitudes. Am J Physiol Regul Integr Comp Physiol 2019; 317:R407-R417. [PMID: 31242021 DOI: 10.1152/ajpregu.00005.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
High-altitude natives have evolved to overcome environmental hypoxia and provide a compelling system to understand physiological function during reductions in oxygen availability. The sympathoadrenal system plays a key role in responses to acute hypoxia, but prolonged activation of this system in chronic hypoxia may be maladaptive. Here, we examined how chronic hypoxia exposure alters adrenal catecholamine secretion and how adrenal function is altered further in high-altitude natives. Populations of deer mice (Peromyscus maniculatus) native to low and high altitudes were each born and raised in captivity at sea level, and adults from each population were exposed to normoxia or hypobaric hypoxia for 5 mo. Using carbon fiber amperometry on adrenal slices, catecholamine secretion evoked by low doses of nicotine (10 µM) or acute hypoxia (Po2 ∼15-20 mmHg) was reduced in lowlanders exposed to hypobaric hypoxia, which was attributable mainly to a decrease in quantal charge rather than event frequency. However, secretion evoked by high doses of nicotine (50 µM) was unaffected. Hypobaric hypoxia also reduced plasma epinephrine and protein expression of 3,4-dihydroxyphenylalanine (DOPA) decarboxylase in the adrenal medulla of lowlanders. In contrast, highlanders were unresponsive to hypobaric hypoxia, exhibiting typically low adrenal catecholamine secretion, plasma epinephrine, and DOPA decarboxylase. Highlanders also had consistently lower catecholamine secretion evoked by high nicotine, smaller adrenal medullae with fewer chromaffin cells, and a larger adrenal cortex compared with lowlanders across both acclimation environments. Our results suggest that plastic responses to chronic hypoxia along with evolved changes in adrenal function attenuate catecholamine release in deer mice at high altitude.
Collapse
Affiliation(s)
- Angela L Scott
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Colin A Nurse
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
26
|
Menon V. Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data. Brief Funct Genomics 2019; 17:240-245. [PMID: 29236955 DOI: 10.1093/bfgp/elx044] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. From a data generation perspective, recent single-cell studies can be classified into two groups: those that distribute reads shallowly over large numbers of cells and those that distribute reads more deeply over a smaller cell population. Although there are advantages to both approaches in terms of cellular and tissue coverage, it is unclear whether different computational cell type identification methods are better suited to one or the other experimental paradigm. This study reviews three cell type clustering algorithms, each representing one of three broad approaches, and finds that PCA-based algorithms appear most suited to low read depth data sets, whereas gene clustering-based and biclustering algorithms perform better on high read depth data sets. In addition, highly related cell classes are better distinguished by higher-depth data, given the same total number of reads; however, simultaneous discovery of distinct and similar types is better served by lower-depth, higher cell number data. Overall, this study suggests that the depth of profiling should be determined by initial assumptions about the diversity of cells in the population, and that the selection of clustering algorithm(s) subsequently based on the depth of profiling will allow for better identification of putative transcriptomic cell types.
Collapse
Affiliation(s)
- Vilas Menon
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA, USA
| |
Collapse
|
27
|
Zhu W, Zhang B, Li M, Mo F, Mi T, Wu Y, Teng Z, Zhou Q, Li W, Hu B. Precisely controlling endogenous protein dosage in hPSCs and derivatives to model FOXG1 syndrome. Nat Commun 2019; 10:928. [PMID: 30804331 PMCID: PMC6389984 DOI: 10.1038/s41467-019-08841-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/23/2019] [Indexed: 01/25/2023] Open
Abstract
Dosage of key regulators impinge on developmental disorders such as FOXG1 syndrome. Since neither knock-out nor knock-down strategy assures flexible and precise protein abundance control, to study hypomorphic or haploinsufficiency expression remains challenging. We develop a system in human pluripotent stem cells (hPSCs) using CRISPR/Cas9 and SMASh technology, with which we can target endogenous proteins for precise dosage control in hPSCs and at multiple stages of neural differentiation. We also reveal FOXG1 dose-dependently affect the cellular constitution of human brain, with 60% mildly affect GABAergic interneuron development while 30% thresholds the production of MGE derived neurons. Abnormal interneuron differentiation accounts for various neurological defects such as epilepsy or seizures, which stimulates future innovative cures of FOXG1 syndrome. By means of its robustness and easiness, dosage-control of proteins in hPSCs and their derivatives will update the understanding and treatment of additional diseases caused by abnormal protein dosage. Altered dosage of developmental regulators such as transcription factors can result in disorders, such as FOXG1 syndrome. Here, the authors demonstrate the utility of SMASh technology for modulating protein dosage by modeling FOXG1 syndrome using human pluripotent stem cell-derived neurons and neural organoids.
Collapse
Affiliation(s)
- Wenliang Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Mengqi Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Tingwei Mi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yihui Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Zhaoqian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
28
|
Ouwenga R, Lake AM, Aryal S, Lagunas T, Dougherty JD. The Differences in Local Translatome across Distinct Neuron Types Is Mediated by Both Baseline Cellular Differences and Post-transcriptional Mechanisms. eNeuro 2018; 5:ENEURO.0320-18.2018. [PMID: 30723792 PMCID: PMC6361723 DOI: 10.1523/eneuro.0320-18.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Local translation in neurites is a phenomenon that enhances the spatial segregation of proteins and their functions away from the cell body, yet it is unclear how local translation varies across neuronal cell types. Further, it is unclear whether differences in local translation across cell types simply reflect differences in transcription or whether there is also a cell type-specific post-transcriptional regulation of the location and translation of specific mRNAs. Most of the mRNAs discovered as being locally translated have been identified from hippocampal neurons because their laminar organization facilitates neurite-specific dissection and microscopy methods. Given the diversity of neurons across the brain, studies have not yet analyzed how locally translated mRNAs differ across cell types. Here, we used the SynapTRAP method to harvest two broad cell types in the mouse forebrain: GABAergic neurons and layer 5 projection neurons. While some transcripts overlap, the majority of the local translatome is not shared across these cell types. In addition to differences driven by baseline expression levels, some transcripts also exhibit cell type-specific post-transcriptional regulation. Finally, we provide evidence that GABAergic neurons specifically localize mRNAs for peptide neurotransmitters, including somatostatin and cortistatin, suggesting localized production of these key signaling molecules in the neurites of GABAergic neurons. Overall, this work suggests that differences in local translation in neurites across neuronal cell types are poised to contribute substantially to the heterogeneity in neuronal phenotypes.
Collapse
Affiliation(s)
- Rebecca Ouwenga
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Allison M. Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Shivani Aryal
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Tomas Lagunas
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
29
|
Prytkova I, Goate A, Hart RP, Slesinger PA. Genetics of Alcohol Use Disorder: A Role for Induced Pluripotent Stem Cells? Alcohol Clin Exp Res 2018; 42:1572-1590. [PMID: 29897633 PMCID: PMC6120805 DOI: 10.1111/acer.13811] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) affects millions of people and costs nearly 250 billion dollars annually. Few effective FDA-approved treatments exist, and more are needed. AUDs have a strong heritability, but only a few genes have been identified with a large effect size on disease phenotype. Genomewide association studies (GWASs) have identified common variants with low effect sizes, most of which are in noncoding regions of the genome. Animal models frequently fail to recapitulate key molecular features of neuropsychiatric disease due to the polygenic nature of the disease, partial conservation of coding regions, and significant disparity in noncoding regions. By contrast, human induced pluripotent stem cells (hiPSCs) derived from patients provide a powerful platform for evaluating genes identified by GWAS and modeling complex interactions in the human genome. hiPSCs can be differentiated into a wide variety of human cells, including neurons, glia, and hepatic cells, which are compatible with numerous functional assays and genome editing techniques. In this review, we focus on current applications and future directions of patient hiPSC-derived central nervous system cells for modeling AUDs in addition to highlighting successful applications of hiPSCs in polygenic neuropsychiatric diseases.
Collapse
Affiliation(s)
- Iya Prytkova
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Alison Goate
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ronald P. Hart
- Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway NJ 08854, USA
| | - Paul A. Slesinger
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| |
Collapse
|
30
|
Tasic B. Single cell transcriptomics in neuroscience: cell classification and beyond. Curr Opin Neurobiol 2018; 50:242-249. [DOI: 10.1016/j.conb.2018.04.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/15/2022]
|
31
|
Karzbrun E, Kshirsagar A, Cohen SR, Hanna JH, Reiner O. Human Brain Organoids on a Chip Reveal the Physics of Folding. NATURE PHYSICS 2018; 14:515-522. [PMID: 29760764 PMCID: PMC5947782 DOI: 10.1038/s41567-018-0046-7] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/08/2018] [Indexed: 05/18/2023]
Abstract
Human brain wrinkling has been implicated in neurodevelopmental disorders and yet its origins remain unknown. Polymer gel models suggest that wrinkling emerges spontaneously due to compression forces arising during differential swelling, but these ideas have not been tested in a living system. Here, we report the appearance of surface wrinkles during the in vitro development and self-organization of human brain organoids in a micro-fabricated compartment that supports in situ imaging over a timescale of weeks. We observe the emergence of convolutions at a critical cell density and maximal nuclear strain, which are indicative of a mechanical instability. We identify two opposing forces contributing to differential growth: cytoskeletal contraction at the organoid core and cell-cycle-dependent nuclear expansion at the organoid perimeter. The wrinkling wavelength exhibits linear scaling with tissue thickness, consistent with balanced bending and stretching energies. Lissencephalic (smooth brain) organoids display reduced convolutions, modified scaling and a reduced elastic modulus. Although the mechanism here does not include the neuronal migration seen in in vivo, it models the physics of the folding brain remarkably well. Our on-chip approach offers a means for studying the emergent properties of organoid development, with implications for the embryonic human brain.
Collapse
Affiliation(s)
- Eyal Karzbrun
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Aditya Kshirsagar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel, 7610001
| |
Collapse
|
32
|
Eid L, Lachance M, Hickson G, Rossignol E. Ex Utero Electroporation and Organotypic Slice Cultures of Embryonic Mouse Brains for Live-Imaging of Migrating GABAergic Interneurons. J Vis Exp 2018. [PMID: 29733310 DOI: 10.3791/57526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
GABAergic interneurons (INs) are critical components of neuronal networks that drive cognition and behavior. INs destined to populate the cortex migrate tangentially from their place of origin in the ventral telencephalon (including from the medial and caudal ganglionic eminences (MGE, CGE)) to the dorsal cortical plate in response to a variety of intrinsic and extrinsic cues. Different methodologies have been developed over the years to genetically manipulate specific pathways and investigate how they regulate the dynamic cytoskeletal changes required for proper IN migration. In utero electroporation has been extensively used to study the effect of gene repression or overexpression in specific IN subtypes while assessing the impact on morphology and final position. However, while this approach is readily used to modify radially migrating pyramidal cells, it is more technically challenging when targeting INs. In utero electroporation generates a low yield given the decreased survival rates of pups when electroporation is conducted before e14.5, as is customary when studying MGE-derived INs. In an alternative approach, MGE explants provide easy access to the MGE and facilitate the imaging of genetically modified INs. However, in these explants, INs migrate into an artificial matrix, devoid of endogenous guidance cues and thalamic inputs. This prompted us to optimize a method where INs can migrate in a more naturalistic environment, while circumventing the technical challenges of in utero approaches. In this paper, we describe the combination of ex utero electroporation of embryonic mouse brains followed by organotypic slice cultures to readily track, image and reconstruct genetically modified INs migrating along their natural paths in response to endogenous cues. This approach allows for both the quantification of the dynamic aspects of IN migration with time-lapse confocal imaging, as well as the detailed analysis of various morphological parameters using neuronal reconstructions on fixed immunolabeled tissue.
Collapse
Affiliation(s)
- Lara Eid
- Centre de recherche du CHU Sainte-Justine; Department of Neuroscience, Université de Montréal
| | | | - Gilles Hickson
- Centre de recherche du CHU Sainte-Justine; Department of pathology and cellular biology, Université de Montréal
| | - Elsa Rossignol
- Centre de recherche du CHU Sainte-Justine; Department of Neuroscience, Université de Montréal; Department of Pediatrics, Université de Montréal;
| |
Collapse
|
33
|
He Z, Yu Q. Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation. BMC Genomics 2018; 19:262. [PMID: 29665773 PMCID: PMC5905132 DOI: 10.1186/s12864-018-4649-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/08/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Neuron maturation is a critical process in neurogenesis, during which neurons gain their morphological, electrophysiological and molecular characteristics for their functions as the central components of the nervous system. RESULTS To better understand the molecular changes during this process, we combined the protein-protein interaction network and public single cell RNA-seq data of mature and immature neurons to identify functional modules relevant to the neuron maturation process in humans. Among the 109 functional modules in total, 33 showed significant gene expression level changes (discriminating modules) which participate in varied functions including energy consumption, synaptic functions and housekeeping functions such as translation and splicing. Based on the identified modules, we trained a neuron maturity index (NMI) model for the quantification of maturation states of single neurons or purified bulk neurons. Applied to multiple single neuron transcriptome data sets of neuron development in humans and mice, the NMI model made estimation of neuron maturity states which were significantly correlated with the neuron maturation trajectories in both species, implying the reproducibility and conservation of the identified transcriptome transition. CONCLUSION We identified 33 discriminating modules whose activities were significantly correlated with single neuron maturity states, which may play important roles in the neuron maturation process.
Collapse
Affiliation(s)
- Zhisong He
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China. .,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Current affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
| | - Qianhui Yu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China.,Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| |
Collapse
|
34
|
Mi D, Li Z, Lim L, Li M, Moissidis M, Yang Y, Gao T, Hu TX, Pratt T, Price DJ, Sestan N, Marín O. Early emergence of cortical interneuron diversity in the mouse embryo. Science 2018; 360:81-85. [PMID: 29472441 PMCID: PMC6195193 DOI: 10.1126/science.aar6821] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
GABAergic interneurons (GABA, γ-aminobutyric acid) regulate neural-circuit activity in the mammalian cerebral cortex. These cortical interneurons are structurally and functionally diverse. Here, we use single-cell transcriptomics to study the origins of this diversity in the mouse. We identify distinct types of progenitor cells and newborn neurons in the ganglionic eminences, the embryonic proliferative regions that give rise to cortical interneurons. These embryonic precursors show temporally and spatially restricted transcriptional patterns that lead to different classes of interneurons in the adult cerebral cortex. Our findings suggest that shortly after the interneurons become postmitotic, their diversity is already patent in their diverse transcriptional programs, which subsequently guide further differentiation in the developing cortex.
Collapse
Affiliation(s)
- Da Mi
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Zhen Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lynette Lim
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Yifei Yang
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Tianliuyun Gao
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tim Xiaoming Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02446, USA
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Thomas Pratt
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - David J Price
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK.
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| |
Collapse
|
35
|
Regulatory networks specifying cortical interneurons from human embryonic stem cells reveal roles for CHD2 in interneuron development. Proc Natl Acad Sci U S A 2017; 114:E11180-E11189. [PMID: 29229852 DOI: 10.1073/pnas.1712365115] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cortical interneurons (cINs) modulate excitatory neuronal activity by providing local inhibition. During fetal development, several cIN subtypes derive from the medial ganglionic eminence (MGE), a transient ventral telencephalic structure. While altered cIN development contributes to neurodevelopmental disorders, the inaccessibility of human fetal brain tissue during development has hampered efforts to define molecular networks controlling this process. Here, we modified protocols for directed differentiation of human embryonic stem cells, obtaining efficient, accelerated production of MGE-like progenitors and MGE-derived cIN subtypes with the expected electrophysiological properties. We defined transcriptome changes accompanying this process and integrated these data with direct transcriptional targets of NKX2-1, a transcription factor controlling MGE specification. This analysis defined NKX2-1-associated genes with enriched expression during MGE specification and cIN differentiation, including known and previously unreported transcription factor targets with likely roles in MGE specification, and other target classes regulating cIN migration and function. NKX2-1-associated peaks were enriched for consensus binding motifs for NKX2-1, LHX, and SOX transcription factors, suggesting roles in coregulating MGE gene expression. Among the NKX2-1 direct target genes with cIN-enriched expression was CHD2, which encodes a chromatin remodeling protein mutated to cause human epilepsies. Accordingly, CHD2 deficiency impaired cIN specification and altered later electrophysiological function, while CHD2 coassociated with NKX2-1 at cis-regulatory elements and was required for their transactivation by NKX2-1 in MGE-like progenitors. This analysis identified several aspects of gene-regulatory networks underlying human MGE specification and suggested mechanisms by which NKX2-1 acts with chromatin remodeling activities to regulate gene expression programs underlying cIN development.
Collapse
|
36
|
Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Molecular and cellular reorganization of neural circuits in the human lineage. Science 2017; 358:1027-1032. [PMID: 29170230 PMCID: PMC5776074 DOI: 10.1126/science.aan3456] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/17/2017] [Indexed: 01/06/2023]
Abstract
To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. Integration with human single-cell transcriptomic data revealed global, regional, and cell-type-specific species expression differences in genes representing distinct functional categories. We validated and further characterized the human specificity of genes enriched in distinct cell types through histological and functional analyses, including rare subpallial-derived interneurons expressing dopamine biosynthesis genes enriched in the human striatum and absent in the nonhuman African ape neocortex. Our integrated analysis of the generated data revealed diverse molecular and cellular features of the phylogenetic reorganization of the human brain across multiple levels, with relevance for brain function and disease.
Collapse
Affiliation(s)
- André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Marco Onorati
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Biology, Unit of Cell and Developmental Biology, University of Pisa, Pisa, Italy
| | - Andrew T N Tebbenkamp
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Bernardo Stutz
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Yuka Imamura Kawasawa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Departments of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Raquel Garcia Perez
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Marta Mele
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Tiago Carvalho
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Mario Skarica
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Akemi Shibata
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alexa R Stephenson
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Melissa K Edler
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, NM, USA
| | - John D Elsworth
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Tamas L Horvath
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Mark Reimers
- Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Matthew W State
- Department of Psychiatry and Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - James A Knowles
- Department of Psychiatry and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Centro Nacional de Analisis Genomico, Barcelona, Catalonia, Spain
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
37
|
Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
Collapse
Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| |
Collapse
|
38
|
Laclef C, Métin C. Conserved rules in embryonic development of cortical interneurons. Semin Cell Dev Biol 2017; 76:86-100. [PMID: 28918121 DOI: 10.1016/j.semcdb.2017.09.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022]
Abstract
This review will focus on early aspects of cortical interneurons (cIN) development from specification to migration and final positioning in the human cerebral cortex. These mechanisms have been largely studied in the mouse model, which provides unique possibilities of genetic analysis, essential to dissect the molecular and cellular events involved in cortical development. An important goal here is to discuss the conservation and the potential divergence of these mechanisms, with a particular interest for the situation in the human embryo. We will thus cover recent works, but also revisit older studies in the light of recent data to better understand the developmental mechanisms underlying cIN differentiation in human. Because cIN are implicated in severe developmental disorders, understanding the molecular and cellular mechanisms controlling their differentiation might clarify some causes and potential therapeutic approaches to these important clinical conditions.
Collapse
Affiliation(s)
- Christine Laclef
- INSERM, UMR-S839, Paris, France; Sorbonne Universités, UPMC University Paris 6, UMR-S839, Paris, France; Institut du Fer à Moulin, Paris, France
| | - Christine Métin
- INSERM, UMR-S839, Paris, France; Sorbonne Universités, UPMC University Paris 6, UMR-S839, Paris, France; Institut du Fer à Moulin, Paris, France.
| |
Collapse
|