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Zhang D, Rubio Rodríguez-Kirby LA, Lin Y, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Wang S, Chen XL, Gao F, Wang D, Xu H, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R. Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605493. [PMID: 39091821 PMCID: PMC11291146 DOI: 10.1101/2024.07.28.605493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The ability to spatially map multiple layers of the omics information over different time points allows for exploring the mechanisms driving brain development, differentiation, arealization, and alterations in disease. Herein we developed and applied spatial tri-omic sequencing technologies, DBiT ARP-seq (spatial ATAC-RNA-Protein-seq) and DBiT CTRP-seq (spatial CUT&Tag-RNA-Protein-seq) together with multiplexed immunofluorescence imaging (CODEX) to map spatial dynamic remodeling in brain development and neuroinflammation. A spatiotemporal tri-omic atlas of the mouse brain was obtained at different stages from postnatal day P0 to P21, and compared to the regions of interest in the human developing brains. Specifically, in the cortical area, we discovered temporal persistence and spatial spreading of chromatin accessibility for the layer-defining transcription factors. In corpus callosum, we observed dynamic chromatin priming of myelin genes across the subregions. Together, it suggests a role for layer specific projection neurons to coordinate axonogenesis and myelination. We further mapped the brain of a lysolecithin (LPC) neuroinflammation mouse model and observed common molecular programs in development and neuroinflammation. Microglia, exhibiting both conserved and distinct programs for inflammation and resolution, are transiently activated not only at the core of the LPC lesion, but also at distal locations presumably through neuronal circuitry. Thus, this work unveiled common and differential mechanisms in brain development and neuroinflammation, resulting in a valuable data resource to investigate brain development, function and disease.
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Affiliation(s)
- Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- These authors contributed equally
| | - Leslie A Rubio Rodríguez-Kirby
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- These authors contributed equally
| | - Yingxin Lin
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mengyi Song
- 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 Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Li Wang
- 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 Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Lijun Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Shigeaki Kanatani
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tony Jimenez-Beristain
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yonglong Dang
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mei Zhong
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Shaohui Wang
- 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 Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Xinyi Lisa Chen
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Fu Gao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Dejiang Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Hang Xu
- Binformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xing Lou
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Jinmiao Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Binformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Per Uhlén
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Arnold Kriegstein
- 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 Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
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2
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Yousefian-Jazi A, Kim S, Choi SH, Chu J, Nguyen PTT, Park U, Lim K, Hwang H, Lee K, Kim Y, Hyeon SJ, Rhim H, Ryu HL, Lim G, Stein TD, Ryu H, Lee J. Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603186. [PMID: 39071309 PMCID: PMC11275751 DOI: 10.1101/2024.07.15.603186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Genetic changes and epigenetic modifications are associated with neuronal dysfunction in the pathogenesis of neurodegenerative disorders. However, the mechanism behind genetic mutations in the non-coding region of genes that affect epigenetic modifications remains unclear. Here, we identified an ALS-associated SNP located in the intronic region of MEF2C (rs304152), residing in a putative enhancer element, using convolutional neural network. The enhancer mutation of MEF2C reduces own gene expression and consequently impairs mitochondrial function in motor neurons. MEF2C localizes and binds to the mitochondria DNA, and directly modulates mitochondria-encoded gene expression. CRISPR/Cas-9-induced mutation of the MEF2C enhancer decreases expression of mitochondria-encoded genes. Moreover, MEF2C mutant cells show reduction of mitochondrial membrane potential, ATP level but elevation of oxidative stress. MEF2C deficiency in the upper and lower motor neurons of mice impairs mitochondria-encoded genes, and leads to mitochondrial metabolic disruption and progressive motor behavioral deficits. Together, MEF2C dysregulation by the enhancer mutation leads to mitochondrial dysfunction and oxidative stress, which are prevalent features in motor neuronal damage and ALS pathogenesis. This genetic and epigenetic crosstalk mechanism provides insights for advancing our understanding of motor neuron disease and developing effective treatments.
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3
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Zhuang K, Leng L, Su X, Wang S, Su Y, Chen Y, Yuan Z, Zi L, Li J, Xie W, Yan S, Xia Y, Wang H, Li H, Chen Z, Yuan T, Zhang J. Menin Deficiency Induces Autism-Like Behaviors by Regulating Foxg1 Transcription and Participates in Foxg1-Related Encephalopathy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307953. [PMID: 38582517 PMCID: PMC11200012 DOI: 10.1002/advs.202307953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/18/2024] [Indexed: 04/08/2024]
Abstract
FOXG1 syndrome is a developmental encephalopathy caused by FOXG1 (Forkhead box G1) mutations, resulting in high phenotypic variability. However, the upstream transcriptional regulation of Foxg1 expression remains unclear. This report demonstrates that both deficiency and overexpression of Men1 (protein: menin, a pathogenic gene of MEN1 syndrome known as multiple endocrine neoplasia type 1) lead to autism-like behaviors, such as social defects, increased repetitive behaviors, and cognitive impairments. Multifaceted transcriptome analyses revealed that Foxg1 signaling is predominantly altered in Men1 deficiency mice, through its regulation of the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (Atrx) factor. Atrx recruits menin to bind to the transcriptional start region of Foxg1 and mediates the regulation of Foxg1 expression by H3K4me3 (Trimethylation of histone H3 lysine 4) modification. The deficits observed in menin deficient mice are rescued by the over-expression of Foxg1, leading to normalized spine growth and restoration of hippocampal synaptic plasticity. These findings suggest that menin may have a putative role in the maintenance of Foxg1 expression, highlighting menin signaling as a potential therapeutic target for Foxg1-related encephalopathy.
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Affiliation(s)
- Kai Zhuang
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Lige Leng
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Xiao Su
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Shuzhong Wang
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Yuemin Su
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Yanbing Chen
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Ziqi Yuan
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Liu Zi
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Jieyin Li
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Wenting Xie
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Sihan Yan
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Yujun Xia
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Han Wang
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Huifang Li
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Zhenyi Chen
- Department of AnesthesiologyFirst Affiliated HospitalCollege of MedicineXiamen UniversityXiamenFujian361105China
| | - Tifei Yuan
- Shanghai Mental Health CenterShanghai Jiaotong University School of MedicineShanghai200030China
| | - Jie Zhang
- Institute of NeuroscienceCollege of MedicineXiamen UniversityXiamenFujian361105China
- Department of AnesthesiologyFirst Affiliated HospitalCollege of MedicineXiamen UniversityXiamenFujian361105China
- The Key Laboratory of Neural and Vascular BiologyMinistry of EducationCollege of Basic MedicineHebei Medical UniversityShijiazhuang050017China
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4
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Umeda K, Tanaka K, Chowdhury G, Nasu K, Kuroyanagi Y, Yamasu K. Evolutionarily conserved roles of foxg1a in the developing subpallium of zebrafish embryos. Dev Growth Differ 2024; 66:219-234. [PMID: 38378191 DOI: 10.1111/dgd.12917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024]
Abstract
The vertebrate telencephalic lobes consist of the pallium (dorsal) and subpallium (ventral). The subpallium gives rise to the basal ganglia, encompassing the pallidum and striatum. The development of this region is believed to depend on Foxg1/Foxg1a functions in both mice and zebrafish. This study aims to elucidate the genetic regulatory network controlled by foxg1a in subpallium development using zebrafish as a model. The expression gradient of foxg1a within the developing telencephalon was examined semi-quantitatively in initial investigations. Utilizing the CRISPR/Cas9 technique, we subsequently established a foxg1a mutant line and observed the resultant phenotypes. Morphological assessment revealed that foxg1a mutants exhibit a thin telencephalon together with a misshapen preoptic area (POA). Notably, accumulation of apoptotic cells was identified in this region. In mutants at 24 h postfertilization, the expression of pallium markers expanded ventrally, while that of subpallium markers was markedly suppressed. Concurrently, the expression of fgf8a, vax2, and six3b was shifted ventrally, causing anomalous expression in regions typical of POA formation in wild-type embryos. Consequently, the foxg1a mutation led to expansion of the pallium and disrupted the subpallium and POA. This highlights a pivotal role of foxg1a in directing the dorsoventral patterning of the telencephalon, particularly in subpallium differentiation, mirroring observations in mice. Additionally, reduced expression of neural progenitor maintenance genes was detected in mutants, suggesting the necessity of foxg1a in preserving neural progenitors. Collectively, these findings underscore evolutionarily conserved functions of foxg1 in the development of the subpallium in vertebrate embryos.
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Affiliation(s)
- Koto Umeda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kaiho Tanaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Gazlima Chowdhury
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- Department of Aquatic Environment and Resource Management, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Kouhei Nasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yuri Kuroyanagi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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5
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Liao K, Xiang Y, Huang F, Huang M, Xu W, Lin Y, Liao P, Wang Z, Yang L, Tian X, Chen D, Wang Z, Liu S, Zhuang Z. Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum. iScience 2024; 27:109009. [PMID: 38333704 PMCID: PMC10850779 DOI: 10.1016/j.isci.2024.109009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The avian optic tectum (OT) has been studied for its diverse functions, yet a comprehensive molecular landscape at the cellular level has been lacking. In this study, we applied spatial transcriptome sequencing and single-nucleus RNA sequencing (snRNA-seq) to explore the cellular organization and molecular characteristics of the avian OT from two species: Columba livia and Taeniopygia guttata. We identified precise layer structures and provided comprehensive layer-specific signatures of avian OT. Furthermore, we elucidated diverse functions in different layers, with the stratum griseum periventriculare (SGP) potentially playing a key role in advanced functions of OT, like fear response and associative learning. We characterized detailed neuronal subtypes and identified a population of FOXG1+ excitatory neurons, resembling those found in the mouse neocortex, potentially involved in neocortex-related functions and expansion of avian OT. These findings could contribute to our understanding of the architecture of OT, shedding light on visual perception and multifunctional association.
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Affiliation(s)
- Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Ya Xiang
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Fubaoqian Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenbo Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Youning Lin
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Pingfang Liao
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zishi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lin Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinmao Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Duoyuan Chen
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenkun Zhuang
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
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6
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Shen Z, Yang J, Zhang Q, Wang K, Lv X, Hu X, Ma J, Shi SH. How variable progenitor clones construct a largely invariant neocortex. Natl Sci Rev 2024; 11:nwad247. [PMID: 38274004 PMCID: PMC10810685 DOI: 10.1093/nsr/nwad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 01/27/2024] Open
Abstract
The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors (RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.
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Affiliation(s)
- Zhongfu Shen
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiajun Yang
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangqiang Zhang
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kuiyu Wang
- Department of Computer Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Lv
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaolin Hu
- Department of Computer Sciences, Tsinghua University, Beijing 100084, China
| | - Jian Ma
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Song-Hai Shi
- New Cornerstone Science Laboratory, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Chinese Institute for Brain Research, Beijing 102206, China
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7
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Wang Z, Tong L, Wang Q, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558077. [PMID: 37790302 PMCID: PMC10542124 DOI: 10.1101/2023.09.18.558077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Systematic analysis of gene function across diverse cell types in vivo is hindered by two challenges: obtaining sufficient cells from live tissues and accurately identifying each cell's perturbation in high-throughput single-cell assays. Leveraging AAV's versatile cell type tropism and high labeling capacity, we expanded the resolution and scale of in vivo CRISPR screens: allowing phenotypic analysis at single-cell resolution across a multitude of cell types in the embryonic brain, adult brain, and peripheral nervous system. We undertook extensive tests of 86 AAV serotypes, combined with a transposon system, to substantially amplify labeling and accelerate in vivo gene delivery from weeks to days. Using this platform, we performed an in utero genetic screen as proof-of-principle and identified pleiotropic regulatory networks of Foxg1 in cortical development, including Layer 6 corticothalamic neurons where it tightly controls distinct networks essential for cell fate specification. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% (mediated by lentivirus), and achieve analysis of over 30,000 cells in one experiment, thus enabling massively parallel in vivo Perturb-seq. Compatible with various perturbation techniques (CRISPRa/i) and phenotypic measurements (single-cell or spatial multi-omics), our platform presents a flexible, modular approach to interrogate gene function across diverse cell types in vivo, connecting gene variants to their causal functions.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Sean K. Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace S. Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
| | - Joshua Z. Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
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8
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Cao G, Sun C, Shen H, Qu D, Shen C, Lu H. Conditional Deletion of Foxg1 Delayed Myelination during Early Postnatal Brain Development. Int J Mol Sci 2023; 24:13921. [PMID: 37762220 PMCID: PMC10530892 DOI: 10.3390/ijms241813921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
FOXG1 (forkhead box G1) syndrome is a neurodevelopmental disorder caused by variants in the Foxg1 gene that affect brain structure and function. Individuals affected by FOXG1 syndrome frequently exhibit delayed myelination in neuroimaging studies, which may impair the rapid conduction of nerve impulses. To date, the specific effects of FOXG1 on oligodendrocyte lineage progression and myelination during early postnatal development remain unclear. Here, we investigated the effects of Foxg1 deficiency on myelin development in the mouse brain by conditional deletion of Foxg1 in neural progenitors using NestinCreER;Foxg1fl/fl mice and tamoxifen induction at postnatal day 0 (P0). We found that Foxg1 deficiency resulted in a transient delay in myelination, evidenced by decreased myelin formation within the first two weeks after birth, but ultimately recovered to the control levels by P30. We also found that Foxg1 deletion prevented the timely attenuation of platelet-derived growth factor receptor alpha (PDGFRα) signaling and reduced the cell cycle exit of oligodendrocyte precursor cells (OPCs), leading to their excessive proliferation and delayed maturation. Additionally, Foxg1 deletion increased the expression of Hes5, a myelin formation inhibitor, as well as Olig2 and Sox10, two promoters of OPC differentiation. Our results reveal the important role of Foxg1 in myelin development and provide new clues for further exploring the pathological mechanisms of FOXG1 syndrome.
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Affiliation(s)
- Guangliang Cao
- Department of Human Anatomy, School of Medicine, Southeast University, Nanjing 210009, China; (G.C.); (H.S.); (D.Q.)
| | - Congli Sun
- Department of Physiology, School of Medicine, Southeast University, Nanjing 210009, China;
| | - Hualin Shen
- Department of Human Anatomy, School of Medicine, Southeast University, Nanjing 210009, China; (G.C.); (H.S.); (D.Q.)
| | - Dewei Qu
- Department of Human Anatomy, School of Medicine, Southeast University, Nanjing 210009, China; (G.C.); (H.S.); (D.Q.)
| | - Chuanlu Shen
- Department of Pathophysiology, School of Medicine, Southeast University, Nanjing 210009, China;
| | - Haiqin Lu
- Department of Human Anatomy, School of Medicine, Southeast University, Nanjing 210009, China; (G.C.); (H.S.); (D.Q.)
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9
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Park J, Moon JH, O'Shea H, Shin D, Hwang SU, Li L, Lee H, Brimble E, Lee J, Clark S, Lee SK, Jeon S. The patient-specific mouse model with Foxg1 frameshift mutation uncovers the pathophysiology of FOXG1 syndrome. RESEARCH SQUARE 2023:rs.3.rs-2953760. [PMID: 37398410 PMCID: PMC10312924 DOI: 10.21203/rs.3.rs-2953760/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Single allelic mutations in the gene encoding the forebrain-specific transcription factor FOXG1 lead to FOXG1 syndrome (FS). Patient-specific animal models are needed to understand the etiology of FS, as FS patients show a wide spectrum of symptoms correlated with location and mutation type in the FOXG1 gene. Here we report the first patient-specific FS mouse model, Q84Pfs heterozygous (Q84Pfs-Het) mice, mimicking one of the most predominant single nucleotide variants in FS. Intriguingly, we found that Q84Pfs-Het mice faithfully recapitulate human FS phenotypes at the cellular, brain structural, and behavioral levels. Importantly, Q84Pfs-Het mice exhibited myelination deficits like FS patients. Further, our transcriptome analysis of Q84Pfs-Het cortex revealed a new role for FOXG1 in synapse and oligodendrocyte development. The dysregulated genes in Q84Pfs-Het brains also predicted motor dysfunction and autism-like phenotypes. Correspondingly, Q84Pfs-Het mice showed movement deficits, repetitive behaviors, increased anxiety, and prolonged behavior arrest. Together, our study revealed the crucial postnatal role of FOXG1 in neuronal maturation and myelination and elucidated the essential pathophysiology mechanisms of FS.
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Ba R, Yang L, Zhang B, Jiang P, Ding Z, Zhou X, Yang Z, Zhao C. FOXG1 drives transcriptomic networks to specify principal neuron subtypes during the development of the medial pallium. SCIENCE ADVANCES 2023; 9:eade2441. [PMID: 36791184 PMCID: PMC9931217 DOI: 10.1126/sciadv.ade2441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The medial pallium (MP) is the major forebrain region underlying learning and memory, spatial navigation, and emotion; however, the mechanisms underlying the specification of its principal neuron subtypes remain largely unexplored. Here, by postmitotic deletion of FOXG1 (a transcription factor linked to autism spectrum disorders and FOXG1 syndrome) and single-cell RNA sequencing of E17.5 MP in mice, we found that FOXG1 controls the specification of upper-layer retrosplenial cortical pyramidal neurons [RSC-PyNs (UL)], subiculum PyNs (SubC-PyNs), CA1-PyNs, CA3-PyNs, and dentate gyrus granule cells (DG-GCs) in the MP. We uncovered subtype-specific and subtype-shared FOXG1-regulated transcriptomic networks orchestrating MP neuron specification. We further demonstrated that FOXG1 transcriptionally represses Zbtb20, Prox1, and Epha4 to prevent CA3-PyN and DG-GC identities during the specification of RSC-PyNs (UL) and SubC-PyNs; FOXG1 directly activates Nr4a2 to promote SubC-PyN identity. We showed that TBR1, controlled by FOXG1 during CA1-PyN specification, was down-regulated. Thus, our study illuminates MP principal neuron subtype specification and related neuropathogenesis.
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Affiliation(s)
- Ru Ba
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
| | - Lin Yang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Fudan University, Shanghai 200032, P.R. China
| | - Baoshen Zhang
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
| | - Pengfei Jiang
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zhipeng Ding
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
| | - Xue Zhou
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, MOE Frontier Research Center for Brain Science, Fudan University, Shanghai 200032, P.R. China
| | - Chunjie Zhao
- Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, School of Medicine, Southeast University, Nanjing 210009, China
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Co M, Barnard RA, Jahncke JN, Grindstaff S, Fedorov LM, Adey AC, Wright KM, O'Roak BJ. Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development. J Neurosci 2022; 42:7166-7181. [PMID: 35944998 PMCID: PMC9480892 DOI: 10.1523/jneurosci.0409-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/06/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022] Open
Abstract
T-Box Brain Transcription Factor 1 (TBR1) plays essential roles in brain development, mediating neuronal migration, fate specification, and axon tract formation. While heterozygous loss-of-function and missense TBR1 mutations are associated with neurodevelopmental conditions, the effects of these heterogeneous mutations on brain development have yet to be fully explored. We characterized multiple mouse lines carrying Tbr1 mutations differing by type and exonic location, including the previously generated Tbr1 exon 2-3 knock-out (KO) line, and we analyzed male and female mice at neonatal and adult stages. The frameshift patient mutation A136PfsX80 (A136fs) caused reduced TBR1 protein in cortex similar to Tbr1 KO, while the missense patient mutation K228E caused significant TBR1 upregulation. Analysis of cortical layer formation found similar defects between KO and A136fs homozygotes in their CUX1+ and CTIP2+ layer positions, while K228E homozygosity produced layering defects distinct from these mutants. Meanwhile, the examination of cortical apoptosis found extensive cell death in KO homozygotes but limited cell death in A136fs or K228E homozygotes. Despite their discordant cortical phenotypes, these Tbr1 mutations produced several congruent phenotypes, including anterior commissure reduction in heterozygotes, which was previously observed in humans with TBR1 mutations. These results indicate that patient-specific Tbr1 mutant mice will be valuable translational models for pinpointing shared and distinct etiologies among patients with TBR1-related developmental conditions.SIGNIFICANCE STATEMENT Mutations of the TBR1 gene increase the likelihood of neurodevelopmental conditions such as intellectual disability and autism. Therefore, the study of TBR1 can offer insights into the biological mechanisms underlying these conditions, which affect millions worldwide. To improve the modeling of TBR1-related conditions over current Tbr1 knock-out mice, we created mouse lines carrying Tbr1 mutations identical to those found in human patients. Mice with one mutant Tbr1 copy show reduced amygdalar connections regardless of mutation type, suggesting a core biomarker for TBR1-related disorders. In mice with two mutant Tbr1 copies, brain phenotypes diverge by mutation type, suggesting differences in Tbr1 gene functionality in different patients. These mouse models will serve as valuable tools for understanding genotype-phenotype relationships among patients with neurodevelopmental conditions.
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Affiliation(s)
- Marissa Co
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Rebecca A Barnard
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
| | - Jennifer N Jahncke
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Sally Grindstaff
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
| | - Lev M Fedorov
- Transgenic Mouse Models Core, Oregon Health & Science University, Portland, Oregon 97239
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
| | - Kevin M Wright
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Brian J O'Roak
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239
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