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Li Y, Zhou X, Chen R, Zhang X, Cao H. STAREG: Statistical replicability analysis of high throughput experiments with applications to spatial transcriptomic studies. PLoS Genet 2024; 20:e1011423. [PMID: 39361716 PMCID: PMC11478871 DOI: 10.1371/journal.pgen.1011423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 10/15/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024] Open
Abstract
Replicable signals from different yet conceptually related studies provide stronger scientific evidence and more powerful inference. We introduce STAREG, a statistical method for replicability analysis of high throughput experiments, and apply it to analyze spatial transcriptomic studies. STAREG uses summary statistics from multiple studies of high throughput experiments and models the the joint distribution of p-values accounting for the heterogeneity of different studies. It effectively controls the false discovery rate (FDR) and has higher power by information borrowing. Moreover, it provides different rankings of important genes. With the EM algorithm in combination with pool-adjacent-violator-algorithm (PAVA), STAREG is scalable to datasets with millions of genes without any tuning parameters. Analyzing two pairs of spatially resolved transcriptomic datasets, we are able to make biological discoveries that otherwise cannot be obtained by using existing methods.
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Affiliation(s)
- Yan Li
- School of Computer Science and Technology, Changchun University of Science and Technology, Changchun, Jilin, China
- School of Mathematics, Jilin University, Changchun, Jilin, China
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xianyang Zhang
- Department of Statistics, Texas A&M University, College Station, Texas, United States of America
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
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Yu H, Liu Y, Xu F, Fu Y, Yang M, Ding L, Wu Y, Tang F, Qiao J, Wen L. A human fetal cerebellar map of the late second trimester reveals developmental molecular characteristics and abnormality in trisomy 21. Cell Rep 2024; 43:114586. [PMID: 39137113 DOI: 10.1016/j.celrep.2024.114586] [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: 02/06/2024] [Revised: 05/29/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Our understanding of human fetal cerebellum development during the late second trimester, a critical period for the generation of astrocytes, oligodendrocytes, and unipolar brush cells (UBCs), remains limited. Here, we performed single-cell RNA sequencing (scRNA-seq) in human fetal cerebellum samples from gestational weeks (GWs) 18-25. We find that proliferating UBC progenitors distribute in the subventricular zone of the rhombic lip (RLSVZ) near white matter (WM), forming a layer structure. We also delineate two trajectories from astrogenic radial glia (ARGs) to Bergmann glial progenitors (BGPs) and recognize oligodendrogenic radial glia (ORGs) as one source of primitive oligodendrocyte progenitor cells (PriOPCs). Additionally, our scRNA-seq analysis of the trisomy 21 fetal cerebellum at this stage reveals abnormal upregulated genes in pathways such as the cell adhesion pathway and focal adhesion pathway, which potentially promote neuronal differentiation. Overall, our research provides valuable insights into normal and abnormal development of the human fetal cerebellum.
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Affiliation(s)
- Hongmin Yu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yun Liu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
| | - Fanqing Xu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuanyuan Fu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Ming Yang
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Ding
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yixuan Wu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
| | - Jie Qiao
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lu Wen
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China.
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Lv ZB, Zhang JJ, Xiang C. GDF10 and IDO1 as a thyroid cancer prognostic biomarker associated with immune infiltration. Heliyon 2024; 10:e27651. [PMID: 38509876 PMCID: PMC10950683 DOI: 10.1016/j.heliyon.2024.e27651] [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: 05/22/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Objection The aim of this work is to screen the immune-related genes to predict the prognosis and provide a new direction of treatment for patients with thyroid cancer (THCA). Methods The mRNA and clinical features of THCA patients were collected from the Cancer Genome Atlas (TCGA) databases. The immune-related genes were obtained from the ImmPort databases. The bio-information methods were performed to screen the differential expression genes (DEGs) and genes related to immunity between the THCA patients and normal individuals. On this basis, the hub prognosis immunity genes were screened by Veen. The related genes were obtained by constructing the protein-protein interaction network. The enrichment analyses were performed based on the protein and protein interaction (PPI) related genes. The hub immune checkpoint was screened by correlation analysis. Finally, the hub gene and the immunity checkpoint-miRNA (or transcription factor, drug) interaction network were constructed. A drug-sensitive analysis also was performed. Results The GDF10 was screened. The PPI genes were enriched in the TGF-beta signaling pathway, signaling pathways regulating, the pluripotency of stem cells, Cytokine-cytokine receptor interaction, and so on. The hub immunity checkpoint IDO1 was obtained. The joint indicator of two hub genes was positively related to the thyroid differentiation score. Three interaction factors were found to be related to the two hub genes, and 7 kinds of drugs screened act on the two hub genes at the same time. Conclusion This work indicated that immune-related gene GDF10 and immune checkpoint IDO1 are important for the prognosis prediction of THCA patients, and immunity is involved in the proliferation, and differentiation of tumor cells.
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Affiliation(s)
- Zhao-bao Lv
- Breast and Thyroid Surgery, The Second Hospital of Liaocheng, Lingqing, 252600, Shandong, China
| | - Jun-jing Zhang
- Breast and Thyroid Surgery, The Second Hospital of Liaocheng, Lingqing, 252600, Shandong, China
| | - Cheng Xiang
- Thyroid Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
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Vera-Montecinos A, Galiano-Landeira J, Roldán M, Vidal-Domènech F, Claro E, Ramos B. A Novel Localization of METTL7A in Bergmann Glial Cells in Human Cerebellum. Int J Mol Sci 2023; 24:ijms24098405. [PMID: 37176112 PMCID: PMC10179429 DOI: 10.3390/ijms24098405] [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: 11/18/2022] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Methyltransferase-like protein 7A (METTL7A) is a member of the METTL family of methyltransferases.Little information is available regarding the cellular expression of METTL7A in the brain. METTL7A is commonly located in the endoplasmic reticulum and to a lesser extent, in the lipid droplets of some cells. Several studies have reported altered protein and RNA levels in different brain areas in schizophrenia. One of these studies found reduced protein levels of METTL7A in the cerebellar cortex in schizophrenia and stress murine models. Since there is limited information in the literature about METTL7A, we characterized its cellular and subcellular localizations in the human cerebellum using immunohistochemical analysis with laser confocal microscopy. Our study reveals a novel METTL7A localization in GFAP-positive cells, with higher expression in the end-feet of the Bergmann glia, which participate in the cerebrospinal fluid-brain parenchyma barrier. Further 3D reconstruction image analysis showed that METTL7A was expressed in the contacts between the Bergmann glia and Purkinje neurons. METTL7A was also detected in lipid droplets in some cells in the white matter. The localization of METTL7A in the human cerebellar glia limitans could suggest a putative role in maintaining the cerebellar parenchyma homeostasis and in the regulation of internal cerebellar circuits by modulating the synaptic activity of Purkinje neurons.
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Affiliation(s)
- América Vera-Montecinos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Spain
| | - Jordi Galiano-Landeira
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Spain
| | - Mònica Roldán
- Unitat de Microscòpia Confocal i Imatge Cel·lular, Servei de Medicina Genètica i Molecular, Institut Pediàtric de Malalties Rares (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Francisco Vidal-Domènech
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Spain
| | - Enrique Claro
- Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Belén Ramos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Dr. Antoni Pujadas, 42, 08830 Sant Boi de Llobregat, Spain
- Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM (Biomedical Network Research Center of Mental Health), Institute of Health Carlos III, 28029 Madrid, Spain
- Faculty of Medicine, University of Vic-Central University of Catalonia, 08500 Vic, Spain
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Kim H, Choo H, Cha J, Jang M, Son J, Jeong T, Choi BH, Lim Y, Chai HH, Lee J, Lim D, Shin D, Park W, Park JE. Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens. Anim Cells Syst (Seoul) 2022; 26:358-368. [PMID: 36605592 PMCID: PMC9809412 DOI: 10.1080/19768354.2022.2146187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p < 0.05) enriched, which were limb development, inner ear development, positive regulation of dendrite development, the KEGG pathway the TGF-beta signaling pathway, and melanogenesis (p < 0.05). These pathways are related to morphological maintenance and growth of the tissues. In addition, the SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r 2 = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.
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Affiliation(s)
- Hana Kim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Hyojun Choo
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, Korea
| | - Jihye Cha
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Myoungjin Jang
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Juhwan Son
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Taejoon Jeong
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Youngjo Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Han-Ha Chai
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Korea
| | - Woncheoul Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
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Khouri-Farah N, Guo Q, Morgan K, Shin J, Li JYH. Integrated single-cell transcriptomic and epigenetic study of cell state transition and lineage commitment in embryonic mouse cerebellum. SCIENCE ADVANCES 2022; 8:eabl9156. [PMID: 35363520 PMCID: PMC10938588 DOI: 10.1126/sciadv.abl9156] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Recent studies using single-cell RNA-sequencing have revealed cellular heterogeneity in the developing mammalian cerebellum, yet the regulatory logic underlying this cellular diversity remains to be elucidated. Using integrated single-cell RNA and ATAC analyses, we resolved developmental trajectories of cerebellar progenitors and identified putative trans- and cis-elements that control cell state transition. We reverse engineered gene regulatory networks (GRNs) of each cerebellar cell type. Through in silico simulations and in vivo experiments, we validated the efficacy of GRN analyses and uncovered the molecular control of a posterior transitory zone (PTZ), a distinct progenitor zone residing immediately anterior to the morphologically defined rhombic lip (RL). We showed that perturbing cell fate specification in the PTZ and RL causes posterior cerebellar vermis hypoplasia, the most common cerebellar birth defect in humans. Our study provides a foundation for comprehensive studies of developmental programs of the mammalian cerebellum.
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Affiliation(s)
- Nagham Khouri-Farah
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Kerry Morgan
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Jihye Shin
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - James Y. H. Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
- Institute for Systems Genomics, University of Connecticut, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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Zhao Q, Xu J, Han X, Zhang Z, Qu J, Cheng Z. Growth differentiation factor 10 induces angiogenesis to promote wound healing in rats with diabetic foot ulcers by activating TGF-β1/Smad3 signaling pathway. Front Endocrinol (Lausanne) 2022; 13:1013018. [PMID: 36714584 PMCID: PMC9880151 DOI: 10.3389/fendo.2022.1013018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/23/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Diabetic foot ulcer (DFU) represents a highly-prevalent complication of diabetes mellitus (DM). Herein, the current study sought to identify the role of growth differentiation factor 10 (GDF-10) in wound healing in DFU via regulation of the transforming growth factor-beta 1 (TGF-β1)/Smad3 pathway. METHODS DM- and DFU-related microarray datasets GSE29221 and GSE134431 were firstly retrieved, and weighted gene co-expression network analysis (WGCNA) was carried out to construct a co-expression network affecting wound healing in DFU, followed by differential analysis. A protein-protein interaction (PPI) network of the DFU-related genes was subsequently constructed, and the core genes and signaling pathways in DFU were screened with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional analyses. A DFU rat model was constructed for mechanism verification of the effect of GDF-10 on wound healing in DFU. RESULTS WGCNA screened five co-expression modules, and the brown module was most closely-related to DM. Clustering analysis screened 4417 candidate genes, of which 175 differential genes were associated with wound healing, further involved in TGF-β1/Smad3 signaling pathway regulation of wound healing in DFU. The PPI network analysis predicted that GDF-10 might regulate the TGF-β1/Smad3 signaling pathway to participate in DFU development. Results of animal experimentation showed that the wound healing rates of NFU, DFU, DFU + GDF and GDF + SIS3 groups on the 22nd day were (87.66 ± 6.80)%, (56.31 ± 7.29)%, (71.64 ± 9.43)% and (55.09 ± 7.13)%, respectively. Besides, the expression of TGF-β1 in NFU, DFU, DFU + GDF and GDF + SIS3 groups was 0.988 ± 0.086, 0.297 ± 0.036, 0.447 ± 0.044, and 0.240 ± 0.050, respectively, and that of Smad3 was 1.009 ± 0.137, 0.145 ± 0.017, 0.368 ± 0.048, and 0.200 ± 0.028, respectively. Specifically, GDF-10 exerted a significant diminishing effect on fasting blood glucose level, and promoted wound healing in DFU rats, in addition to up-regulation of VEGF, FGF, Ang-1, TGF-β1, Smad3 and enhancement of IL-1b, IL-6, TNF-a and MMP-9, thereby promoting fibroblast proliferation, collagen deposition and angiogenesis. CONCLUSIONS Our findings highlight that GDF-10 may promote angiogenesis by activating TGF-β1/Smad3 signaling, thereby promoting wound healing in DFU rats.
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Bayin NS, Mizrak D, Stephen DN, Lao Z, Sims PA, Joyner AL. Injury-induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. SCIENCE ADVANCES 2021; 7:eabj1598. [PMID: 34878841 PMCID: PMC8654303 DOI: 10.1126/sciadv.abj1598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/20/2021] [Indexed: 05/23/2023]
Abstract
To understand repair processes, it is critical to identify the molecular foundations underlying progenitor diversity and plasticity. Upon injury to the neonatal cerebellum, a normally gliogenic nestin-expressing progenitor (NEP) in the Bergmann glia layer (BgL) undergoes adaptive reprograming to restore granule cell production. However, the cellular states and genes regulating the NEP fate switch are unknown. Using single-cell RNA sequencing and fate mapping, we defined molecular subtypes of NEPs and their lineages under homeostasis and repair. NEPs contain two major subtypes: Hopx+ astrogliogenic and Ascl1+ neurogenic NEPs that are further subdivided based on their location, lineage, and differentiation status. Upon injury, an Ascl1+ transitory cellular state arises from Hopx+ BgL-NEPs. Furthermore, mutational analysis revealed that induction of Ascl1 is required for adaptive reprogramming by orchestrating a glial-to-neural switch in vivo following injury. Thus, we provide molecular and cellular insights into context-dependent progenitor plasticity and repair mechanisms in the brain.
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Affiliation(s)
- N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Dogukan Mizrak
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Daniel N. Stephen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Zhimin Lao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biochemistry and Biophysics, Columbia University, New York, NY, USA
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
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Wang F, Wang Q, Liu B, Mei L, Ma S, Wang S, Wang R, Zhang Y, Niu C, Xiong Z, Zheng Y, Zhang Z, Shi J, Song X. The long noncoding RNA Synage regulates synapse stability and neuronal function in the cerebellum. Cell Death Differ 2021; 28:2634-2650. [PMID: 33762741 PMCID: PMC8408218 DOI: 10.1038/s41418-021-00774-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
The brain is known to express many long noncoding RNAs (lncRNAs); however, whether and how these lncRNAs function in modulating synaptic stability remains unclear. Here, we report a cerebellum highly expressed lncRNA, Synage, regulating synaptic stability via at least two mechanisms. One is through the function of Synage as a sponge for the microRNA miR-325-3p, to regulate expression of the known cerebellar synapse organizer Cbln1. The other function is to serve as a scaffold for organizing the assembly of the LRP1-HSP90AA1-PSD-95 complex in PF-PC synapses. Although somewhat divergent in its mature mRNA sequence, the locus encoding Synage is positioned adjacent to the Cbln1 loci in mouse, rhesus macaque, and human, and Synage is highly expressed in the cerebella of all three species. Synage deletion causes a full-spectrum cerebellar ablation phenotype that proceeds from cerebellar atrophy, through neuron loss, on to synapse density reduction, synaptic vesicle loss, and finally to a reduction in synaptic activity during cerebellar development; these deficits are accompanied by motor dysfunction in adult mice, which can be rescued by AAV-mediated Synage overexpression from birth. Thus, our study demonstrates roles for the lncRNA Synage in regulating synaptic stability and function during cerebellar development.
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Affiliation(s)
- Fei Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Qianqian Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Baowei Liu
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Lisheng Mei
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Sisi Ma
- grid.506261.60000 0001 0706 7839National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS and PUMC, Beijing, China
| | - Shujuan Wang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Ruoyu Wang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China ,grid.240145.60000 0001 2291 4776Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX USA
| | - Yan Zhang
- grid.59053.3a0000000121679639Stroke Center & Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Chaoshi Niu
- grid.59053.3a0000000121679639Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Zhiqi Xiong
- grid.9227.e0000000119573309Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yong Zheng
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhi Zhang
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui China
| | - Juan Shi
- grid.506261.60000 0001 0706 7839National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, CAMS and PUMC, Beijing, China
| | - Xiaoyuan Song
- grid.59053.3a0000000121679639MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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10
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Kantzer CG, Parmigiani E, Cerrato V, Tomiuk S, Knauel M, Jungblut M, Buffo A, Bosio A. ACSA-2 and GLAST classify subpopulations of multipotent and glial-restricted cerebellar precursors. J Neurosci Res 2021; 99:2228-2249. [PMID: 34060113 PMCID: PMC8453861 DOI: 10.1002/jnr.24842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022]
Abstract
The formation of the cerebellum is highly coordinated to obtain its characteristic morphology and all cerebellar cell types. During mouse postnatal development, cerebellar progenitors with astroglial‐like characteristics generate mainly astrocytes and oligodendrocytes. However, a subset of astroglial‐like progenitors found in the prospective white matter (PWM) produces astroglia and interneurons. Characterizing these cerebellar astroglia‐like progenitors and distinguishing their developmental fates is still elusive. Here, we reveal that astrocyte cell surface antigen‐2 (ACSA‐2), lately identified as ATPase, Na+/K+ transporting, beta 2 polypeptide, is expressed by glial precursors throughout postnatal cerebellar development. In contrast to common astrocyte markers, ACSA‐2 appears on PWM cells but is absent on Bergmann glia (BG) precursors. In the adult cerebellum, ACSA‐2 is broadly expressed extending to velate astrocytes in the granular layer, white matter astrocytes, and to a lesser extent to BG. Cell transplantation and transcriptomic analysis revealed that marker staining discriminates two postnatal progenitor pools. One subset is defined by the co‐expression of ACSA‐2 and GLAST and the expression of markers typical of parenchymal astrocytes. These are PWM precursors that are exclusively gliogenic. They produce predominantly white matter and granular layer astrocytes. Another subset is constituted by GLAST positive/ACSA‐2 negative precursors that express neurogenic and BG‐like progenitor genes. This population displays multipotency and gives rise to interneurons besides all glial types, including BG. In conclusion, this work reports about ACSA‐2, a marker that in combination with GLAST enables for the discrimination and isolation of multipotent and glia‐committed progenitors, which generate different types of cerebellar astrocytes.
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Affiliation(s)
- Christina Geraldine Kantzer
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany.,Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy.,Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Italy.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy.,Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Italy.,Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Stefan Tomiuk
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Michail Knauel
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | | | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy.,Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Italy
| | - Andreas Bosio
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
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11
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Hughes LJ, Park R, Lee MJ, Terry BK, Lee DJ, Kim H, Cho SH, Kim S. Yap/Taz are required for establishing the cerebellar radial glia scaffold and proper foliation. Dev Biol 2019; 457:150-162. [PMID: 31586559 DOI: 10.1016/j.ydbio.2019.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 01/20/2023]
Abstract
Yap/Taz are well-established downstream effectors of the Hippo pathway, known to regulate organ size by directing proliferation and apoptosis. Although the functions of Yap/Taz have been extensively studied, little is known about their role in brain development. Here, through genetic ablation, we show that Yap/Taz are required for cerebellar morphogenesis. Yap/Taz deletion in neural progenitors causes defects in secondary fissure formation, leading to abnormal folia development. Although they seemed very likely to serve an important function in the development of cerebellar granule cell precursors, Yap/Taz are dispensable for their proliferation. Furthermore, Yap/Taz loss does not rescue the medulloblastoma phenotype caused by constitutively active Smoothened. Importantly, Yap/Taz are highly expressed in radial glia and play a crucial role in establishing the radial scaffold and cellular polarity of neural progenitors during embryogenesis. We found that Yap/Taz are necessary to establish and maintain junctional integrity of cerebellar neuroepithelium as prominent junction proteins are not maintained at the apical junction in the absence of Yap/Taz. Our study identifies a novel function of Yap/Taz in cerebellar foliation and finds that they are required to establish the radial glia scaffold and junctional stability.
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Affiliation(s)
- Lucinda J Hughes
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA; Graduate Program of Biomedical Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Raehee Park
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Min Jung Lee
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Bethany K Terry
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA; Graduate Program of Biomedical Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - David J Lee
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Hansol Kim
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Seo-Hee Cho
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Seonhee Kim
- Shriners Hospitals Pediatrics Research Center, Department of Anatomy and Cell Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
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12
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Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 2018; 36:nbt.4259. [PMID: 30320766 DOI: 10.1038/nbt.4259] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/20/2018] [Indexed: 01/10/2023]
Abstract
Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. Although single splicing events have been described for ≤200 single cells with statistical confidence, full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled. We developed a method that starts with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. Using single-cell isoform RNA-Seq (ScISOr-Seq), we identified RNA isoforms in neurons, astrocytes, microglia, and cell subtypes such as Purkinje and Granule cells, and cell-type-specific combination patterns of distant splice sites. We used ScISOr-Seq to improve genome annotation in mouse Gencode version 10 by determining the cell-type-specific expression of 18,173 known and 16,872 novel isoforms.
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Affiliation(s)
- Ishaan Gupta
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
| | - Paul G Collier
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
| | | | - Ahmed Mahfouz
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Anoushka Joglekar
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
| | - Taylor Floyd
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
| | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, the Netherlands
| | - Ben Barres
- Department of Neurobiology, Stanford University, Stanford, California, USA
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, the Netherlands
| | - Steven A Sloan
- Department of Neurobiology, Stanford University, Stanford, California, USA
| | - Wenjie Luo
- Brain and Mind Research Institute and Appel Alzheimer's Research Institute, Weill Cornell Medicine, New York, New York, USA
| | | | - M Elizabeth Ross
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA
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13
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Cerrato V, Parmigiani E, Figueres-Oñate M, Betizeau M, Aprato J, Nanavaty I, Berchialla P, Luzzati F, de’Sperati C, López-Mascaraque L, Buffo A. Multiple origins and modularity in the spatiotemporal emergence of cerebellar astrocyte heterogeneity. PLoS Biol 2018; 16:e2005513. [PMID: 30260948 PMCID: PMC6178385 DOI: 10.1371/journal.pbio.2005513] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 10/09/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
The morphological, molecular, and functional heterogeneity of astrocytes is under intense scrutiny, but how this diversity is ontogenetically achieved remains largely unknown. Here, by quantitative in vivo clonal analyses and proliferation studies, we demonstrate that the major cerebellar astrocyte types emerge according to an unprecedented and remarkably orderly developmental program comprising (i) a time-dependent decline in both clone size and progenitor multipotency, associated with clone allocation first to the hemispheres and then to the vermis(ii) distinctive clonal relationships among astrocyte types, revealing diverse lineage potentials of embryonic and postnatal progenitors; and (iii) stereotyped clone architectures and recurrent modularities that correlate to layer-specific dynamics of postnatal proliferation/differentiation. In silico simulations indicate that the sole presence of a unique multipotent progenitor at the source of the whole astrogliogenic program is unlikely and rather suggest the involvement of additional committed components. Astrocytes are abundant cells of the brain essential to support and shape neuronal activity. They can be grouped in different subclasses based on their remarkable variety of morphologies, molecular profiles, and specialized functions. Although different astrocyte types likely display specialized interactions with distinct neuron categories, the different classes of astrocytes have only partially been unmasked. How astrocyte heterogeneity is ontogenetically achieved remains largely unknown. Here we approached this question by studying the development of the main astrocyte types of the cerebellum. The reconstruction of developmental lineages in the mouse embryo combined with proliferation studies and computational modeling demonstrate that cerebellar astrocyte types emerge according to an unprecedented and remarkably orderly developmental program. Embryonic progenitor cells produce either only a single astrocyte type or more types. These distinct astrocyte lineages display stereotyped architectures and recurrent modularities. Moreover, the generation of astrocytes follows a well-defined spatiotemporal pattern, defined by a time-dependent allocation of astrocytes to distinct cerebellar territories and an inside-out sequence of differentiation, coupled with a decline over time in both progenitor amplification and capability to produce distinct astrocyte types. These results provide the first evidence that an ontogenetic program, tightly regulated in space and time, determines astrocyte heterogeneity.
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Affiliation(s)
- Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - María Figueres-Oñate
- Department of Molecular, Cellular, and Developmental Neurobiology, Cajal Institute -CSIC-, Spanish National Research Council, Madrid, Spain
| | - Marion Betizeau
- Brain Research Institute, University of Zurich Irchel, Zurich, Switzerland
| | - Jessica Aprato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - Ishira Nanavaty
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - Paola Berchialla
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Federico Luzzati
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Claudio de’Sperati
- Laboratory of Action, Perception and Cognition, Vita-Salute San Raffaele University, Milan, Italy
- Experimental Psychology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura López-Mascaraque
- Department of Molecular, Cellular, and Developmental Neurobiology, Cajal Institute -CSIC-, Spanish National Research Council, Madrid, Spain
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
- * E-mail:
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14
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Carter RA, Bihannic L, Rosencrance C, Hadley JL, Tong Y, Phoenix TN, Natarajan S, Easton J, Northcott PA, Gawad C. A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum. Curr Biol 2018; 28:2910-2920.e2. [PMID: 30220501 DOI: 10.1016/j.cub.2018.07.062] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/30/2018] [Accepted: 07/25/2018] [Indexed: 01/31/2023]
Abstract
The cerebellum develops from a restricted number of cell types that precisely organize to form the circuitry that controls sensory-motor coordination and some higher-order cognitive processes. To acquire an enhanced understanding of the molecular processes that mediate cerebellar development, we performed single-cell RNA-sequencing of 39,245 murine cerebellar cells at twelve critical developmental time points. Using recognized lineage markers, we confirmed that the single-cell data accurately recapitulate cerebellar development. We then followed distinct populations from emergence through migration and differentiation, and determined the associated transcriptional cascades. After identifying key lineage commitment decisions, focused analyses uncovered waves of transcription factor expression at those branching points. Finally, we created Cell Seek, a flexible online interface that facilitates exploration of the dataset. Our study provides a transcriptional summarization of cerebellar development at single-cell resolution that will serve as a valuable resource for future investigations of cerebellar development, neurobiology, and disease.
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Affiliation(s)
- Robert A Carter
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Celeste Rosencrance
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiai Tong
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy N Phoenix
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Charles Gawad
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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15
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Bernal A, Arranz L. Nestin-expressing progenitor cells: function, identity and therapeutic implications. Cell Mol Life Sci 2018; 75:2177-2195. [PMID: 29541793 PMCID: PMC5948302 DOI: 10.1007/s00018-018-2794-z] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/28/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023]
Abstract
The neuroepithelial stem cell protein, or Nestin, is a cytoskeletal intermediate filament initially characterized in neural stem cells. However, current extensive evidence obtained in in vivo models and humans shows presence of Nestin+ cells with progenitor and/or regulatory functions in a number of additional tissues, remarkably bone marrow. This review presents the current knowledge on the role of Nestin in essential stem cell functions, including self-renewal/proliferation, differentiation and migration, in the context of the cytoskeleton. We further discuss the available in vivo models for the study of Nestin+ cells and their progeny, their function and elusive nature in nervous system and bone marrow, and their potential mechanistic role and promising therapeutic value in preclinical models of disease. Future improved in vivo models and detection methods will allow to determine the true essence of Nestin+ cells and confirm their potential application as therapeutic target in a range of diseases.
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Affiliation(s)
- Aurora Bernal
- Stem Cell Aging and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway, MH Building Level 6, 9019, Tromsø, Norway
| | - Lorena Arranz
- Stem Cell Aging and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway, MH Building Level 6, 9019, Tromsø, Norway.
- Department of Hematology, University Hospital of North Norway, Tromsø, Norway.
- Young Associate Investigator, Norwegian Center for Molecular Medicine (NCMM), Oslo, Norway.
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16
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Schilling K. Moving into shape: cell migration during the development and histogenesis of the cerebellum. Histochem Cell Biol 2018; 150:13-36. [DOI: 10.1007/s00418-018-1677-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
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17
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Leung AW, Li JYH. The Molecular Pathway Regulating Bergmann Glia and Folia Generation in the Cerebellum. CEREBELLUM (LONDON, ENGLAND) 2018; 17:42-48. [PMID: 29218544 PMCID: PMC5809181 DOI: 10.1007/s12311-017-0904-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Evolution of complex behaviors in higher vertebrates and primates require the development of sophisticated neuronal circuitry and the expansion of brain surface area to accommodate the vast number of neuronal and glial populations. To achieve these goals, the neocortex in primates and the cerebellum in amniotes have developed specialized types of basal progenitors to aid the folding of their cortices. In the cerebellum, Bergmann glia constitute such a basal progenitor population, having a distinctive morphology and playing a critical role in cerebellar corticogenesis. Here, we review recent studies on the induction of Bergmann glia and their crucial role in mediating folding of the cerebellar cortex. These studies uncover a key function of FGF-ERK-ETV signaling cascade in the transformation of Bergmann glia from radial glia in the ventricular zone. Remarkably, in the neocortex, the same signaling axis operates to facilitate the transformation of ventricular radial glia into basal radial glia, a Bergmann glia-like basal progenitor population, which have been implicated in the establishment of neocortical gyri. These new findings draw a striking similarity in the function and ontogeny of the two basal progenitor populations born in distinct brain compartments.
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Affiliation(s)
- Alan W Leung
- Department of Genetics and Yale Stem Cell Center, Yale University, 10 Amistad Street, New Haven, CT, 06520-8073, USA
| | - James Y H Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030-6403, USA.
- Institute for Systems Genomics, University of Connecticut, 400 Farmington Avenue, Farmington, CT, 06030-6403, USA.
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18
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Transcriptional Regulator ZEB2 Is Essential for Bergmann Glia Development. J Neurosci 2018; 38:1575-1587. [PMID: 29326173 DOI: 10.1523/jneurosci.2674-17.2018] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/25/2017] [Accepted: 01/05/2018] [Indexed: 11/21/2022] Open
Abstract
Bergmann glia facilitate granule neuron migration during development and maintain the cerebellar organization and functional integrity. At present, molecular control of Bergmann glia specification from cerebellar radial glia is not fully understood. In this report, we show that ZEB2 (aka, SIP1 or ZFHX1B), a Mowat-Wilson syndrome-associated transcriptional regulator, is highly expressed in Bergmann glia, but hardly detectable in astrocytes in the cerebellum. The mice lacking Zeb2 in cerebellar radial glia exhibit severe deficits in Bergmann glia specification, and develop cerebellar cortical lamination dysgenesis and locomotion defects. In developing Zeb2-mutant cerebella, inward migration of granule neuron progenitors is compromised, the proliferation of glial precursors is reduced, and radial glia fail to differentiate into Bergmann glia in the Purkinje cell layer. In contrast, Zeb2 ablation in granule neuron precursors or oligodendrocyte progenitors does not affect Bergmann glia formation, despite myelination deficits caused by Zeb2 mutation in the oligodendrocyte lineage. Transcriptome profiling identified that ZEB2 regulates a set of Bergmann glia-related genes and FGF, NOTCH, and TGFβ/BMP signaling pathway components. Our data reveal that ZEB2 acts as an integral regulator of Bergmann glia formation ensuring maintenance of cerebellar integrity, suggesting that ZEB2 dysfunction in Bergmann gliogenesis might contribute to motor deficits in Mowat-Wilson syndrome.SIGNIFICANCE STATEMENT Bergmann glia are essential for proper cerebellar organization and functional circuitry, however, the molecular mechanisms that control the specification of Bergmann glia remain elusive. Here, we show that transcriptional factor ZEB2 is highly expressed in mature Bergmann glia, but not in cerebellar astrocytes. The mice lacking Zeb2 in cerebellar radial glia, but not oligodendrocyte progenitors or granular neuron progenitors, exhibit severe defects in Bergmann glia formation. The orderly radial scaffolding formed by Bergmann glial fibers critical for cerebellar lamination was not established in Zeb2 mutants, displaying motor behavior deficits. This finding demonstrates a previously unrecognized critical role for ZEB2 in Bergmann glia specification, and points to an important contribution of ZEB2 dysfunction to cerebellar motor disorders in Mowat-Wilson syndrome.
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19
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Takeuchi M, Yamaguchi S, Sakakibara Y, Hayashi T, Matsuda K, Hara Y, Tanegashima C, Shimizu T, Kuraku S, Hibi M. Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum. J Comp Neurol 2016; 525:1558-1585. [DOI: 10.1002/cne.24114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/03/2016] [Accepted: 09/04/2016] [Indexed: 02/02/2023]
Affiliation(s)
- Miki Takeuchi
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology; Nagoya University; Nagoya Aichi 464-8601 Japan
| | - Shingo Yamaguchi
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Yoshimasa Sakakibara
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Takuto Hayashi
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Koji Matsuda
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology; Nagoya University; Nagoya Aichi 464-8601 Japan
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies; Kobe Hyogo 650-0047 Japan
| | - Chiharu Tanegashima
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies; Kobe Hyogo 650-0047 Japan
| | - Takashi Shimizu
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology; Nagoya University; Nagoya Aichi 464-8601 Japan
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies; Kobe Hyogo 650-0047 Japan
| | - Masahiko Hibi
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology; Nagoya University; Nagoya Aichi 464-8601 Japan
- Division of Biological Science, Graduate School of Science; Nagoya University; Nagoya Aichi 464-8602 Japan
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20
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Gerling M, Büller NVJA, Kirn LM, Joost S, Frings O, Englert B, Bergström Å, Kuiper RV, Blaas L, Wielenga MCB, Almer S, Kühl AA, Fredlund E, van den Brink GR, Toftgård R. Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth. Nat Commun 2016; 7:12321. [PMID: 27492255 PMCID: PMC4980446 DOI: 10.1038/ncomms12321] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/21/2016] [Indexed: 01/07/2023] Open
Abstract
A role for Hedgehog (Hh) signalling in the development of colorectal cancer (CRC) has been proposed. In CRC and other solid tumours, Hh ligands are upregulated; however, a specific Hh antagonist provided no benefit in a clinical trial. Here we use Hh reporter mice to show that downstream Hh activity is unexpectedly diminished in a mouse model of colitis-associated colon cancer, and that downstream Hh signalling is restricted to the stroma. Functionally, stroma-specific Hh activation in mice markedly reduces the tumour load and blocks progression of advanced neoplasms, partly via the modulation of BMP signalling and restriction of the colonic stem cell signature. By contrast, attenuated Hh signalling accelerates colonic tumourigenesis. In human CRC, downstream Hh activity is similarly reduced and canonical Hh signalling remains predominantly paracrine. Our results suggest that diminished downstream Hh signalling enhances CRC development, and that stromal Hh activation can act as a colonic tumour suppressor. The Hedgehog signalling pathway can drive tumorigenesis. Here, the authors show that in a colitis-associated colon cancer model downstream Hedgehog signalling is restricted to the stroma and its over-activation can inhibit tumorigenesis, associated with activation of BMP signaling.
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Affiliation(s)
- Marco Gerling
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden
| | - Nikè V J A Büller
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology and Hepatology, Academic Medical Center, Meibergdreef 69-71, AZ1105 Amsterdam, The Netherlands
| | - Leonard M Kirn
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden.,Department of Medicine I for Gastroenterology, Infectious Diseases and Rheumatology, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Simon Joost
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden
| | - Oliver Frings
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Benjamin Englert
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden.,Department of Medicine I for Gastroenterology, Infectious Diseases and Rheumatology, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Åsa Bergström
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden
| | - Raoul V Kuiper
- Core Facility for Morphologic Phenotype Analysis, Clinical Research Center, Karolinska Institutet, Hälsovägen 7-9, 14183 Huddinge, Sweden
| | - Leander Blaas
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden
| | - Mattheus C B Wielenga
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology and Hepatology, Academic Medical Center, Meibergdreef 69-71, AZ1105 Amsterdam, The Netherlands
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, 17176 Stockholm, Sweden.,Center for Digestive Diseases, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Anja A Kühl
- Department of Medicine I for Gastroenterology, Infectious Diseases and Rheumatology, Charité, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Erik Fredlund
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Gijs R van den Brink
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology and Hepatology, Academic Medical Center, Meibergdreef 69-71, AZ1105 Amsterdam, The Netherlands
| | - Rune Toftgård
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, Hälsovägen 7, 14183 Huddinge, Sweden
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21
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Chrobak AA, Soltys Z. Bergmann Glia, Long-Term Depression, and Autism Spectrum Disorder. Mol Neurobiol 2016; 54:1156-1166. [PMID: 26809583 PMCID: PMC5310553 DOI: 10.1007/s12035-016-9719-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/12/2016] [Indexed: 12/22/2022]
Abstract
Bergmann glia (BG), a specific type of radial astrocytes in the cerebellum, play a variety of vital functions in the development of this structure. However, the possible role of BG in the development of abnormalities observed in individuals with autism spectrum disorder (ASD) seems to be underestimated. One of the most consistent findings observed in ASD patients is loss of Purkinje cells (PCs). Such a defect may be caused by dysregulation of glutamate homeostasis, which is maintained mainly by BG. Moreover, these glial cells are involved in long-term depression (LTD), a form of plasticity which can additionally subserve neuroprotective functions. The aim of presented review is to summarize the current knowledge about interactions which occur between PC and BG, with special emphasis on those which are relevant to the survival and proper functioning of cerebellar neurons.
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Affiliation(s)
- Adrian Andrzej Chrobak
- Department of Neuroanatomy, Institute of Zoology, Jagiellonian University, Gronostajowa St. 9, Cracow, 30-387, Poland. .,Faculty of Medicine, Jagiellonian University Medical College, Kopernika St. 21A, Cracow, 31-501, Poland.
| | - Zbigniew Soltys
- Department of Neuroanatomy, Institute of Zoology, Jagiellonian University, Gronostajowa St. 9, Cracow, 30-387, Poland
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22
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De Luca A, Cerrato V, Fucà E, Parmigiani E, Buffo A, Leto K. Sonic hedgehog patterning during cerebellar development. Cell Mol Life Sci 2016; 73:291-303. [PMID: 26499980 PMCID: PMC11108499 DOI: 10.1007/s00018-015-2065-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 10/06/2015] [Accepted: 10/08/2015] [Indexed: 01/30/2023]
Abstract
The morphogenic factor sonic hedgehog (Shh) actively orchestrates many aspects of cerebellar development and maturation. During embryogenesis, Shh signaling is active in the ventricular germinal zone (VZ) and represents an essential signal for proliferation of VZ-derived progenitors. Later, Shh secreted by Purkinje cells sustains the amplification of postnatal neurogenic niches: the external granular layer and the prospective white matter, where excitatory granule cells and inhibitory interneurons are produced, respectively. Moreover, Shh signaling affects Bergmann glial differentiation and promotes cerebellar foliation during development. Here we review the most relevant functions of Shh during cerebellar ontogenesis, underlying its role in physiological and pathological conditions.
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Affiliation(s)
- Annarita De Luca
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Elisa Fucà
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
| | - Ketty Leto
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126, Turin, Italy.
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
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