1
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Banu MA, Dovas A, Argenziano MG, Zhao W, Sperring CP, Cuervo Grajal H, Liu Z, Higgins DM, Amini M, Pereira B, Ye LF, Mahajan A, Humala N, Furnari JL, Upadhyayula PS, Zandkarimi F, Nguyen TT, Teasley D, Wu PB, Hai L, Karan C, Dowdy T, Razavilar A, Siegelin MD, Kitajewski J, Larion M, Bruce JN, Stockwell BR, Sims PA, Canoll P. A cell state-specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. EMBO J 2024:10.1038/s44318-024-00176-4. [PMID: 39192032 DOI: 10.1038/s44318-024-00176-4] [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: 04/23/2024] [Revised: 06/12/2024] [Accepted: 07/01/2024] [Indexed: 08/29/2024] Open
Abstract
Glioma cells hijack developmental programs to control cell state. Here, we uncover a glioma cell state-specific metabolic liability that can be therapeutically targeted. To model cell conditions at brain tumor inception, we generated genetically engineered murine gliomas, with deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling astrocyte differentiation during brain development. N1IC tumors harbored quiescent astrocyte-like transformed cell populations while p53 tumors were predominantly comprised of proliferating progenitor-like cell states. Further, N1IC transformed cells exhibited increased mitochondrial lipid peroxidation, high ROS production and depletion of reduced glutathione. This altered mitochondrial phenotype rendered the astrocyte-like, quiescent populations more sensitive to pharmacologic or genetic inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Treatment of patient-derived early-passage cell lines and glioma slice cultures generated from surgical samples with a GPX4 inhibitor induced selective depletion of quiescent astrocyte-like glioma cell populations with similar metabolic profiles. Collectively, these findings reveal a specific therapeutic vulnerability to ferroptosis linked to mitochondrial redox imbalance in a subpopulation of quiescent astrocyte-like glioma cells resistant to standard forms of treatment.
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Affiliation(s)
- Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael G Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Colin P Sperring
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Zhouzerui Liu
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Dominique Mo Higgins
- Department of Neurological Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Misha Amini
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ling F Ye
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia L Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Pavan S Upadhyayula
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Zandkarimi
- Department of Biological Sciences, Department of Chemistry and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Trang Tt Nguyen
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Damian Teasley
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter B Wu
- Department of Neurological Surgery, UCLA Geffen School of Medicine, Los Angeles, CA, USA
| | - Li Hai
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | | | - Aida Razavilar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Markus D Siegelin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jan Kitajewski
- University of Illinois Cancer Center, Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, USA
| | | | - Jeffrey N Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Department of Chemistry and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Peter A Sims
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Peter Canoll
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
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2
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Norton ES, Whaley LA, Jones VK, Brooks MM, Russo MN, Morderer D, Jessen E, Schiapparelli P, Ramos-Fresnedo A, Zarco N, Carrano A, Rossoll W, Asmann YW, Lam TT, Chaichana KL, Anastasiadis PZ, Quiñones-Hinojosa A, Guerrero-Cázares H. Cell-specific cross-talk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone. SCIENCE ADVANCES 2024; 10:eadn1607. [PMID: 39110807 PMCID: PMC11305394 DOI: 10.1126/sciadv.adn1607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Glioblastoma (GBM) is the most prevalent and aggressive malignant primary brain tumor. GBM proximal to the lateral ventricles (LVs) is more aggressive, potentially because of subventricular zone contact. Despite this, cross-talk between GBM and neural stem/progenitor cells (NSC/NPCs) is not well understood. Using cell-specific proteomics, we show that LV-proximal GBM prevents neuronal maturation of NSCs through induction of senescence. In addition, GBM brain tumor-initiating cells (BTICs) increase expression of cathepsin B (CTSB) upon interaction with NPCs. Lentiviral knockdown and recombinant protein experiments reveal that both cell-intrinsic and soluble CTSB promote malignancy-associated phenotypes in BTICs. Soluble CTSB stalls neuronal maturation in NPCs while promoting senescence, providing a link between LV-tumor proximity and neurogenesis disruption. Last, we show LV-proximal CTSB up-regulation in patients, showing the relevance of this cross-talk in human GBM biology. These results demonstrate the value of proteomic analysis in tumor microenvironment research and provide direction for new therapeutic strategies in GBM.
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Affiliation(s)
- Emily S. Norton
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
- Regenerative Sciences Training Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Lauren A. Whaley
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Vanessa K. Jones
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Mieu M. Brooks
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Marissa N. Russo
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dmytro Morderer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Erik Jessen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | | | - Natanael Zarco
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Anna Carrano
- Department of Neurosurgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yan W. Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - TuKiet T. Lam
- Keck MS and Proteomics Resource, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510, USA
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3
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Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600691. [PMID: 39091792 PMCID: PMC11291010 DOI: 10.1101/2024.06.25.600691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.
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4
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Ma Z, Zhang W, Wang C, Su Y, Yi C, Niu J. A New Acquaintance of Oligodendrocyte Precursor Cells in the Central Nervous System. Neurosci Bull 2024:10.1007/s12264-024-01261-8. [PMID: 39042298 DOI: 10.1007/s12264-024-01261-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 07/24/2024] Open
Abstract
Oligodendrocyte precursor cells (OPCs) are a heterogeneous multipotent population in the central nervous system (CNS) that appear during embryogenesis and persist as resident cells in the adult brain parenchyma. OPCs could generate oligodendrocytes to participate in myelination. Recent advances have renewed our knowledge of OPC biology by discovering novel markers of oligodendroglial cells, the myelin-independent roles of OPCs, and the regulatory mechanism of OPC development. In this review, we will explore the updated knowledge on OPC identity, their multifaceted roles in the CNS in health and diseases, as well as the regulatory mechanisms that are involved in their developmental stages, which hopefully would contribute to a further understanding of OPCs and attract attention in the field of OPC biology.
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Affiliation(s)
- Zexuan Ma
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
| | - Wei Zhang
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
| | - Chenmeng Wang
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yixun Su
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Chenju Yi
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, China.
- Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen, 518107, China.
| | - Jianqin Niu
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China.
- Chongqing Key Laboratory of Neurobiology, Chongqing, 400038, China.
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5
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Kopsidas CA, Lowe CC, McDaniel DP, Zhou X, Feng Y. Sustained generation of neurons destined for neocortex with oxidative metabolic upregulation upon filamin abrogation. iScience 2024; 27:110199. [PMID: 38989458 PMCID: PMC11233971 DOI: 10.1016/j.isci.2024.110199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Neurons in the neocortex are generated during embryonic development. While the adult ventricular-subventricular zone (V-SVZ) contains cells with neural stem/progenitors' characteristics, it remains unclear whether it has the capacity of producing neocortical neurons. Here, we show that generating neurons with transcriptomic resemblance to upper layer neocortical neurons continues in the V-SVZ of mouse models of a human condition known as periventricular heterotopia by abrogating Flna and Flnb. We found such surplus neurogenesis was associated with V-SVZ's upregulation of oxidative phosphorylation, mitochondrial biogenesis, and vascular abundance. Additionally, spatial transcriptomics analyses showed V-SVZ's neurogenic activation was coupled with transcriptional enrichment of genes in diverse pathways for energy metabolism, angiogenesis, cell signaling, synaptic transmission, and turnovers of nucleic acids and proteins in upper cortical layers. These findings support the potential of generating neocortical neurons in adulthood through boosting brain-wide vascular circulation, aerobic adenosine triphosphate synthesis, metabolic turnover, and neuronal activity.
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Affiliation(s)
- Caroline A. Kopsidas
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Clara C. Lowe
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Dennis P. McDaniel
- Biomedical Instrumentation Center, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Yuanyi Feng
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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6
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Grobecker P, Sakoparnig T, van Nimwegen E. Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. PLoS Comput Biol 2024; 20:e1012224. [PMID: 38995959 DOI: 10.1371/journal.pcbi.1012224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/04/2024] [Indexed: 07/14/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a popular experimental method to study variation of gene expression within a population of cells. However, obtaining an accurate picture of the diversity of distinct gene expression states that are present in a given dataset is highly challenging because the sparsity of the scRNA-seq data and its inhomogeneous measurement noise properties. Although a vast number of different methods is applied in the literature for clustering cells into subsets with 'similar' expression profiles, these methods generally lack rigorously specified objectives, involve multiple complex layers of normalization, filtering, feature selection, dimensionality-reduction, employ ad hoc measures of distance or similarity between cells, often ignore the known measurement noise properties of scRNA-seq measurements, and include a large number of tunable parameters. Consequently, it is virtually impossible to assign concrete biophysical meaning to the clusterings that result from these methods. Here we address the following problem: Given raw unique molecule identifier (UMI) counts of an scRNA-seq dataset, partition the cells into subsets such that the gene expression states of the cells in each subset are statistically indistinguishable, and each subset corresponds to a distinct gene expression state. That is, we aim to partition cells so as to maximally reduce the complexity of the dataset without removing any of its meaningful structure. We show that, given the known measurement noise structure of scRNA-seq data, this problem is mathematically well-defined and derive its unique solution from first principles. We have implemented this solution in a tool called Cellstates which operates directly on the raw data and automatically determines the optimal partition and cluster number, with zero tunable parameters. We show that, on synthetic datasets, Cellstates almost perfectly recovers optimal partitions. On real data, Cellstates robustly identifies subtle substructure within groups of cells that are traditionally annotated as a common cell type. Moreover, we show that the diversity of gene expression states that Cellstates identifies systematically depends on the tissue of origin and not on technical features of the experiments such as the total number of cells and total UMI count per cell. In addition to the Cellstates tool we also provide a small toolbox of software to place the identified cellstates into a hierarchical tree of higher-order clusters, to identify the most important differentially expressed genes at each branch of this hierarchy, and to visualize these results.
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Affiliation(s)
- Pascal Grobecker
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas Sakoparnig
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
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7
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Ouzikov S, Edwards KM, Anandampillai T, Watanabe S, Lozano Casasbuenas D, Siu KK, Harkins D, Dou A, Jeong D, Lee JE, Yuzwa SA. LRIG1 controls proliferation of adult neural stem cells by facilitating TGFβ and BMP signalling pathways. Commun Biol 2024; 7:845. [PMID: 38987622 PMCID: PMC11237139 DOI: 10.1038/s42003-024-06524-8] [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: 11/23/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Adult Neural Stem Cells (aNSCs) in the ventricular-subventricular zone (V-SVZ) are largely quiescent. Here, we characterize the mechanism underlying the functional role of a cell-signalling inhibitory protein, LRIG1, in the control of aNSCs proliferation. Using Lrig1 knockout models, we show that Lrig1 ablation results in increased aNSCs proliferation with no change in neuronal progeny and that this hyperproliferation likely does not result solely from activation of the epidermal growth factor receptor (EGFR). Loss of LRIG1, however, also leads to impaired activation of transforming growth factor beta (TGFβ) and bone morphogenic protein (BMP) signalling. Biochemically, we show that LRIG1 binds TGFβ/BMP receptors and the TGFβ1 ligand. Finally, we show that the consequences of these interactions are to facilitate SMAD phosphorylation. Collectively, these data suggest that unlike in embryonic NSCs where EGFR may be the primary mechanism of action, in aNSCs, LRIG1 and TGFβ pathways function together to fulfill their inhibitory roles.
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Affiliation(s)
- Stephanie Ouzikov
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Kyshona M Edwards
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Tanvi Anandampillai
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Samuel Watanabe
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Daniela Lozano Casasbuenas
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Karen K Siu
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Danyon Harkins
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Aaron Dou
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Danielle Jeong
- Institute of Medical Science, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Program in Neurosciences and Mental Health, Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Scott A Yuzwa
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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8
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Cebrian-Silla A, Assis Nascimento M, Mancia W, Gonzalez-Granero S, Romero-Rodriguez R, Obernier K, Steffen DM, Lim DA, Garcia-Verdugo JM, Alvarez-Buylla A. Neural Stem Cell Relay from B1 to B2 cells in the adult mouse Ventricular-Subventricular Zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.600695. [PMID: 39005355 PMCID: PMC11244865 DOI: 10.1101/2024.06.28.600695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Neurogenesis and gliogenesis continue in the Ventricular-Subventricular Zone (V-SVZ) of the adult rodent brain. B1 cells are astroglial cells derived from radial glia that function as primary progenitors or neural stem cells (NSCs) in the V-SVZ. B1 cells, which have a small apical contact with the ventricle, decline in numbers during early postnatal life, yet neurogenesis continues into adulthood. Here we found that a second population of V-SVZ astroglial cells (B2 cells), that do not contact the ventricle, function as NSCs in the adult brain. B2 cell numbers increase postnatally, remain constant in 12-month-old mice and decrease by 18 months. Transcriptomic analysis of ventricular-contacting and non-contacting B cells revealed key molecular differences to distinguish B1 from B2 cells. Transplantation and lineage tracing of B2 cells demonstrate their function as primary progenitors for adult neurogenesis. This study reveals how NSC function is relayed from B1 to B2 progenitors to maintain adult neurogenesis.
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9
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Iqbal MA, Bilen M, Liu Y, Jabre V, Fong BC, Chakroun I, Paul S, Chen J, Wade S, Kanaan M, Harper M, Khacho M, Slack RS. The integrated stress response promotes neural stem cell survival under conditions of mitochondrial dysfunction in neurodegeneration. Aging Cell 2024; 23:e14165. [PMID: 38757355 PMCID: PMC11258489 DOI: 10.1111/acel.14165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/27/2024] [Accepted: 03/18/2024] [Indexed: 05/18/2024] Open
Abstract
Impaired mitochondrial function is a hallmark of aging and a major contributor to neurodegenerative diseases. We have shown that disrupted mitochondrial dynamics typically found in aging alters the fate of neural stem cells (NSCs) leading to impairments in learning and memory. At present, little is known regarding the mechanisms by which neural stem and progenitor cells survive and adapt to mitochondrial dysfunction. Using Opa1-inducible knockout as a model of aging and neurodegeneration, we identify a decline in neurogenesis due to impaired stem cell activation and progenitor proliferation, which can be rescued by the mitigation of oxidative stress through hypoxia. Through sc-RNA-seq, we identify the ATF4 pathway as a critical mechanism underlying cellular adaptation to metabolic stress. ATF4 knockdown in Opa1-deficient NSCs accelerates cell death, while the increased expression of ATF4 enhances proliferation and survival. Using a Slc7a11 mutant, an ATF4 target, we show that ATF4-mediated glutathione production plays a critical role in maintaining NSC survival and function under stress conditions. Together, we show that the activation of the integrated stress response (ISR) pathway enables NSCs to adapt to metabolic stress due to mitochondrial dysfunction and metabolic stress and may serve as a therapeutic target to enhance NSC survival and function in aging and neurodegeneration.
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Affiliation(s)
- Mohamed Ariff Iqbal
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Maria Bilen
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Yubing Liu
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Vanessa Jabre
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Bensun C. Fong
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Imane Chakroun
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Smitha Paul
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Jingwei Chen
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Steven Wade
- Department of Biochemistry, Microbiology and Immunology, Center for Neuromuscular Disease (CNMD), Ottawa Institute of Systems Biology (OISB), Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Michel Kanaan
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology (OISB), Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Mary‐Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology (OISB), Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Mireille Khacho
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
- Department of Biochemistry, Microbiology and Immunology, Center for Neuromuscular Disease (CNMD), Ottawa Institute of Systems Biology (OISB), Faculty of MedicineUniversity of OttawaOttawaOntarioCanada
| | - Ruth S. Slack
- Department of Cellular and Molecular MedicineUniversity of Ottawa Brain and Mind Research InstituteUniversity of OttawaOttawaOntarioCanada
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10
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Hosen S, Ikeda-Yorifuji I, Yamashita T. Asporin and CD109, expressed in the injured neonatal spinal cord, attenuate axonal re-growth in vitro. Neurosci Lett 2024; 833:137832. [PMID: 38796094 DOI: 10.1016/j.neulet.2024.137832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
Axonal regeneration is restricted in adults and causes irreversible motor dysfunction following spinal cord injury (SCI). In contrast, neonates have prominent regenerative potential and can restore their neural function. Although the distinct cellular responses in neonates have been studied, how they contribute to neural recovery remains unclear. To assess whether the secreted molecules in neonatal SCI can enhance neural regeneration, we re-analyzed the previously performed single-nucleus RNA-seq (snRNA-seq) and focused on Asporin and Cd109, the highly expressed genes in the injured neonatal spinal cord. In the present study, we showed that both these molecules were expressed in the injured spinal cords of adults and neonates. We treated the cortical neurons with recombinant Asporin or CD109 to observe their direct effects on neurons in vitro. We demonstrated that these molecules enhance neurite outgrowth in neurons. However, these molecules did not enhance re-growth of severed axons. Our results suggest that Asporin and CD109 influence neurites at the lesion site, rather than promoting axon regeneration, to restore neural function in neonates after SCI.
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Affiliation(s)
- Sakura Hosen
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Iyo Ikeda-Yorifuji
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan; Department of Molecular Neuroscience, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan; Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Suita, Japan.
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11
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Xu S, Zhang X, Li Z, Liu C, Liu Q, Chai H, Yao H, Luo Y, Li S, Li C. Characteristics of quiescent adult neural stem cells induced by the bFGF/BMP4 combination or BMP4 alone in vitro. Front Cell Neurosci 2024; 18:1391556. [PMID: 38841203 PMCID: PMC11151745 DOI: 10.3389/fncel.2024.1391556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Bone morphogenetic protein-4 (BMP4) is involved in regulation of neural stem cells (NSCs) proliferation, differentiation, migration and survival. It was previously thought that the treatment of NSCs with BMP4 alone induces astrocytes, whereas the treatment of NSCs with the bFGF/BMP4 combination induces quiescent neural stem cells (qNSCs). In this study, we performed bulk RNA sequencing (RNA-Seq) to compare the transcriptome profiles of BMP4-treated NSCs and bFGF/BMP4-treated NSCs, and found that both NSCs treated by these two methods were Sox2 positive qNSCs which were able to generate neurospheres. However, NSCs treated by those two methods exhibited different characteristics in state and the potential for neuronal differentiation based on transcriptome analysis and experimental results. We found that BMP4-treated NSCs tended to be in a deeper quiescent state than bFGF/BMP4-treated NSCs as the percentage of ki67-positive cells were lower in BMP4-treated NSCs. And after exposure to differentiated environment, bFGF/BMP4-treated NSCs generated more DCX-positive immature neurons and MAP2-positive neurons than BMP4-treated NSCs. Our study characterized qNSCs treated with BMP4 alone and bFGF/BMP4 combination, providing a reference for the scientific use of BMP4 and bFGF/BMP4-induced qNSCs models.
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Affiliation(s)
- Sutong Xu
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Zhang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhuoqun Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chenming Liu
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiulu Liu
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huazhen Chai
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hongkai Yao
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siguang Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chun Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, China
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12
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Huang J, He B, Yang X, Long X, Wei Y, Li L, Tang M, Gao Y, Fang Y, Ying W, Wang Z, Li C, Zhou Y, Li S, Shi L, Choi S, Zhou H, Guo F, Yang H, Wu J. Generation of rat forebrain tissues in mice. Cell 2024; 187:2129-2142.e17. [PMID: 38670071 DOI: 10.1016/j.cell.2024.03.017] [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: 04/24/2023] [Revised: 11/14/2023] [Accepted: 03/13/2024] [Indexed: 04/28/2024]
Abstract
Interspecies blastocyst complementation (IBC) provides a unique platform to study development and holds the potential to overcome worldwide organ shortages. Despite recent successes, brain tissue has not been achieved through IBC. Here, we developed an optimized IBC strategy based on C-CRISPR, which facilitated rapid screening of candidate genes and identified that Hesx1 deficiency supported the generation of rat forebrain tissue in mice via IBC. Xenogeneic rat forebrain tissues in adult mice were structurally and functionally intact. Cross-species comparative analyses revealed that rat forebrain tissues developed at the same pace as the mouse host but maintained rat-like transcriptome profiles. The chimeric rate of rat cells gradually decreased as development progressed, suggesting xenogeneic barriers during mid-to-late pre-natal development. Interspecies forebrain complementation opens the door for studying evolutionarily conserved and divergent mechanisms underlying brain development and cognitive function. The C-CRISPR-based IBC strategy holds great potential to broaden the study and application of interspecies organogenesis.
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Affiliation(s)
- Jia Huang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bingbing He
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiali Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xin Long
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yinghui Wei
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leijie Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Tang
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yanxia Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuan Fang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqin Ying
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zikang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yingsi Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuaishuai Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Linyu Shi
- Huidagene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Seungwon Choi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haibo Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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13
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Morizet D, Foucher I, Alunni A, Bally-Cuif L. Reconstruction of macroglia and adult neurogenesis evolution through cross-species single-cell transcriptomic analyses. Nat Commun 2024; 15:3306. [PMID: 38632253 PMCID: PMC11024210 DOI: 10.1038/s41467-024-47484-1] [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: 04/14/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
Macroglia fulfill essential functions in the adult vertebrate brain, producing and maintaining neurons and regulating neuronal communication. However, we still know little about their emergence and diversification. We used the zebrafish D. rerio as a distant vertebrate model with moderate glial diversity as anchor to reanalyze datasets covering over 600 million years of evolution. We identify core features of adult neurogenesis and innovations in the mammalian lineage with a potential link to the rarity of radial glia-like cells in adult humans. Our results also suggest that functions associated with astrocytes originated in a multifunctional cell type fulfilling both neural stem cell and astrocytic functions before these diverged. Finally, we identify conserved elements of macroglial cell identity and function and their time of emergence during evolution.
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Affiliation(s)
- David Morizet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France.
- Sorbonne Université, Collège doctoral, F-75005, Paris, France.
| | - Isabelle Foucher
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France
| | - Alessandro Alunni
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France
- Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, CNRS UMR9197, F-91190, Gif-sur-Yvette, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France.
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14
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Kakogiannis D, Kourla M, Dimitrakopoulos D, Kazanis I. Reversal of Postnatal Brain Astrocytes and Ependymal Cells towards a Progenitor Phenotype in Culture. Cells 2024; 13:668. [PMID: 38667283 PMCID: PMC11049274 DOI: 10.3390/cells13080668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Astrocytes and ependymal cells have been reported to be able to switch from a mature cell identity towards that of a neural stem/progenitor cell. Astrocytes are widely scattered in the brain where they exert multiple functions and are routinely targeted for in vitro and in vivo reprogramming. Ependymal cells serve more specialized functions, lining the ventricles and the central canal, and are multiciliated, epithelial-like cells that, in the spinal cord, act as bi-potent progenitors in response to injury. Here, we isolate or generate ependymal cells and post-mitotic astrocytes, respectively, from the lateral ventricles of the mouse brain and we investigate their capacity to reverse towards a progenitor-like identity in culture. Inhibition of the GSK3 and TGFβ pathways facilitates the switch of mature astrocytes to Sox2-expressing, mitotic cells that generate oligodendrocytes. Although this medium allows for the expansion of quiescent NSCs, isolated from live rats by "milking of the brain", it does not fully reverse astrocytes towards the bona fide NSC identity; this is a failure correlated with a concomitant lack of neurogenic activity. Ependymal cells could be induced to enter mitosis either via exposure to neuraminidase-dependent stress or by culturing them in the presence of FGF2 and EGF. Overall, our data confirm that astrocytes and ependymal cells retain a high capacity to reverse to a progenitor identity and set up a simple and highly controlled platform for the elucidation of the molecular mechanisms that regulate this reversal.
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Affiliation(s)
- Dimitrios Kakogiannis
- Lab of Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece; (D.K.); (M.K.); (D.D.)
- Institute of Physiological Chemistry, University Medical Center, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Michaela Kourla
- Lab of Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece; (D.K.); (M.K.); (D.D.)
- Biology-Biochemistry Lab, Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Dimitrakopoulos
- Lab of Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece; (D.K.); (M.K.); (D.D.)
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ilias Kazanis
- Lab of Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece; (D.K.); (M.K.); (D.D.)
- School of Life Sciences, University of Westminster, London W1W 6UW, UK
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15
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Labusch M, Thetiot M, Than-Trong E, Morizet D, Coolen M, Varet H, Legendre R, Ortica S, Mancini L, Bally-Cuif L. Prosaposin maintains adult neural stem cells in a state associated with deep quiescence. Stem Cell Reports 2024; 19:515-528. [PMID: 38518783 PMCID: PMC11096431 DOI: 10.1016/j.stemcr.2024.02.007] [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: 08/12/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024] Open
Abstract
In most vertebrates, adult neural stem cells (NSCs) continuously give rise to neurons in discrete brain regions. A critical process for maintaining NSC pools over long periods of time in the adult brain is NSC quiescence, a reversible and tightly regulated state of cell-cycle arrest. Recently, lysosomes were identified to regulate the NSC quiescence-proliferation balance. However, it remains controversial whether lysosomal activity promotes NSC proliferation or quiescence, and a finer influence of lysosomal activity on NSC quiescence duration or depth remains unexplored. Using RNA sequencing and pharmacological manipulations, we show that lysosomes are necessary for NSC quiescence maintenance. In addition, we reveal that expression of psap, encoding the lysosomal regulator Prosaposin, is enriched in quiescent NSCs (qNSCs) that reside upstream in the NSC lineage and display a deep/long quiescence phase in the adult zebrafish telencephalon. We show that shRNA-mediated psap knockdown increases the proportion of activated NSCs (aNSCs) as well as NSCs that reside in shallower quiescence states (signed by ascl1a and deltaA expression). Collectively, our results identify the lysosomal protein Psap as a (direct or indirect) quiescence regulator and unfold the interplay between lysosomal function and NSC quiescence heterogeneities.
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Affiliation(s)
- Miriam Labusch
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Melina Thetiot
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Emmanuel Than-Trong
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - David Morizet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Marion Coolen
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Platform Biomics, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Platform Biomics, 75015 Paris, France
| | - Sara Ortica
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France
| | - Laure Mancini
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, 75015 Paris, France.
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16
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Xu L, Ramirez-Matias J, Hauptschein M, Sun ED, Lunger JC, Buckley MT, Brunet A. Restoration of neuronal progenitors by partial reprogramming in the aged neurogenic niche. NATURE AGING 2024; 4:546-567. [PMID: 38553564 DOI: 10.1038/s43587-024-00594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 02/13/2024] [Indexed: 04/21/2024]
Abstract
Partial reprogramming (pulsed expression of reprogramming transcription factors) improves the function of several tissues in old mice. However, it remains largely unknown how partial reprogramming impacts the old brain. Here we use single-cell transcriptomics to systematically examine how partial reprogramming influences the subventricular zone neurogenic niche in aged mouse brains. Whole-body partial reprogramming mainly improves neuroblasts (cells committed to give rise to new neurons) in the old neurogenic niche, restoring neuroblast proportion to more youthful levels. Interestingly, targeting partial reprogramming specifically to the neurogenic niche also boosts the proportion of neuroblasts and their precursors (neural stem cells) in old mice and improves several molecular signatures of aging, suggesting that the beneficial effects of reprogramming are niche intrinsic. In old neural stem cell cultures, partial reprogramming cell autonomously restores the proportion of neuroblasts during differentiation and blunts some age-related transcriptomic changes. Importantly, partial reprogramming improves the production of new neurons in vitro and in old brains. Our work suggests that partial reprogramming could be used to rejuvenate the neurogenic niche and counter brain decline in old individuals.
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Affiliation(s)
- Lucy Xu
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Max Hauptschein
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Eric D Sun
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Judith C Lunger
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA.
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17
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Puvogel S, Alsema A, North HF, Webster MJ, Weickert CS, Eggen BJL. Single-Nucleus RNA-Seq Characterizes the Cell Types Along the Neuronal Lineage in the Adult Human Subependymal Zone and Reveals Reduced Oligodendrocyte Progenitor Abundance with Age. eNeuro 2024; 11:ENEURO.0246-23.2024. [PMID: 38351133 PMCID: PMC10913050 DOI: 10.1523/eneuro.0246-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during postnatal life. In humans, the neurogenic potential of the SEZ declines after the first year of life. However, studies discovering markers of stem and progenitor cells highlight the neurogenic capacity of progenitors in the adult human SEZ, with increased neurogenic activity occurring under pathological conditions. In the present study, the complete cellular niche of the adult human SEZ was characterized by single-nucleus RNA sequencing, and compared between four youth (age 16-22) and four middle-aged adults (age 44-53). We identified 11 cellular clusters including clusters expressing marker genes for neural stem cells (NSCs), neuroblasts, immature neurons, and oligodendrocyte progenitor cells. The relative abundance of NSC and neuroblast clusters did not differ between the two age groups, indicating that the pool of SEZ NSCs does not decline in this age range. The relative abundance of oligodendrocyte progenitors and microglia decreased in middle-age, indicating that the cellular composition of human SEZ is remodeled between youth and adulthood. The expression of genes related to nervous system development was higher across different cell types, including NSCs, in youth as compared with middle-age. These transcriptional changes suggest ongoing central nervous system plasticity in the SEZ in youth, which declined in middle-age.
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Affiliation(s)
- Sofía Puvogel
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 HB, The Netherlands
| | - Astrid Alsema
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
| | - Hayley F North
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, Rockville 20850, Maryland
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York 13201
| | - Bart J L Eggen
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
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18
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Janeckova L, Knotek T, Kriska J, Hermanova Z, Kirdajova D, Kubovciak J, Berkova L, Tureckova J, Camacho Garcia S, Galuskova K, Kolar M, Anderova M, Korinek V. Astrocyte-like subpopulation of NG2 glia in the adult mouse cortex exhibits characteristics of neural progenitor cells. Glia 2024; 72:245-273. [PMID: 37772368 DOI: 10.1002/glia.24471] [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: 02/20/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Glial cells expressing neuron-glial antigen 2 (NG2), also known as oligodendrocyte progenitor cells (OPCs), play a critical role in maintaining brain health. However, their ability to differentiate after ischemic injury is poorly understood. The aim of this study was to investigate the properties and functions of NG2 glia in the ischemic brain. Using transgenic mice, we selectively labeled NG2-expressing cells and their progeny in both healthy brain and after focal cerebral ischemia (FCI). Using single-cell RNA sequencing, we classified the labeled glial cells into five distinct subpopulations based on their gene expression patterns. Additionally, we examined the membrane properties of these cells using the patch-clamp technique. Of the identified subpopulations, three were identified as OPCs, whereas the fourth subpopulation had characteristics indicative of cells likely to develop into oligodendrocytes. The fifth subpopulation of NG2 glia showed astrocytic markers and had similarities to neural progenitor cells. Interestingly, this subpopulation was present in both healthy and post-ischemic tissue; however, its gene expression profile changed after ischemia, with increased numbers of genes related to neurogenesis. Immunohistochemical analysis confirmed the temporal expression of neurogenic genes and showed an increased presence of NG2 cells positive for Purkinje cell protein-4 at the periphery of the ischemic lesion 12 days after FCI, as well as NeuN-positive NG2 cells 28 and 60 days after injury. These results suggest the potential development of neuron-like cells arising from NG2 glia in the ischemic tissue. Our study provides insights into the plasticity of NG2 glia and their capacity for neurogenesis after stroke.
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Affiliation(s)
- Lucie Janeckova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Knotek
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Hermanova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Denisa Kirdajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kubovciak
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Linda Berkova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sara Camacho Garcia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Galuskova
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolar
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimir Korinek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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19
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Péron S, Miyakoshi LM, Brill MS, Manzano-Franco D, Serrano-López J, Fan W, Marichal N, Ghanem A, Conzelmann KK, Karow M, Ortega F, Gascón S, Berninger B. Programming of neural progenitors of the adult subependymal zone towards a glutamatergic neuron lineage by neurogenin 2. Stem Cell Reports 2023; 18:2418-2433. [PMID: 37995703 PMCID: PMC10724369 DOI: 10.1016/j.stemcr.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Although adult subependymal zone (SEZ) neural stem cells mostly generate GABAergic interneurons, a small progenitor population expresses the proneural gene Neurog2 and produces glutamatergic neurons. Here, we determined whether Neurog2 could respecify SEZ neural stem cells and their progeny toward a glutamatergic fate. Retrovirus-mediated expression of Neurog2 induced the glutamatergic lineage markers TBR2 and TBR1 in cultured SEZ progenitors, which differentiated into functional glutamatergic neurons. Likewise, Neurog2-transduced SEZ progenitors acquired glutamatergic neuron hallmarks in vivo. Intriguingly, they failed to migrate toward the olfactory bulb and instead differentiated within the SEZ or the adjacent striatum, where they received connections from local neurons, as indicated by rabies virus-mediated monosynaptic tracing. In contrast, lentivirus-mediated expression of Neurog2 failed to reprogram early SEZ neurons, which maintained GABAergic identity and migrated to the olfactory bulb. Our data show that NEUROG2 can program SEZ progenitors toward a glutamatergic identity but fails to reprogram their neuronal progeny.
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Affiliation(s)
- Sophie Péron
- Research Group "Adult Neurogenesis and Cellular Reprogramming", Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany; Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Leo M Miyakoshi
- Physiological Genomics, Institute of Physiology, Ludwig-Maximilians University Munich, Munich, Germany
| | - Monika S Brill
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Diana Manzano-Franco
- Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute - CSIC, Madrid, Spain
| | - Julia Serrano-López
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary, Universidad Complutense de Madrid (UCM), Madrid, Spain; Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain; Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Wenqiang Fan
- Research Group "Adult Neurogenesis and Cellular Reprogramming", Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany
| | - Nicolás Marichal
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Alexander Ghanem
- Max von Pettenkofer Institute and Gene Center, Ludwig Maximilians-University Munich, Munich, Germany
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer Institute and Gene Center, Ludwig Maximilians-University Munich, Munich, Germany
| | - Marisa Karow
- Institute of Biochemistry, Friedrich-Alexander Universität Nürnberg-Erlangen, Erlangen, Germany
| | - Felipe Ortega
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary, Universidad Complutense de Madrid (UCM), Madrid, Spain; Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain; Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Sergio Gascón
- Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute - CSIC, Madrid, Spain.
| | - Benedikt Berninger
- Research Group "Adult Neurogenesis and Cellular Reprogramming", Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, Mainz, Germany; Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK; Focus Program Translational Neurosciences, Johannes Gutenberg University, Mainz, Germany.
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20
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Kempermann G. Giving birth gives birth to neurons. Science 2023; 382:881-882. [PMID: 37995245 DOI: 10.1126/science.adl2399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
In mice, pregnancy results in new neurons that support recognition of pups.
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Affiliation(s)
- Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
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21
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Wu L, Wang F, Moncman CL, Pandey M, Clarke HA, Frazier HN, Young LE, Gentry MS, Cai W, Thibault O, Sun RC, Andres DA. RIT1 regulation of CNS lipids RIT1 deficiency Alters cerebral lipid metabolism and reduces white matter tract oligodendrocytes and conduction velocities. Heliyon 2023; 9:e20384. [PMID: 37780758 PMCID: PMC10539968 DOI: 10.1016/j.heliyon.2023.e20384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/21/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023] Open
Abstract
Oligodendrocytes (OLs) generate lipid-rich myelin membranes that wrap axons to enable efficient transmission of electrical impulses. Using a RIT1 knockout mouse model and in situ high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) coupled with MS-based lipidomic analysis to determine the contribution of RIT1 to lipid homeostasis. Here, we report that RIT1 loss is associated with altered lipid levels in the central nervous system (CNS), including myelin-associated lipids within the corpus callosum (CC). Perturbed lipid metabolism was correlated with reduced numbers of OLs, but increased numbers of GFAP+ glia, in the CC, but not in grey matter. This was accompanied by reduced myelin protein expression and axonal conduction deficits. Behavioral analyses revealed significant changes in voluntary locomotor activity and anxiety-like behavior in RIT1KO mice. Together, these data reveal an unexpected role for RIT1 in the regulation of cerebral lipid metabolism, which coincide with altered white matter tract oligodendrocyte levels, reduced axonal conduction velocity, and behavioral abnormalities in the CNS.
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Affiliation(s)
- Lei Wu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Fang Wang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Carole L. Moncman
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Mritunjay Pandey
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
| | - Harrison A. Clarke
- Department of Neuroscience, College of Medicine, University of Kentucky, KY 40536, USA
| | - Hilaree N. Frazier
- Department of Pharmacological and Nutritional Sciences, College of Medicine, University of Kentucky, KY 40536, USA
| | - Lyndsay E.A. Young
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32611, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, College of Medicine, Gainesville, FL 32611, USA
| | - Weikang Cai
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, NY 11568, USA
| | - Olivier Thibault
- Department of Pharmacological and Nutritional Sciences, College of Medicine, University of Kentucky, KY 40536, USA
| | - Ramon C. Sun
- Department of Neuroscience, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32611, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, College of Medicine, Gainesville, FL 32611, USA
| | - Douglas A. Andres
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY 40536, USA
- Markey Cancer Center, Lexington, KY 40536, USA
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, KY 40536, USA
- Gill Heart and Vascular Institute, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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22
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Gao MY, Wang JQ, He J, Gao R, Zhang Y, Li X. Single-Cell RNA-Sequencing in Astrocyte Development, Heterogeneity, and Disease. Cell Mol Neurobiol 2023; 43:3449-3464. [PMID: 37552355 DOI: 10.1007/s10571-023-01397-7] [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: 01/07/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023]
Abstract
Astrocytes are the most plentiful cell type in the central nervous system (CNS) and perform complicated functions in health and disease. It is obvious that different astrocyte subpopulations, or activation states, are relevant with specific genomic programs and functions. In recent years, the emergence of new technologies such as single-cell RNA sequencing (scRNA-seq) has made substantial advance in the characterization of astrocyte heterogeneity, astrocyte developmental trajectory, and its role in CNS diseases which has had a significant impact on neuroscience. In this review, we present an overview of astrocyte development, heterogeneity, and its essential role in the physiological and pathological environments of the CNS. We focused on the critical role of single-cell sequencing in revealing astrocyte development, heterogeneity, and its role in different CNS diseases.
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Affiliation(s)
- Meng-Yuan Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jia-Qi Wang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Jin He
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Rui Gao
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yuan Zhang
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Xing Li
- A National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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23
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Yang Q, Zhang L, Li M, Xu Y, Chen X, Yuan R, Ou X, He M, Liao M, Zhang L, Dai H, Lv M, Xie X, Liang W, Chen X. Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury. Genome Res 2023; 33:1818-1832. [PMID: 37730437 PMCID: PMC10691476 DOI: 10.1101/gr.277881.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
The subventricular zone (SVZ) is a neurogenic niche that contributes to homeostasis and repair after brain injury. However, the effects of mild traumatic brain injury (mTBI) on the divergence of the regulatory DNA landscape within the SVZ and its link to functional alterations remain unexplored. In this study, we mapped the transcriptome atlas of murine SVZ and its responses to mTBI at the single-cell level. We observed cell-specific gene expression changes following mTBI and unveiled diverse cell-to-cell interaction networks that influence a wide array of cellular processes. Moreover, we report novel neurogenesis lineage trajectories and related key transcription factors, which we validate through loss-of-function experiments. Specifically, we validate the role of Tcf7l1, a cell cycle gene regulator, in promoting neural stem cell differentiation toward the neuronal lineage after mTBI, providing a potential target for regenerative medicine. Overall, our study profiles an SVZ transcriptome reference map, which underlies the differential cellular behavior in response to mTBI. The identified key genes and pathways that may ameliorate brain damage or facilitate neural repair serve as a comprehensive resource for drug discovery in the context of mTBI.
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Affiliation(s)
- Qiuyun Yang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
- West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Lingxuan Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Manrui Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Yang Xu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Xiaogang Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Ruixuan Yuan
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Xiaofeng Ou
- Department of Critical Care Medicine, Sichuan University, Chengdu 610000, China
| | - Min He
- Department of Critical Care Medicine, Sichuan University, Chengdu 610000, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Lin Zhang
- Sichuan University, Chengdu 610041, China
| | - Hao Dai
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China
| | - Xiaoqi Xie
- Department of Critical Care Medicine, Sichuan University, Chengdu 610000, China;
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China;
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610000, China;
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24
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Lu Z, Zhang M, Lee J, Sziraki A, Anderson S, Zhang Z, Xu Z, Jiang W, Ge S, Nelson PT, Zhou W, Cao J. Tracking cell-type-specific temporal dynamics in human and mouse brains. Cell 2023; 186:4345-4364.e24. [PMID: 37774676 PMCID: PMC10545416 DOI: 10.1016/j.cell.2023.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Progenitor cells are critical in preserving organismal homeostasis, yet their diversity and dynamics in the aged brain remain underexplored. We introduced TrackerSci, a single-cell genomic method that combines newborn cell labeling and combinatorial indexing to characterize the transcriptome and chromatin landscape of proliferating progenitor cells in vivo. Using TrackerSci, we investigated the dynamics of newborn cells in mouse brains across various ages and in a mouse model of Alzheimer's disease. Our dataset revealed diverse progenitor cell types in the brain and their epigenetic signatures. We further quantified aging-associated shifts in cell-type-specific proliferation and differentiation and deciphered the associated molecular programs. Extending our study to the progenitor cells in the aged human brain, we identified conserved genetic signatures across species and pinpointed region-specific cellular dynamics, such as the reduced oligodendrogenesis in the cerebellum. We anticipate that TrackerSci will be broadly applicable to unveil cell-type-specific temporal dynamics in diverse systems.
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Affiliation(s)
- Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Melissa Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Sonya Anderson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA; The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Shaoyu Ge
- Department of Neurobiology & Behavior, SUNY at Stony Brook, Stony Brook, NY, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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25
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Feng Y, Gao C, Xie D, Liu L, Chen B, Liu S, Yang H, Gao Z, Wilson DA, Tu Y, Peng F. Directed Neural Stem Cells Differentiation via Signal Communication with Ni-Zn Micromotors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301736. [PMID: 37402480 DOI: 10.1002/adma.202301736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/06/2023] [Accepted: 07/02/2023] [Indexed: 07/06/2023]
Abstract
Neural stem cells (NSCs), with the capability of self-renewal, differentiation, and environment modulation, are considered promising for stroke, brain injury therapy, and neuron regeneration. Activation of endogenous NSCs, is attracting increasing research enthusiasm, which avoids immune rejection and ethical issues of exogenous cell transplantation. Yet, how to induce directed growth and differentiation in situ remain a major challenge. In this study, a pure water-driven Ni-Zn micromotor via a self-established electric-chemical field is proposed. The micromotors can be magnetically guided and precisely approach target NSCs. Through the electric-chemical field, bioelectrical signal exchange and communication with endogenous NSCs are allowed, thus allowing for regulated proliferation and directed neuron differentiation in vivo. Therefore, the Ni-Zn micromotor provides a platform for controlling cell fate via a self-established electrochemical field and targeted activation of endogenous NSCs.
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Affiliation(s)
- Ye Feng
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Chao Gao
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Dazhi Xie
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Lu Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Bin Chen
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Suyi Liu
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Haihong Yang
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zhan Gao
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Yingfeng Tu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fei Peng
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
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26
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Brockman AA, Khurana R, Bartkowiak T, Thomas PL, Sivagnanam S, Betts CB, Coussens LM, Lovly CM, Irish JM, Ihrie RA. Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2023; 104:344-355. [PMID: 36748312 PMCID: PMC10404643 DOI: 10.1002/cyto.b.22114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/22/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
Cyclic immunohistochemistry (cycIHC) uses sequential rounds of colorimetric immunostaining and imaging for quantitative mapping of location and number of cells of interest. Additionally, cycIHC benefits from the speed and simplicity of brightfield microscopy, making the collection of entire tissue sections and slides possible at a trivial cost compared to other high dimensional imaging modalities. However, large cycIHC datasets currently require an expert data scientist to concatenate separate open-source tools for each step of image pre-processing, registration, and segmentation, or the use of proprietary software. Here, we present a unified and user-friendly pipeline for processing, aligning, and analyzing cycIHC data - Cyclic Analysis of Single-Cell Subsets and Tissue Territories (CASSATT). CASSATT registers scanned slide images across all rounds of staining, segments individual nuclei, and measures marker expression on each detected cell. Beyond straightforward single cell data analysis outputs, CASSATT explores the spatial relationships between cell populations. By calculating the log odds of interaction frequencies between cell populations within tissues and tissue regions, this pipeline helps users identify populations of cells that interact-or do not interact-at frequencies that are greater than those occurring by chance. It also identifies specific neighborhoods of cells based on the assortment of neighboring cell types that surround each cell in the sample. The presence and location of these neighborhoods can be compared across slides or within distinct regions within a tissue. CASSATT is a fully open source workflow tool developed to process cycIHC data and will allow greater utilization of this powerful staining technique.
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Affiliation(s)
- Asa A. Brockman
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Rohit Khurana
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Todd Bartkowiak
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Departments of Pathology, Microbiology, & Immunology
| | - Portia L. Thomas
- Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, Tennessee
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
| | - Shamilene Sivagnanam
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Courtney B Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Lisa M. Coussens
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
- Department of Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Christine M. Lovly
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
- Departments of Division of Hematology-Oncology, Department of Medicine
| | - Jonathan M. Irish
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Departments of Pathology, Microbiology, & Immunology
- Departments of Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Rebecca A. Ihrie
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of School of Graduate Studies & Research, Meharry Medical College, Nashville, Tennessee
- Neurological Surgery
- Departments of Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232
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27
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Mancini L, Guirao B, Ortica S, Labusch M, Cheysson F, Bonnet V, Phan MS, Herbert S, Mahou P, Menant E, Bedu S, Tinevez JY, Baroud C, Beaurepaire E, Bellaiche Y, Bally-Cuif L, Dray N. Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression. SCIENCE ADVANCES 2023; 9:eadg7519. [PMID: 37656795 PMCID: PMC10854430 DOI: 10.1126/sciadv.adg7519] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
The maintenance of neural stem cells (NSCs) in the adult brain depends on their activation frequency and division mode. Using long-term intravital imaging of NSCs in the zebrafish adult telencephalon, we reveal that apical surface area and expression of the Notch ligand DeltaA predict these NSC decisions. deltaA-negative NSCs constitute a bona fide self-renewing NSC pool and systematically engage in asymmetric divisions generating a self-renewing deltaAneg daughter, which regains the size and behavior of its mother, and a neurogenic deltaApos daughter, eventually engaged in neuronal production following further quiescence-division phases. Pharmacological and genetic manipulations of Notch, DeltaA, and apical size further show that the prediction of activation frequency by apical size and the asymmetric divisions of deltaAneg NSCs are functionally independent of Notch. These results provide dynamic qualitative and quantitative readouts of NSC lineage progression in vivo and support a hierarchical organization of NSCs in differently fated subpopulations.
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Affiliation(s)
- Laure Mancini
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris F-75005, France
| | - Boris Guirao
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, Paris 75005, France
| | - Sara Ortica
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Miriam Labusch
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris F-75005, France
| | - Felix Cheysson
- LPSM, Sorbonne Université, UMR CNRS 8001, Paris 75005, France
| | - Valentin Bonnet
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris F-75015, France
- LadHyX, CNRS, Ecole Polytechnique, IP Paris, Palaiseau 91120, France
| | - Minh Son Phan
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Sébastien Herbert
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Emilie Menant
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Sébastien Bedu
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Charles Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris F-75015, France
- LadHyX, CNRS, Ecole Polytechnique, IP Paris, Palaiseau 91120, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Yohanns Bellaiche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, Paris 75005, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Nicolas Dray
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
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Norton ES, Whaley LA, Jones VK, Brooks MM, Russo MN, Morderer D, Jessen E, Schiapparelli P, Ramos-Fresnedo A, Zarco N, Carrano A, Rossoll W, Asmann YW, Lam TT, Chaichana KL, Anastasiadis PZ, Quiñones-Hinojosa A, Guerrero-Cázares H. Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553966. [PMID: 37662251 PMCID: PMC10473635 DOI: 10.1101/2023.08.19.553966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Glioblastoma (GBM) is the most prevalent and aggressive malignant primary brain tumor. GBM proximal to the lateral ventricles (LVs) is more aggressive, potentially due to subventricular zone (SVZ) contact. Despite this, crosstalk between GBM and neural stem/progenitor cells (NSC/NPCs) is not well understood. Using cell-specific proteomics, we show that LV-proximal GBM prevents neuronal maturation of NSCs through induction of senescence. Additionally, GBM brain tumor initiating cells (BTICs) increase expression of CTSB upon interaction with NPCs. Lentiviral knockdown and recombinant protein experiments reveal both cell-intrinsic and soluble CTSB promote malignancy-associated phenotypes in BTICs. Soluble CTSB stalls neuronal maturation in NPCs while promoting senescence, providing a link between LV-tumor proximity and neurogenesis disruption. Finally, we show LV-proximal CTSB upregulation in patients, showing the relevance of this crosstalk in human GBM biology. These results demonstrate the value of proteomic analysis in tumor microenvironment research and provide direction for new therapeutic strategies in GBM. Highlights Periventricular GBM is more malignant and disrupts neurogenesis in a rodent model.Cell-specific proteomics elucidates tumor-promoting crosstalk between GBM and NPCs.NPCs induce upregulated CTSB expression in GBM, promoting tumor progression.GBM stalls neurogenesis and promotes NPC senescence via CTSB.
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29
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Tang W, Jørgensen ACS, Marguerat S, Thomas P, Shahrezaei V. Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics. Bioinformatics 2023; 39:btad395. [PMID: 37354494 PMCID: PMC10318389 DOI: 10.1093/bioinformatics/btad395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/18/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023] Open
Abstract
MOTIVATION Gene expression is characterized by stochastic bursts of transcription that occur at brief and random periods of promoter activity. The kinetics of gene expression burstiness differs across the genome and is dependent on the promoter sequence, among other factors. Single-cell RNA sequencing (scRNA-seq) has made it possible to quantify the cell-to-cell variability in transcription at a global genome-wide level. However, scRNA-seq data are prone to technical variability, including low and variable capture efficiency of transcripts from individual cells. RESULTS Here, we propose a novel mathematical theory for the observed variability in scRNA-seq data. Our method captures burst kinetics and variability in both the cell size and capture efficiency, which allows us to propose several likelihood-based and simulation-based methods for the inference of burst kinetics from scRNA-seq data. Using both synthetic and real data, we show that the simulation-based methods provide an accurate, robust and flexible tool for inferring burst kinetics from scRNA-seq data. In particular, in a supervised manner, a simulation-based inference method based on neural networks proves to be accurate and useful when applied to both allele and nonallele-specific scRNA-seq data. AVAILABILITY AND IMPLEMENTATION The code for Neural Network and Approximate Bayesian Computation inference is available at https://github.com/WT215/nnRNA and https://github.com/WT215/Julia_ABC, respectively.
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Affiliation(s)
- Wenhao Tang
- Department of Mathematics, Imperial College London, London SW7 2BX, United Kingdom
| | - Andreas Christ Sølvsten Jørgensen
- Department of Mathematics, Imperial College London, London SW7 2BX, United Kingdom
- I-X Centre for AI in Science, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College London, London SW7 2BX, United Kingdom
| | - Vahid Shahrezaei
- Department of Mathematics, Imperial College London, London SW7 2BX, United Kingdom
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30
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Lampada A, Taylor V. Notch signaling as a master regulator of adult neurogenesis. Front Neurosci 2023; 17:1179011. [PMID: 37457009 PMCID: PMC10339389 DOI: 10.3389/fnins.2023.1179011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Neurogenesis ceases in most regions of the mammalian brain before or shortly after birth, however, in a few restricted brain regions, the production of new neurons proceeds into adulthood. Neural stem cells (NSCs) in these neurogenic zones are integrated into niches that control their activity and fate. Most stem cells in the adult brain are mitotically inactive and these cells can remain quiescent for months or even years. One of the key questions is what are the molecular mechanisms that regulate NSC maintenance and differentiation. Notch signaling has been shown to be a critical regulator of stem cell activity and maintenance in many tissues including in the nervous system. In this mini-review we discuss the roles of Notch signaling and the functions of the different Notch receptors and ligands in regulating neurogenesis in the adult murine brain. We review the functions of Notch signaling components in controlling NSC quiescence and entry into cell cycle and neurogenesis.
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31
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Garcia-Diaz C, Pöysti A, Mereu E, Clements MP, Brooks LJ, Galvez-Cancino F, Castillo SP, Tang W, Beattie G, Courtot L, Ruiz S, Roncaroli F, Yuan Y, Marguerat S, Quezada SA, Heyn H, Parrinello S. Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin. Cell Rep 2023; 42:112472. [PMID: 37149862 DOI: 10.1016/j.celrep.2023.112472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 03/14/2023] [Accepted: 04/19/2023] [Indexed: 05/09/2023] Open
Abstract
Glioblastoma (GBM) recurrence originates from invasive margin cells that escape surgical debulking, but to what extent these cells resemble their bulk counterparts remains unclear. Here, we generated three immunocompetent somatic GBM mouse models, driven by subtype-associated mutations, to compare matched bulk and margin cells. We find that, regardless of mutations, tumors converge on common sets of neural-like cellular states. However, bulk and margin have distinct biology. Injury-like programs associated with immune infiltration dominate in the bulk, leading to the generation of lowly proliferative injured neural progenitor-like cells (iNPCs). iNPCs account for a significant proportion of dormant GBM cells and are induced by interferon signaling within T cell niches. In contrast, developmental-like trajectories are favored within the immune-cold margin microenvironment resulting in differentiation toward invasive astrocyte-like cells. These findings suggest that the regional tumor microenvironment dominantly controls GBM cell fate and biological vulnerabilities identified in the bulk may not extend to the margin residuum.
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Affiliation(s)
- Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Anni Pöysti
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Melanie P Clements
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Lucy J Brooks
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Simon P Castillo
- Division of Molecular Pathology & Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
| | - Wenhao Tang
- Department of Mathematics, Imperial College London, London, UK
| | - Gordon Beattie
- CRUK City of London Centre Single Cell Genomics Facility, UCL Cancer Institute, University College London, London, UK; Genomics Translational Technology Platform, UCL Cancer Institute, University College London, London, UK
| | - Lilas Courtot
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Sara Ruiz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Federico Roncaroli
- Geoffrey Jefferson Brain Research Centre, Division of Neuroscience, School of Biological Sciences, Faculty of Brain and Mental Health, University of Manchester, Manchester, UK
| | - Yinyin Yuan
- Division of Molecular Pathology & Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, UK
| | - Samuel Marguerat
- Genomics Translational Technology Platform, UCL Cancer Institute, University College London, London, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK.
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32
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Amodeo V, Davies T, Martinez-Segura A, Clements MP, Ragdale HS, Bailey A, Dos Santos MS, MacRae JI, Mokochinski J, Kramer H, Garcia-Diaz C, Gould AP, Marguerat S, Parrinello S. Diet suppresses glioblastoma initiation in mice by maintaining quiescence of mutation-bearing neural stem cells. Dev Cell 2023; 58:836-846.e6. [PMID: 37084728 PMCID: PMC10618406 DOI: 10.1016/j.devcel.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 12/09/2021] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Glioblastoma is thought to originate from neural stem cells (NSCs) of the subventricular zone that acquire genetic alterations. In the adult brain, NSCs are largely quiescent, suggesting that deregulation of quiescence maintenance may be a prerequisite for tumor initiation. Although inactivation of the tumor suppressor p53 is a frequent event in gliomagenesis, whether or how it affects quiescent NSCs (qNSCs) remains unclear. Here, we show that p53 maintains quiescence by inducing fatty-acid oxidation (FAO) and that acute p53 deletion in qNSCs results in their premature activation to a proliferative state. Mechanistically, this occurs through direct transcriptional induction of PPARGC1a, which in turn activates PPARα to upregulate FAO genes. Dietary supplementation with fish oil containing omega-3 fatty acids, natural PPARα ligands, fully restores quiescence of p53-deficient NSCs and delays tumor initiation in a glioblastoma mouse model. Thus, diet can silence glioblastoma driver mutations, with important implications for cancer prevention.
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Affiliation(s)
- Valeria Amodeo
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Timothy Davies
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Amalia Martinez-Segura
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Melanie P Clements
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | | | - Andrew Bailey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | | | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | - Joao Mokochinski
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Alex P Gould
- The Francis Crick Institute, 1 Midland Road, London NW1 1AA, UK
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK.
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33
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Marcy G, Foucault L, Babina E, Capeliez T, Texeraud E, Zweifel S, Heinrich C, Hernandez-Vargas H, Parras C, Jabaudon D, Raineteau O. Single-cell analysis of the postnatal dorsal V-SVZ reveals a role for Bmpr1a signaling in silencing pallial germinal activity. SCIENCE ADVANCES 2023; 9:eabq7553. [PMID: 37146152 PMCID: PMC10162676 DOI: 10.1126/sciadv.abq7553] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The ventricular-subventricular zone (V-SVZ) is the largest neurogenic region of the postnatal forebrain, containing neural stem cells (NSCs) that emerge from both the embryonic pallium and subpallium. Despite of this dual origin, glutamatergic neurogenesis declines rapidly after birth, while GABAergic neurogenesis persists throughout life. We performed single-cell RNA sequencing of the postnatal dorsal V-SVZ for unraveling the mechanisms leading to pallial lineage germinal activity silencing. We show that pallial NSCs enter a state of deep quiescence, characterized by high bone morphogenetic protein (BMP) signaling, reduced transcriptional activity and Hopx expression, while in contrast, subpallial NSCs remain primed for activation. Induction of deep quiescence is paralleled by a rapid blockade of glutamatergic neuron production and differentiation. Last, manipulation of Bmpr1a demonstrates its key role in mediating these effects. Together, our results highlight a central role of BMP signaling in synchronizing quiescence induction and blockade of neuronal differentiation to rapidly silence pallial germinal activity after birth.
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Affiliation(s)
- Guillaume Marcy
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
- Univ Lyon, Université Claude Bernard Lyon 1, Bioinformatic Platform of the Labex Cortex, 69008 Lyon, France
| | - Louis Foucault
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Elodie Babina
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Timothy Capeliez
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Emeric Texeraud
- Univ Lyon, Université Claude Bernard Lyon 1, Bioinformatic Platform of the Labex Cortex, 69008 Lyon, France
| | - Stefan Zweifel
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Christophe Heinrich
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Hector Hernandez-Vargas
- Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373 Lyon Cedex 08, France
| | - Carlos Parras
- Paris Brain Institute, Sorbonne Université, Inserm U1127, CNRS UMR 7225, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Geneva University Hospital, Geneva, Switzerland
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
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Qian Z, Qin J, Lai Y, Zhang C, Zhang X. Large-Scale Integration of Single-Cell RNA-Seq Data Reveals Astrocyte Diversity and Transcriptomic Modules across Six Central Nervous System Disorders. Biomolecules 2023; 13:692. [PMID: 37189441 PMCID: PMC10135484 DOI: 10.3390/biom13040692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The dysfunction of astrocytes in response to environmental factors contributes to many neurological diseases by impacting neuroinflammation responses, glutamate and ion homeostasis, and cholesterol and sphingolipid metabolism, which calls for comprehensive and high-resolution analysis. However, single-cell transcriptome analyses of astrocytes have been hampered by the sparseness of human brain specimens. Here, we demonstrate how large-scale integration of multi-omics data, including single-cell and spatial transcriptomic and proteomic data, overcomes these limitations. We created a single-cell transcriptomic dataset of human brains by integration, consensus annotation, and analyzing 302 publicly available single-cell RNA-sequencing (scRNA-seq) datasets, highlighting the power to resolve previously unidentifiable astrocyte subpopulations. The resulting dataset includes nearly one million cells that span a wide variety of diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), multiple sclerosis (MS), epilepsy (Epi), and chronic traumatic encephalopathy (CTE). We profiled the astrocytes at three levels, subtype compositions, regulatory modules, and cell-cell communications, and comprehensively depicted the heterogeneity of pathological astrocytes. We constructed seven transcriptomic modules that are involved in the onset and progress of disease development, such as the M2 ECM and M4 stress modules. We validated that the M2 ECM module could furnish potential markers for AD early diagnosis at both the transcriptome and protein levels. In order to accomplish a high-resolution, local identification of astrocyte subtypes, we also carried out a spatial transcriptome analysis of mouse brains using the integrated dataset as a reference. We found that astrocyte subtypes are regionally heterogeneous. We identified dynamic cell-cell interactions in different disorders and found that astrocytes participate in key signaling pathways, such as NRG3-ERBB4, in epilepsy. Our work supports the utility of large-scale integration of single-cell transcriptomic data, which offers new insights into underlying multiple CNS disease mechanisms where astrocytes are involved.
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Affiliation(s)
- Zhenwei Qian
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Jinglin Qin
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Yiwen Lai
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Chen Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Beijing 102206, China
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Nanjing 210000, China
| | - Xiannian Zhang
- School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
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35
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Murtaj V, Butti E, Martino G, Panina-Bordignon P. Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease. Front Cell Neurosci 2023; 17:1125785. [PMID: 37091923 PMCID: PMC10113633 DOI: 10.3389/fncel.2023.1125785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Neural stem cells (NSCs), an invaluable source of neuronal and glial progeny, have been widely interrogated in the last twenty years, mainly to understand their therapeutic potential. Most of the studies were performed with cells derived from pluripotent stem cells of either rodents or humans, and have mainly focused on their potential in regenerative medicine. High-throughput omics technologies, such as transcriptomics, epigenetics, proteomics, and metabolomics, which exploded in the past decade, represent a powerful tool to investigate the molecular mechanisms characterizing the heterogeneity of endogenous NSCs. The transition from bulk studies to single cell approaches brought significant insights by revealing complex system phenotypes, from the molecular to the organism level. Here, we will discuss the current literature that has been greatly enriched in the “omics era”, successfully exploring the nature and function of endogenous NSCs and the process of neurogenesis. Overall, the information obtained from omics studies of endogenous NSCs provides a sharper picture of NSCs function during neurodevelopment in healthy and in perturbed environments.
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Affiliation(s)
- Valentina Murtaj
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Erica Butti
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Gianvito Martino
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Panina-Bordignon
- Division of Neuroscience, San Raffaele Vita-Salute University, Milan, Italy
- Neuroimmunology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele, Milan, Italy
- *Correspondence: Paola Panina-Bordignon
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36
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The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool. Cell Rep 2023; 42:112242. [PMID: 36924490 DOI: 10.1016/j.celrep.2023.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/19/2023] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that these NPCs are transcriptionally primed to differentiate and that the primed mRNAs are associated with the translational repressor 4E-T. 4E-T also broadly associates with other NPC mRNAs encoding transcriptional regulators, and these are preferentially depleted from ribosomes, consistent with repression. By contrast, a second translational regulator, Cpeb4, associates with diverse target mRNAs that are largely ribosome associated. The 4E-T-dependent mRNA association is functionally important because 4E-T knockdown or conditional knockout derepresses proneurogenic mRNA translation and perturbs maintenance versus differentiation of early postnatal NPCs in culture and in vivo. Thus, early postnatal NPCs are primed to differentiate, and 4E-T regulates the balance between cell genesis and stem cell expansion by sequestering and repressing mRNAs encoding transcriptional regulators.
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37
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Kang H, Liu Q, Seim I, Zhang W, Li H, Gao H, Lin W, Lin M, Zhang P, Zhang Y, Gao H, Wang Y, Qin Y, Liu M, Dong L, Yang Z, Zhang Y, Han L, Fan G, Li S. A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour 2023. [PMID: 36826393 DOI: 10.1111/1755-0998.13775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.
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Affiliation(s)
- Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, Qingdao, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenwei Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Haiyu Gao
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | | | - Yang Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yating Qin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Mingming Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zixin Yang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Lei Han
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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38
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Banu MA, Dovas A, Argenziano MG, Zhao W, Grajal HC, Higgins DM, Sperring CP, Pereira B, Ye LF, Mahajan A, Humala N, Furnari JL, Upadhyayula PS, Zandkarimi F, Nguyen TTT, Wu PB, Hai L, Karan C, Razavilar A, Siegelin MD, Kitajewski J, Bruce JN, Stockwell BR, Sims PA, Canoll PD. A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529581. [PMID: 36865302 PMCID: PMC9980114 DOI: 10.1101/2023.02.22.529581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Glioma cells hijack developmental transcriptional programs to control cell state. During neural development, lineage trajectories rely on specialized metabolic pathways. However, the link between tumor cell state and metabolic programs is poorly understood in glioma. Here we uncover a glioma cell state-specific metabolic liability that can be leveraged therapeutically. To model cell state diversity, we generated genetically engineered murine gliomas, induced by deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling cellular fate. N1IC tumors harbored quiescent astrocyte-like transformed cell states while p53 tumors were predominantly comprised of proliferating progenitor-like cell states. N1IC cells exhibit distinct metabolic alterations, with mitochondrial uncoupling and increased ROS production rendering them more sensitive to inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Importantly, treating patient-derived organotypic slices with a GPX4 inhibitor induced selective depletion of quiescent astrocyte-like glioma cell populations with similar metabolic profiles.
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Affiliation(s)
- Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael G. Argenziano
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenting Zhao
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Dominique M.O. Higgins
- Department of Neurological Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Colin P. Sperring
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brianna Pereira
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ling F. Ye
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nelson Humala
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia L. Furnari
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Pavan S. Upadhyayula
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Zandkarimi
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Trang T. T. Nguyen
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter B. Wu
- Department of Neurological Surgery, UCLA Geffen School of Medicine, Los Angeles, CA, USA
| | - Li Hai
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Charles Karan
- Sulzberger Columbia Genome Center, Columbia University, New York, NY, USA
| | - Aida Razavilar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Markus D. Siegelin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jan Kitajewski
- University of Illinois Cancer Center, Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, USA
| | - Jeffrey N. Bruce
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Brent R. Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Peter A. Sims
- Department of System Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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Li J, Godoy MI, Zhang AJ, Diamante G, Ahn IS, Cebrian-Silla A, Alvarez-Buylla A, Yang X, Novitch BG, Zhang Y. Prdm16 and Vcam1 regulate the postnatal disappearance of embryonic radial glia and the ending of cortical neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528567. [PMID: 36824905 PMCID: PMC9949035 DOI: 10.1101/2023.02.14.528567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Embryonic neural stem cells (NSCs, i.e., radial glia) in the ventricular-subventricular zone (V-SVZ) generate the majority of neurons and glia in the forebrain. Postnatally, embryonic radial glia disappear and a subpopulation of radial glia transition into adult NSCs. As this transition occurs, widespread neurogenesis in brain regions such as the cerebral cortex ends. The mechanisms that regulate the postnatal disappearance of radial glia and the ending of embryonic neurogenesis remain poorly understood. Here, we show that PR domain-containing 16 (Prdm16) promotes the disappearance of radial glia and the ending of neurogenesis in the cerebral cortex. Genetic deletion of Prdm16 from NSCs leads to the persistence of radial glia in the adult V-SVZ and prolonged postnatal cortical neurogenesis. Mechanistically, Prdm16 induces the postnatal reduction in Vascular Cell Adhesion Molecule 1 (Vcam1). The postnatal disappearance of radial glia and the ending of cortical neurogenesis occur normally in Prdm16-Vcam1 double conditional knockout mice. These observations reveal novel molecular regulators of the postnatal disappearance of radial glia and the ending of embryonic neurogenesis, filling a key knowledge gap in NSC biology.
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Affiliation(s)
- Jiwen Li
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | - Marlesa I. Godoy
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | - Alice J. Zhang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | | | - In Sook Ahn
- Department of Integrative Biology and Physiology, UCLA
| | - Arantxa Cebrian-Silla
- Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, Department of Neurological Surgery, University of California, San Francisco, San Francisco, USA
| | - Arturo Alvarez-Buylla
- Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, Department of Neurological Surgery, University of California, San Francisco, San Francisco, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, UCLA
- Brain Research Institute at UCLA
- Institute for Quantitative and Computational Biosciences at UCLA
- Molecular Biology Institute at UCLA
| | - Bennett G. Novitch
- Brain Research Institute at UCLA
- Molecular Biology Institute at UCLA
- Department of Neurobiology, UCLA
- Intellectual and Developmental Disabilities Research Center at UCLA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA
| | - Ye Zhang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
- Brain Research Institute at UCLA
- Molecular Biology Institute at UCLA
- Intellectual and Developmental Disabilities Research Center at UCLA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA
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40
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Bagnoli S, Chiavacci E, Cellerino A, Terzibasi Tozzini E. Localization and Characterization of Major Neurogenic Niches in the Brain of the Lesser-Spotted Dogfish Scyliorhinus canicula. Int J Mol Sci 2023; 24:ijms24043650. [PMID: 36835066 PMCID: PMC9967623 DOI: 10.3390/ijms24043650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Adult neurogenesis is defined as the ability of specialized cells in the postnatal brain to produce new functional neurons and to integrate them into the already-established neuronal network. This phenomenon is common in all vertebrates and has been found to be extremely relevant for numerous processes, such as long-term memory, learning, and anxiety responses, and it has been also found to be involved in neurodegenerative and psychiatric disorders. Adult neurogenesis has been studied extensively in many vertebrate models, from fish to human, and observed also in the more basal cartilaginous fish, such as the lesser-spotted dogfish, Scyliorhinus canicula, but a detailed description of neurogenic niches in this animal is, to date, limited to the telencephalic areas. With this article, we aim to extend the characterization of the neurogenic niches of S. canicula in other main areas of the brain: we analyzed via double immunofluorescence sections of telencephalon, optic tectum, and cerebellum with markers of proliferation (PCNA) and mitosis (pH3) in conjunction with glial cell (S100β) and stem cell (Msi1) markers, to identify the actively proliferating cells inside the neurogenic niches. We also labeled adult postmitotic neurons (NeuN) to exclude double labeling with actively proliferating cells (PCNA). Lastly, we observed the presence of the autofluorescent aging marker, lipofuscin, contained inside lysosomes in neurogenic areas.
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Affiliation(s)
- Sara Bagnoli
- Biology Laboratory (BIO@SNS), Scuola Normale Superiore, 56126 Pisa, Italy
| | - Elena Chiavacci
- Biology Laboratory (BIO@SNS), Scuola Normale Superiore, 56126 Pisa, Italy
- Biology and Evolution of Marine Organisms Department (BEOM), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Alessandro Cellerino
- Biology Laboratory (BIO@SNS), Scuola Normale Superiore, 56126 Pisa, Italy
- Fritz Lipmann Institute for Age Research, Leibniz Institute, 07745 Jena, Germany
| | - Eva Terzibasi Tozzini
- Biology and Evolution of Marine Organisms Department (BEOM), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
- Correspondence:
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Huang T, Cheng J, Feng H, Zhou W, Qiu P, Zhou D, Yang D, Zhang J, Willer C, Chen YE, Mizrak D, Yang B. Bicuspid Aortic Valve-Associated Regulatory Regions Reveal GATA4 Regulation and Function During Human-Induced Pluripotent Stem Cell-Based Endothelial-Mesenchymal Transition-Brief Report. Arterioscler Thromb Vasc Biol 2023; 43:312-322. [PMID: 36519469 PMCID: PMC10038164 DOI: 10.1161/atvbaha.122.318566] [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: 03/13/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The endothelial-mesenchymal transition (EndoMT) is a fundamental process for heart valve formation and defects in EndoMT cause aortic valve abnormalities. Our previous genome-wide association study identified multiple variants in a large chromosome 8 segment as significantly associated with bicuspid aortic valve (BAV). The objective of this study is to determine the biological effects of this large noncoding segment in human induced pluripotent stem cell (hiPSC)-based EndoMT. METHODS A large genomic segment enriched for BAV-associated variants was deleted in hiPSCs using 2-step CRISPR/Cas9 editing. To address the effects of the variants on GATA4 expression, we generated CRISPR repression hiPSC lines (CRISPRi) as well as hiPSCs from BAV patients. The resulting hiPSCs were differentiated to mesenchymal/myofibroblast-like cells through cardiovascular-lineage endothelial cells for molecular and cellular analysis. Single-cell RNA sequencing was also performed at different stages of EndoMT induction. RESULTS The large deletion impaired hiPSC-based EndoMT in multiple biallelic clones compared with their isogenic control. It also reduced GATA4 transcript and protein levels during EndoMT, sparing the other genes nearby the deletion segment. Single-cell trajectory analysis revealed the molecular reprogramming during EndoMT. Putative GATA-binding protein targets during EndoMT were uncovered, including genes implicated in endocardial cushion formation and EndoMT process. Differentiation of cells derived from BAV patients carrying the rs117430032 variant as well as CRISPRi repression of the rs117430032 locus resulted in lower GATA4 expression in a stage-specific manner. TWIST1 was identified as a potential regulator of GATA4 expression, showing specificity to the locus tagged by rs117430032. CONCLUSIONS BAV-associated distal regions regulate GATA4 expression during hiPSC-based EndoMT, which in turn promotes EndoMT progression, implicating its contribution to heart valve development.
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Affiliation(s)
- Tingting Huang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiaxi Cheng
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Hao Feng
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ping Qiu
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Dong Zhou
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Dongshan Yang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jifeng Zhang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Cristen Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Y. Eugene Chen
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dogukan Mizrak
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
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42
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Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma. Front Med 2023; 17:240-262. [PMID: 36645634 DOI: 10.1007/s11684-022-0936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 01/17/2023]
Abstract
Detailed characterizations of genomic alterations have not identified subtype-specific vulnerabilities in adult gliomas. Mapping gliomas into developmental programs may uncover new vulnerabilities that are not strictly related to genomic alterations. After identifying conserved gene modules co-expressed with EGFR or PDGFRA (EM or PM), we recently proposed an EM/PM classification scheme for adult gliomas in a histological subtype- and grade-independent manner. By using cohorts of bulk samples, paired primary and recurrent samples, multi-region samples from the same glioma, single-cell RNA-seq samples, and clinical samples, we here demonstrate the temporal and spatial stability of the EM and PM subtypes. The EM and PM subtypes, which progress in a subtype-specific mode, are robustly maintained in paired longitudinal samples. Elevated activities of cell proliferation, genomic instability and microenvironment, rather than subtype switching, mark recurrent gliomas. Within individual gliomas, the EM/PM subtype was preserved across regions and single cells. Malignant cells in the EM and PM gliomas were correlated to neural stem cell and oligodendrocyte progenitor cell compartment, respectively. Thus, while genetic makeup may change during progression and/or within different tumor areas, adult gliomas evolve within a neurodevelopmental framework of the EM and PM molecular subtypes. The dysregulated developmental pathways embedded in these molecular subtypes may contain subtype-specific vulnerabilities.
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Nam HS, Capecchi MR. Lrig1 expression identifies quiescent stem cells in the ventricular-subventricular zone from postnatal development to adulthood and limits their persistent hyperproliferation. Neural Dev 2023; 18:1. [PMID: 36631891 PMCID: PMC9832784 DOI: 10.1186/s13064-022-00169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/26/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND We previously identified Leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1) as a marker of long-term neurogenic stem cells in the lateral wall of the adult mouse brain. The morphology of the stem cells thus identified differed from the canonical B1 type stem cells, raising a question about their cellular origin. Thus, we investigated the development of these stem cells in the postnatal and juvenile brain. Furthermore, because Lrig1 is a known regulator of quiescence, we also investigated the effect(s) of its deletion on the cellular proliferation in the lateral wall. METHODS To observe the development of the Lrig1-lineage stem cells, genetic inducible fate mapping studies in combination with thymidine analog administration were conducted using a previously published Lrig1T2A-iCreERT2 mouse line. To identify the long-term consequence(s) of Lrig1 germline deletion, old Lrig1 knock-out mice were generated using two different Lrig1 null alleles in the C57BL/6J background. The lateral walls from these mice were analyzed using an optimized whole mount immunofluorescence protocol and confocal microscopy. RESULTS We observed the Lrig1-lineage labeled cells with morphologies consistent with neurogenic stem cell identity in postnatal, juvenile, and adult mouse brains. Interestingly, when induced at postnatal or juvenile ages, morphologically distinct cells were revealed, including cells with the canonical B1 type stem cell morphology. Almost all of the presumptive stem cells labeled were non-proliferative at these ages. In the old Lrig1 germline knock-out mice, increased proliferation was observed compared to wildtype littermates without concomitant increase in apoptosis. CONCLUSIONS Once set aside during embryogenesis, the Lrig1-lineage stem cells remain largely quiescent during postnatal and juvenile development until activation in adult age. The absence of premature proliferative exhaustion in the Lrig1 knock-out stem cell niche during aging is likely due to a complex cascade of effects on the adult stem cell pool. Thus, we suggest that the adult stem cell pool size may be genetically constrained via Lrig1.
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Affiliation(s)
- Hyung-song Nam
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5331 USA
| | - Mario R. Capecchi
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5331 USA
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Davinelli S, Medoro A, Ali S, Passarella D, Intrieri M, Scapagnini G. Dietary Flavonoids and Adult Neurogenesis: Potential Implications for Brain Aging. Curr Neuropharmacol 2023; 21:651-668. [PMID: 36321225 PMCID: PMC10207917 DOI: 10.2174/1570159x21666221031103909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 02/10/2023] Open
Abstract
Adult neurogenesis deficiency has been proposed to be a common hallmark in different age-related neurodegenerative diseases. The administration of flavonoids is currently reported as a potentially beneficial strategy for preventing brain aging alterations, including adult neurogenesis decline. Flavonoids are a class of plant-derived dietary polyphenols that have drawn attention for their neuroprotective and pro-cognitive effects. Although they undergo extensive metabolism and localize in the brain at low concentrations, flavonoids are now believed to improve cerebral vasculature and interact with signal transduction cascades involved in the regulation of adult neurogenesis. Furthermore, many dietary flavonoids have been shown to reduce oxidative stress and neuroinflammation, improving the neuronal microenvironment where adult neurogenesis occurs. The overall goal of this review is to summarize the evidence supporting the role of flavonoids in modulating adult neurogenesis as well as to highlight how these dietary agents may be promising candidates in restoring healthy brain function during physiological and pathological aging.
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Affiliation(s)
- Sergio Davinelli
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Alessandro Medoro
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Sawan Ali
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Daniela Passarella
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Mariano Intrieri
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
| | - Giovanni Scapagnini
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, Campobasso 86100, Italy
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Becker J, Sun B, Alammari F, Haerty W, Vance KW, Szele FG. What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone? Stem Cell Reports 2022; 18:354-376. [PMID: 36525965 PMCID: PMC9860170 DOI: 10.1016/j.stemcr.2022.11.011] [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: 04/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) function is mediated by the process of transcription or through transcript-dependent associations with proteins or nucleic acids to control gene regulatory networks. Many lncRNAs are transcribed in the ventricular-subventricular zone (V-SVZ), a postnatal neural stem cell niche. lncRNAs in the V-SVZ are implicated in neurodevelopmental disorders, cancer, and brain disease, but their functions are poorly understood. V-SVZ neurogenesis capacity declines with age due to stem cell depletion and resistance to neural stem cell activation. Here we analyzed V-SVZ transcriptomics by pooling current single-cell RNA-seq data. They showed consistent lncRNA expression during stem cell activation, lineage progression, and aging. In conjunction with epigenetic and genetic data, we predicted V-SVZ lncRNAs that regulate stem cell activation and differentiation. Some of the lncRNAs validate known epigenetic mechanisms, but most remain uninvestigated. Our analysis points to several lncRNAs that likely participate in key aspects of V-SVZ stem cell activation and neurogenesis in health and disease.
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Affiliation(s)
- Jemima Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia,Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Keith W. Vance
- Department of Life Sciences, University of Bath, Bath, UK
| | - Francis George Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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Neural precursor cells tune striatal connectivity through the release of IGFBPL1. Nat Commun 2022; 13:7579. [PMID: 36482070 PMCID: PMC9731988 DOI: 10.1038/s41467-022-35341-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
The adult brain retains over life endogenous neural stem/precursor cells (eNPCs) within the subventricular zone (SVZ). Whether or not these cells exert physiological functions is still unclear. In the present work, we provide evidence that SVZ-eNPCs tune structural, electrophysiological, and behavioural aspects of striatal function via secretion of insulin-like growth factor binding protein-like 1 (IGFBPL1). In mice, selective ablation of SVZ-eNPCs or selective abrogation of IGFBPL1 determined an impairment of striatal medium spiny neuron morphology, a higher failure rate in GABAergic transmission mediated by fast-spiking interneurons, and striatum-related behavioural dysfunctions. We also found IGFBPL1 expression in the human SVZ, foetal and induced-pluripotent stem cell-derived NPCs. Finally, we found a significant correlation between SVZ damage, reduction of striatum volume, and impairment of information processing speed in neurological patients. Our results highlight the physiological role of adult SVZ-eNPCs in supporting cognitive functions by regulating striatal neuronal activity.
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Zhang C, Xue P, Zhang H, Tan C, Zhao S, Li X, Sun L, Zheng H, Wang J, Zhang B, Lang W. Gut brain interaction theory reveals gut microbiota mediated neurogenesis and traditional Chinese medicine research strategies. Front Cell Infect Microbiol 2022; 12:1072341. [PMID: 36569198 PMCID: PMC9772886 DOI: 10.3389/fcimb.2022.1072341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Adult neurogenesis is the process of differentiation of neural stem cells (NSCs) into neurons and glial cells in certain areas of the adult brain. Defects in neurogenesis can lead to neurodegenerative diseases, mental disorders, and other maladies. This process is directionally regulated by transcription factors, the Wnt and Notch pathway, the extracellular matrix, and various growth factors. External factors like stress, physical exercise, diet, medications, etc., affect neurogenesis and the gut microbiota. The gut microbiota may affect NSCs through vagal, immune and chemical pathways, and other pathways. Traditional Chinese medicine (TCM) has been proven to affect NSCs proliferation and differentiation and can regulate the abundance and metabolites produced by intestinal microorganisms. However, the underlying mechanisms by which these factors regulate neurogenesis through the gut microbiota are not fully understood. In this review, we describe the recent evidence on the role of the gut microbiota in neurogenesis. Moreover, we hypothesize on the characteristics of the microbiota-gut-brain axis based on bacterial phyla, including microbiota's metabolites, and neuronal and immune pathways while providing an outlook on TCM's potential effects on adult neurogenesis by regulating gut microbiota.
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Affiliation(s)
- Chenxi Zhang
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, China
| | - Peng Xue
- Medical School of Nantong University, Nantong University, Nantong, China
| | - Haiyan Zhang
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, China
| | - Chenxi Tan
- Department of Infection Control, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Shiyao Zhao
- Department of Nuclear Medicine, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Xudong Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lihui Sun
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, China
| | - Huihui Zheng
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, China
| | - Jun Wang
- The Academic Affairs Office, Qiqihar Medical University, Qiqihar, China
| | - Baoling Zhang
- Department of Operating Room, Qiqihar First Hospital, Qiqihar, China
| | - Weiya Lang
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, China,*Correspondence: Weiya Lang,
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Jung GA, Kim JA, Park HW, Lee H, Chang MS, Cho KO, Song BW, Kim HJ, Kwon YK, Oh IH. Induction of Nanog in neural progenitor cells for adaptive regeneration of ischemic brain. Exp Mol Med 2022; 54:1955-1966. [PMID: 36376495 PMCID: PMC9722910 DOI: 10.1038/s12276-022-00880-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
NANOG plays a key role in cellular plasticity and the acquisition of the stem cell state during reprogramming, but its role in the regenerative process remains unclear. Here, we show that the induction of NANOG in neuronal cells is necessary for the physiological initiation of neuronal regeneration in response to ischemic stress. Specifically, we found that NANOG was preferentially expressed in undifferentiated neuronal cells, and forced expression of Nanog in neural progenitor cells (NPCs) promoted their self-renewing expansion both in ex-vivo slice cultures and in vitro limiting dilution analysis. Notably, the upstream region of the Nanog gene contains sequence motifs for hypoxia-inducible factor-1 alpha (HIF-1α). Therefore, cerebral neurons exposed to hypoxia significantly upregulated NANOG expression selectively in primitive (CD133+) cells, but not in mature cells, leading to the expansion of NPCs. Notably, up to 80% of the neuronal expansion induced by hypoxia was attributed to NANOG-expressing neuronal cells, whereas knockdown during hypoxia abolished this expansion and was accompanied by the downregulation of other pluripotency-related genes. Moreover, the number of NANOG-expressing neuronal cells were transiently increased in response to ischemic insult, predominantly in the infarct area of brain regions undergoing neurogenesis, but not in non-neurogenic loci. Together, these findings reveal a functional effect of NANOG-induction for the initiation of adaptive neuronal regeneration among heterogeneous NPC subsets, pointing to cellular plasticity as a potential link between regeneration and reprogramming processes.
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Affiliation(s)
- Gyung-Ah Jung
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin-A Kim
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hwan-Woo Park
- grid.31501.360000 0004 0470 5905Department of Oral Anatomy, Dental Research Institute & School of Dentistry, Seoul National University, Seoul, Korea ,grid.411143.20000 0000 8674 9741Present Address: Department of Cell Biology, Myunggok Medical Research Institute, Konyang University College of Medicine, Daejeon, Korea
| | - Hyemi Lee
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Mi-Sook Chang
- grid.31501.360000 0004 0470 5905Department of Oral Anatomy, Dental Research Institute & School of Dentistry, Seoul National University, Seoul, Korea
| | - Kyung-Ok Cho
- grid.411947.e0000 0004 0470 4224Department of Pharmacology, Department of Biomedicine & Health Sciences, Catholic Neuroscience Institute, Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byeong-Wook Song
- grid.411199.50000 0004 0470 5702College of Medicine, Institute for Bio-Medical Convergence, Catholic Kwandong University, Gangneung-si, 25601 Korea
| | - Hyun-Ju Kim
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Yunhee Kim Kwon
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Il-Hoan Oh
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea ,Institute for Regenerative Medical Research, StemMeditech Inc., Seoul, Korea
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Wang J, Ware K, Bedolla A, Allgire E, Turcato FC, Weed M, Sah R, Luo Y. Disruption of Sonic Hedgehog Signaling Accelerates Age-Related Neurogenesis Decline and Abolishes Stroke-Induced Neurogenesis and Leads to Increased Anxiety Behavior in Stroke Mice. Transl Stroke Res 2022; 13:830-844. [PMID: 35146631 PMCID: PMC10114538 DOI: 10.1007/s12975-022-00994-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/10/2022] [Accepted: 01/31/2022] [Indexed: 02/03/2023]
Abstract
Sonic Hedgehog (SHH) signaling has a critical role in mediating developmental neurogenesis and has been implicated in adult subventricular (SVZ) neurogenesis. However, the precise role of Smoothened (SMO) receptor-mediated SHH signaling in adult neurogenesis during aging especially in hippocampal subgranular zone (SGZ) neurogenesis remains undefined. Additionally, our previous study showed that stimulation of SHH signaling post-stroke leads to increased neurogenesis and improved behavioral functions after stroke. However, it is not clear whether SHH signaling in neural stem cells (NSCs) is required for stroke-induced neurogenesis and functional recovery post-stroke. In this study, using conditional knockout (cKO) of SHH signaling receptor Smo gene in NSCs, we show a decreased neurogenesis at both SVZ and SGZ in young-adult mice and an accelerated depletion of neurogenic cells in the process of aging suggesting that SHH signaling is critical in maintaining neurogenesis during aging. Behavior studies revealed that compromised neurogenesis in Smo cKO mice leads to increased anxiety/depression-like behaviors without affecting general locomotor function or spatial and fear-related learning. Importantly, we also show that NSCs with a cKO of SHH signaling abolishes stroke-induced neurogenesis in Smo cKO mice. Compared to control mice, Smo cKO mice also show delayed motor function recovery and increased anxiety level after stroke. Our data highlights the essential role of Smo function in regulating adult neurogenesis and emotional behaviors during both aging and CNS injury such as stroke.
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Affiliation(s)
- Jiapeng Wang
- Department of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Kierra Ware
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Alicia Bedolla
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Neuroscience Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Emily Allgire
- Neuroscience Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Department of Pharmacology & Systems Physiology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Flavia Correa Turcato
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Maxwell Weed
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Renu Sah
- Neuroscience Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Department of Pharmacology & Systems Physiology, University of Cincinnati, Cincinnati, OH, 45267, USA
- Cincinnati VA Medical Center, Cincinnati, OH, 45220, USA
| | - Yu Luo
- Department of Molecular Genetics, Biochemistry and Microbiology, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA.
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Expression of Transcription Factor ZBTB20 in the Adult Primate Neurogenic Niche under Physiological Conditions or after Ischemia. Genes (Basel) 2022; 13:genes13091559. [PMID: 36140727 PMCID: PMC9498320 DOI: 10.3390/genes13091559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
The Zbtb20 gene encodes for a transcription factor that plays an important role in mammalian cortical development. Recently, its expression was reported in the adult mouse subventricular zone (SVZ), a major neurogenic niche containing neural stem cells throughout life. Here, we analyzed its expression in the adult primate anterior SVZ (SVZa) and rostral migratory stream (RMS) using macaque monkeys (Macaca fuscata). We report that the majority of Ki67+ cells, 71.4% in the SVZa and 85.7% in the RMS, co-label for ZBTB20. Nearly all neuroblasts, identified by their Doublecortin expression, were positive for ZBTB20 in both regions. Nearly all GFAP+ neural stem cells/astrocytes were also positive for ZBTB20. Analysis of images derived from a public database of gene expression in control/ischemic monkey SVZa, showed evidence for ZBTB20 upregulation in postischemic monkey SVZa. Furthermore, the co-localization of ZBTB20 with Doublecortin and Ki67 was increased in the postischemic SVZa. Our results suggest that ZBTB20 expression is evolutionarily conserved in the mammalian neurogenic niche and is reactive to ischemia. This opens the possibility for further functional studies on the role of this transcription factor in neurogenesis in primates.
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