1
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Lee Y, Kim KH, Park J, Kang HM, Kim SH, Jeong H, Lee B, Lee N, Cho Y, Kim GD, Yu S, Gee HY, Bok J, Hamilton MS, Gewin L, Aronow BJ, Lim KM, Coffey RJ, Nam KT. Regenerative Role of Lrig1+ Cells in Kidney Repair. J Am Soc Nephrol 2024:00001751-990000000-00388. [PMID: 39120954 DOI: 10.1681/asn.0000000000000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/05/2024] [Indexed: 08/11/2024] Open
Abstract
Key Points
Lrig1
+
cells exist long term during kidney homeostasis and become activated upon injury, contributing to regeneration.
Lrig1
+
cells and their progeny emerge during tubulogenesis and contribute to proximal tubule and inner medullary collecting duct development.
Lrig1
+
cells expand and differentiate into a mature nephron lineage in response to AKI to repair the proximal tubule.
Background
In response to severe kidney injury, the kidney epithelium displays remarkable regenerative capabilities driven by adaptable resident epithelial cells. To date, it has been widely considered that the adult kidney lacks multipotent stem cells; thus, the cellular lineages responsible for repairing proximal tubule damage are incompletely understood. Leucine-rich repeats and immunoglobulin-like domain protein 1–expressing cells (Lrig1
+ cells) have been identified as a long-lived cell in various tissues that can induce epithelial tissue repair. Therefore, we hypothesized that Lrig1
+ cells participate in kidney development and tissue regeneration.
Methods
We investigated the role of Lrig1
+
cells in kidney injury using mouse models. The localization of Lrig1
+
cells in the kidney was examined throughout mouse development. The function of Lrig1
+
progeny cells in AKI repair was examined in vivo using a tamoxifen-inducible Lrig1-specific Cre recombinase-based lineage tracing in three different kidney injury mouse models. In addition, we conducted single-cell RNA sequencing to characterize the transcriptional signature of Lrig1
+
cells and trace their progeny.
Results
Lrig1
+ cells were present during kidney development and contributed to formation of the proximal tubule and collecting duct structures in mature mouse kidneys. In three-dimensional culture, single Lrig1
+ cells demonstrated long-lasting propagation and differentiated into the proximal tubule and collecting duct lineages. These Lrig1
+ proximal tubule cells highly expressed progenitor-like and quiescence-related genes, giving rise to a novel cluster of cells with regenerative potential in adult kidneys. Moreover, these long-lived Lrig1
+ cells expanded and repaired damaged proximal tubule in response to three types of AKIs in mice.
Conclusions
These findings highlight the critical role of Lrig1
+ cells in kidney regeneration.
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Affiliation(s)
- Yura Lee
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang H Kim
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Hyun Mi Kang
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung-Hee Kim
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Haengdueng Jeong
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Buhyun Lee
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Nakyum Lee
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yejin Cho
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Seyoung Yu
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Heon Yung Gee
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jinwoong Bok
- Department of Anatomy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Maxwell S Hamilton
- Epithelial Biology Center and Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Leslie Gewin
- Division of Nephrology and Hypertension, Department of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Medicine, Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Bruce J Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kyung-Min Lim
- College of Pharmacy, Ewha Womans University, Seoul, Korea
| | - Robert J Coffey
- Epithelial Biology Center and Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Medicine, Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Ki Taek Nam
- Department of Biomedical Sciences, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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2
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Sun Z, Zhang B, Zhou J, Luo Y, Zhu X, Wang Y, He Y, Zheng P, Zhang L, Yang J, Wang G. Integrated Single-Cell RNA-seq and ATAC-seq Reveals Heterogeneous Differentiation of CD4 + Naive T Cell Subsets is Associated with Response to Antidepressant Treatment in Major Depressive Disorder. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308393. [PMID: 38867657 PMCID: PMC11321657 DOI: 10.1002/advs.202308393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/08/2024] [Indexed: 06/14/2024]
Abstract
The mechanism involved in major depressive disorder (MDD) is well-studied but the mechanistic origin of the heterogeneous antidepressant effect remains largely unknown. Single-cell RNA-sequencing (scRNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) on peripheral blood mononuclear cells from 8 healthy individuals and 8 MDD patients before or after 12 weeks of antidepressant treatment is performed. scRNA-seq analysis reveals a lower proportion of naive T cells, particularly CD4+ naive T cells, in MDD patients compared to controls, and in nonresponders versus responders at the baseline. Flow cytometry data analysis of an independent cohort of 35 patients and 40 healthy individuals confirms the findings. Enrichment analysis of differentially expressed genes indicated obvious immune activation in responders. A specific activated CD4+ naive T population in responders characterized by enhanced mitogen-activated protein kinases (MAPK) pathway is identified. E-twenty six (ETS) is proposed as an upstream regulator of the MAPK pathway and heterogeneous differentiation in activated CD4+ naive T population is associated with the response to antidepressant treatment in MDD patients. A distinct immune feature manifested by CD4+ naive T cells during antidepressant treatment in MDD is identified. Collectively, this proposes the molecular mechanism that underlies the heterogeneous antidepressant outcomes for MDD.
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Affiliation(s)
- Zuoli Sun
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Bowen Zhang
- College of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Jingjing Zhou
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Yanting Luo
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Xuequan Zhu
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Yaping Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Yi He
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Peng Zheng
- Department of NeurologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional DiseasesThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Ling Zhang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
| | - Jian Yang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
- Advanced Innovation Center for Human Brain ProtectionCapital Medical UniversityBeijing100069China
| | - Gang Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental DisordersBeijing Anding HospitalCapital Medical UniversityBeijing100088China
- Advanced Innovation Center for Human Brain ProtectionCapital Medical UniversityBeijing100069China
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3
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Tan Z, Chen P, Dong X, Guo S, Leung VYL, Cheung JPY, Chan D, Richardson SM, Hoyland JA, To MKT, Cheah KSE. Progenitor-like cells contributing to cellular heterogeneity in the nucleus pulposus are lost in intervertebral disc degeneration. Cell Rep 2024; 43:114342. [PMID: 38865240 DOI: 10.1016/j.celrep.2024.114342] [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: 11/13/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
The nucleus pulposus (NP) in the intervertebral disc (IVD) arises from embryonic notochord. Loss of notochordal-like cells in humans correlates with onset of IVD degeneration, suggesting that they are critical for healthy NP homeostasis and function. Comparative transcriptomic analyses identified expression of progenitor-associated genes (GREM1, KRT18, and TAGLN) in the young mouse and non-degenerated human NP, with TAGLN expression reducing with aging. Lineage tracing using Tagln-CreERt2 mice identified peripherally located proliferative NP (PeriNP) cells in developing and postnatal NP that provide a continuous supply of cells to the entire NP. PeriNP cells were diminished in aged mice and absent in puncture-induced degenerated discs. Single-cell transcriptomes of postnatal Tagln-CreERt2 IVD cells indicate enrichment for TGF-β signaling in Tagln descendant NP sub-populations. Notochord-specific removal of TGF-β/BMP mediator Smad4 results in loss of Tagln+ cells and abnormal NP morphologies. We propose Tagln+ PeriNP cells are potential progenitors crucial for NP homeostasis.
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Affiliation(s)
- Zhijia Tan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Peikai Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Artificial Intelligence and Big Data Lab, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Xiaonan Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shuang Guo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Victor Y L Leung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jason P Y Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stephen M Richardson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Judith A Hoyland
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Michael K T To
- Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Shenzhen Clinical Research Center for Rare Diseases, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China; Department of Orthopaedics and Traumatology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kathryn S E Cheah
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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4
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [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: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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5
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Guo Y, Feng Y, Jiang F, Hu L, Shan T, Li H, Liao H, Bao H, Shi H, Si Y. Down-regulating nuclear factor of activated T cells 1 alleviates cognitive deficits in a mouse model of sepsis-associated encephalopathy, possibly by stimulating hippocampal neurogenesis. Brain Res 2024; 1826:148731. [PMID: 38154504 DOI: 10.1016/j.brainres.2023.148731] [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: 08/14/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Sepsis-associated encephalopathy (SAE) is a common complication of sepsis, and has been associated with increased morbidity and mortality. Nuclear factor of activated T cells (NFATs) 1, a transcriptional factor that regulates T cell development, activation and differentiation, has been implicated in neuronal plasticity. Here we examined the potential role of NFAT1 in sepsis-associated encephalopathy in mice. Adult male C57BL/6J mice received intracerebroventricular injections of short interfering RNA against NFAT1 or sex-determining region Y-box 2 (SOX2), or a scrambled control siRNA prior to cecal ligation and perforation (CLP). A group of mice receiving sham surgery were included as an additional control. CLP increased escape latency and decreased the number of crossings into, and total time spent within, the target quadrant in the Morris water maze test. CLP also decreased the freezing time in context-dependent, but not context-independent, fear conditioning test. Knockdown of either NFAT1 or SOX2 attenuated these behavioral deficits. NFAT1 knockdown also attenuated CLP-induced upregulation of SOX2, increased the numbers of nestin-positive cells and newborn astrocytes, reduced the number of immature newborn neurons, and promoted the G1 to S transition of neural stem cells in hippocampus. These findings suggest that NFAT1 may contribute to sepsis-induced behavioral deficits, possibly by promoting SOX2 signaling and neurogenesis.
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Affiliation(s)
- Yaoyi Guo
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Yue Feng
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Fan Jiang
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Liang Hu
- Department of Pharmacology, Nanjing Medical University, No. 101 Longmiandadao Road, Jiangning District, Nanjing, Jiangsu Province 211166, People's Republic of China
| | - Tao Shan
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Haojia Li
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Hongsen Liao
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Hongguang Bao
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Hongwei Shi
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China
| | - Yanna Si
- Department of Anesthesiology, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Qinhuai District, Nanjing, Jiangsu Province 210006, People's Republic of China.
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6
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Jimenez-Vergara AC, Avina J, Block TJ, Sheldrake A, Koch C, Gonzalez A, Steele J, Díaz-Lasprilla AM, Munoz-Pinto DJ. A Bioinspired Astrocyte-Derived Coating Promotes the In Vitro Proliferation of Human Neural Stem Cells While Maintaining Their Stemness. Biomimetics (Basel) 2023; 8:589. [PMID: 38132528 PMCID: PMC10741944 DOI: 10.3390/biomimetics8080589] [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: 10/10/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The repair of neuronal tissue is a challenging process due to the limited proliferative capacity of neurons. Neural stem cells (NSCs) can aid in the regeneration process of neural tissue due to their high proliferation potential and capacity to differentiate into neurons. The therapeutic potential of these cells can only be achieved if sufficient cells are obtained without losing their differentiation potential. Toward this end, an astrocyte-derived coating (HAc) was evaluated as a promising substrate to promote the proliferation of NSCs. Mass spectroscopy and scanning electron microscopy were used to characterize the HAc. The proliferation rate and the expression of stemness and differentiation markers in NSCs cultured on the HAc were evaluated and compared to the responses of these cells to commonly used coating materials including Poly-L-Ornithine (PLO), and a Human Induced Pluripotent Stem Cell (HiPSC)-based coating. The use of the HAc promotes the in vitro cell growth of NSCs. The expression of the stemness markers Sox2 and Nestin, and the differentiation marker DCX in the HAc group was akin to the expression of these markers in the controls. In summary, HAc supported the proliferation of NSCs while maintaining their stemness and neural differentiation potential.
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Affiliation(s)
- Andrea C. Jimenez-Vergara
- Engineering Science Department, Trinity University, San Antonio, TX 78212, USA; (A.C.J.-V.); (J.A.); (A.G.); (A.M.D.-L.)
| | - Jacob Avina
- Engineering Science Department, Trinity University, San Antonio, TX 78212, USA; (A.C.J.-V.); (J.A.); (A.G.); (A.M.D.-L.)
| | | | - Anne Sheldrake
- StemBioSys, San Antonio, TX 78229, USA; (T.J.B.); (A.S.)
| | - Carson Koch
- Neuroscience Program, Trinity University, San Antonio, TX 78212, USA;
| | - Anna Gonzalez
- Engineering Science Department, Trinity University, San Antonio, TX 78212, USA; (A.C.J.-V.); (J.A.); (A.G.); (A.M.D.-L.)
| | - Jennifer Steele
- Physics and Astronomy Department, Trinity University, San Antonio, TX 78212, USA;
| | - Ana M. Díaz-Lasprilla
- Engineering Science Department, Trinity University, San Antonio, TX 78212, USA; (A.C.J.-V.); (J.A.); (A.G.); (A.M.D.-L.)
| | - Dany J. Munoz-Pinto
- Engineering Science Department, Trinity University, San Antonio, TX 78212, USA; (A.C.J.-V.); (J.A.); (A.G.); (A.M.D.-L.)
- Neuroscience Program, Trinity University, San Antonio, TX 78212, USA;
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7
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Noack F, Vangelisti S, Ditzer N, Chong F, Albert M, Bonev B. Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids. Nat Cell Biol 2023; 25:1873-1883. [PMID: 37996647 PMCID: PMC10709149 DOI: 10.1038/s41556-023-01296-5] [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: 09/20/2022] [Accepted: 10/17/2023] [Indexed: 11/25/2023]
Abstract
Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomics methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a method-3D genome, RNA, accessibility and methylation sequencing (3DRAM-seq)-that simultaneously interrogates spatial genome organization, chromatin accessibility and DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA sequencing in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay to profile cell-type-specific enhancer activity in organoids and to functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues.
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Affiliation(s)
- Florian Noack
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Silvia Vangelisti
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nora Ditzer
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Faye Chong
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mareike Albert
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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8
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Magalhães F, Andrade C, Simões B, Brigham F, Valente R, Martinez P, Rino J, Sugni M, Coelho AV. Regeneration of starfish radial nerve cord restores animal mobility and unveils a new coelomocyte population. Cell Tissue Res 2023; 394:293-308. [PMID: 37606764 PMCID: PMC10638123 DOI: 10.1007/s00441-023-03818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/21/2023] [Indexed: 08/23/2023]
Abstract
The potential to regenerate a damaged body part is expressed to a different extent in animals. Echinoderms, in particular starfish, are known for their outstanding regenerating potential. Differently, humans have restricted abilities to restore organ systems being dependent on limited sources of stem cells. In particular, the potential to regenerate the central nervous system is extremely limited, explaining the lack of natural mechanisms that could overcome the development of neurodegenerative diseases and the occurrence of trauma. Therefore, understanding the molecular and cellular mechanisms of regeneration in starfish could help the development of new therapeutic approaches in humans. In this study, we tackle the problem of starfish central nervous system regeneration by examining the external and internal anatomical and behavioral traits, the dynamics of coelomocyte populations, and neuronal tissue architecture after radial nerve cord (RNC) partial ablation. We noticed that the removal of part of RNC generated several anatomic anomalies and induced behavioral modifications (injured arm could not be used anymore to lead the starfish movement). Those alterations seem to be related to defense mechanisms and protection of the wound. In particular, histology showed that tissue patterns during regeneration resemble those described in holothurians and in starfish arm tip regeneration. Flow cytometry coupled with imaging flow cytometry unveiled a new coelomocyte population during the late phase of the regeneration process. Morphotypes of these and previously characterized coelomocyte populations were described based on IFC data. Further studies of this new coelomocyte population might provide insights on their involvement in radial nerve cord regeneration.
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Affiliation(s)
- Filipe Magalhães
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Claúdia Andrade
- NOVA Medical School/Faculdade de Ciências Médicas, Lisbon, Portugal
| | - Beatriz Simões
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fredi Brigham
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ruben Valente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- ICREA (Institut Català de Recerca i Estudis Avancats), Barcelona, Spain
| | - José Rino
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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9
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Challa NVD, Chen S, Yuan H, Duncan MR, Moreno WJ, Bramlett H, Dietrich WD, Benny M, Schmidt AF, Young K, Wu S. GSDMD gene knockout alleviates hyperoxia-induced hippocampal brain injury in neonatal mice. J Neuroinflammation 2023; 20:205. [PMID: 37679766 PMCID: PMC10486051 DOI: 10.1186/s12974-023-02878-8] [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: 06/12/2023] [Accepted: 08/19/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Neonatal hyperoxia exposure is associated with brain injury and poor neurodevelopment outcomes in preterm infants. Our previous studies in neonatal rodent models have shown that hyperoxia stimulates the brain's inflammasome pathway, leading to the activation of gasdermin D (GSDMD), a key executor of pyroptotic inflammatory cell death. Moreover, we found pharmacological inhibition of caspase-1, which blocks GSDMD activation, attenuates hyperoxia-induced brain injury in neonatal mice. We hypothesized that GSDMD plays a pathogenic role in hyperoxia-induced neonatal brain injury and that GSDMD gene knockout (KO) will alleviate hyperoxia-induced brain injury. METHODS Newborn GSDMD knockout mice and their wildtype (WT) littermates were randomized within 24 h after birth to be exposed to room air or hyperoxia (85% O2) from postnatal days 1 to 14. Hippocampal brain inflammatory injury was assessed in brain sections by immunohistology for allograft inflammatory factor 1 (AIF1) and CD68, markers of microglial activation. Cell proliferation was evaluated by Ki-67 staining, and cell death was determined by TUNEL assay. RNA sequencing of the hippocampus was performed to identify the transcriptional effects of hyperoxia and GSDMD-KO, and qRT-PCR was performed to confirm some of the significantly regulated genes. RESULTS Hyperoxia-exposed WT mice had increased microglia consistent with activation, which was associated with decreased cell proliferation and increased cell death in the hippocampal area. Conversely, hyperoxia-exposed GSDMD-KO mice exhibited considerable resistance to hyperoxia as O2 exposure did not increase AIF1 + , CD68 + , or TUNEL + cell numbers or decrease cell proliferation. Hyperoxia exposure differentially regulated 258 genes in WT and only 16 in GSDMD-KO mice compared to room air-exposed WT and GSDMD-KO, respectively. Gene set enrichment analysis showed that in the WT brain, hyperoxia differentially regulated genes associated with neuronal and vascular development and differentiation, axonogenesis, glial cell differentiation, hypoxia-induced factor 1 pathway, and neuronal growth factor pathways. These changes were prevented by GSDMD-KO. CONCLUSIONS GSDMD-KO alleviates hyperoxia-induced inflammatory injury, cell survival and death, and alterations of transcriptional gene expression of pathways involved in neuronal growth, development, and differentiation in the hippocampus of neonatal mice. This suggests that GSDMD plays a pathogenic role in preterm brain injury, and targeting GSDMD may be beneficial in preventing and treating brain injury and poor neurodevelopmental outcomes in preterm infants.
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Affiliation(s)
- Naga Venkata Divya Challa
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaoyi Chen
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Huijun Yuan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Matthew R Duncan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William Javier Moreno
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Helen Bramlett
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - W Dalton Dietrich
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Merline Benny
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Augusto F Schmidt
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Karen Young
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shu Wu
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA.
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10
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Mercurio S. SOX2-Sensing: Insights into the Role of SOX2 in the Generation of Sensory Cell Types in Vertebrates. Int J Mol Sci 2023; 24:ijms24087637. [PMID: 37108798 PMCID: PMC10141063 DOI: 10.3390/ijms24087637] [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: 03/28/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The SOX2 transcription factor is a key regulator of nervous system development, and its mutation in humans leads to a rare disease characterized by severe eye defects, cognitive defects, hearing defects, abnormalities of the CNS and motor control problems. SOX2 has an essential role in neural stem cell maintenance in specific regions of the brain, and it is one of the master genes required for the generation of induced pluripotent stem cells. Sox2 is expressed in sensory organs, and this review will illustrate how it regulates the differentiation of sensory cell types required for hearing, touching, tasting and smelling in vertebrates and, in particular, in mice.
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Affiliation(s)
- Sara Mercurio
- Department of Biotechnologies and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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11
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Guyer RA, Stavely R, Robertson K, Bhave S, Mueller JL, Picard NM, Hotta R, Kaltschmidt JA, Goldstein AM. Single-cell multiome sequencing clarifies enteric glial diversity and identifies an intraganglionic population poised for neurogenesis. Cell Rep 2023; 42:112194. [PMID: 36857184 PMCID: PMC10123761 DOI: 10.1016/j.celrep.2023.112194] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/24/2022] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
The enteric nervous system (ENS) consists of glial cells (EGCs) and neurons derived from neural crest precursors. EGCs retain capacity for large-scale neurogenesis in culture, and in vivo lineage tracing has identified neurons derived from glial cells in response to inflammation. We thus hypothesize that EGCs possess a chromatin structure poised for neurogenesis. We use single-cell multiome sequencing to simultaneously assess transcription and chromatin accessibility in EGCs undergoing spontaneous neurogenesis in culture, as well as small intestine myenteric plexus EGCs. Cultured EGCs maintain open chromatin at genomic loci accessible in neurons, and neurogenesis from EGCs involves dynamic chromatin rearrangements with a net decrease in accessible chromatin. A subset of in vivo EGCs, highly enriched within the myenteric ganglia and that persist into adulthood, have a gene expression program and chromatin state consistent with neurogenic potential. These results clarify the mechanisms underlying EGC potential for neuronal fate transition.
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Affiliation(s)
- Richard A Guyer
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Rhian Stavely
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Keiramarie Robertson
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Sukhada Bhave
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica L Mueller
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole M Picard
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Julia A Kaltschmidt
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan M Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA, USA.
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12
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Seo Y, Han S, Song BW, Chang JW, Na YC, Chang WS. Endogenous Neural Stem Cell Activation after Low-Intensity Focused Ultrasound-Induced Blood–Brain Barrier Modulation. Int J Mol Sci 2023; 24:ijms24065712. [PMID: 36982785 PMCID: PMC10056062 DOI: 10.3390/ijms24065712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Endogenous neural stem cells (eNSCs) in the adult brain, which have the potential to self-renew and differentiate into functional, tissue-appropriate cell types, have raised new expectations for neurological disease therapy. Low-intensity focused ultrasound (LIFUS)-induced blood–brain barrier modulation has been reported to promote neurogenesis. Although these studies have reported improved behavioral performance and enhanced expression of brain biomarkers after LIFUS, indicating increased neurogenesis, the precise mechanism remains unclear. In this study, we evaluated eNSC activation as a mechanism for neurogenesis after LIFUS-induced blood–brain barrier modulation. We evaluated the specific eNSC markers, Sox-2 and nestin, to confirm the activation of eNSCs. We also performed 3′-deoxy-3′[18F] fluoro-L-thymidine positron emission tomography ([18F] FLT-PET) to evaluate the activation of eNSCs. The expression of Sox-2 and nestin was significantly upregulated 1 week after LIFUS. After 1 week, the upregulated expression decreased sequentially; after 4 weeks, the upregulated expression returned to that of the control group. [18F] FLT-PET images also showed higher stem cell activity after 1 week. The results of this study indicated that LIFUS could activate eNSCs and induce adult neurogenesis. These results show that LIFUS may be useful as an effective treatment for patients with neurological damage or neurological disorders in clinical settings.
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Affiliation(s)
- Younghee Seo
- Department of Neurosurgery and Brain Research Institute, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sangheon Han
- Department of Neurosurgery and Brain Research Institute, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Byeong-Wook Song
- Department for Medical Science, College of Medicine, Catholic Kwandong University, Gangwon-do, Gangneung City 25601, Republic of Korea
| | - Jin Woo Chang
- Department of Neurosurgery and Brain Research Institute, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Cheol Na
- Department of Neurosurgery and Brain Research Institute, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
- Department of Neurosurgery, Catholic Kwandong University College of Medicine, International St. Mary’s Hospital, Seo-gu, Incheon Metropolitan City 22711, Republic of Korea
- Correspondence: (Y.C.N.); (W.S.C.)
| | - Won Seok Chang
- Department of Neurosurgery and Brain Research Institute, Yonsei University College of Medicine, Seodaemun-gu, Seoul 03722, Republic of Korea
- Correspondence: (Y.C.N.); (W.S.C.)
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13
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Fetit R, Barbato MI, Theil T, Pratt T, Price DJ. 16p11.2 deletion accelerates subpallial maturation and increases variability in human iPSC-derived ventral telencephalic organoids. Development 2023; 150:dev201227. [PMID: 36826401 PMCID: PMC10110424 DOI: 10.1242/dev.201227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
Inhibitory interneurons regulate cortical circuit activity, and their dysfunction has been implicated in autism spectrum disorder (ASD). 16p11.2 microdeletions are genetically linked to 1% of ASD cases. However, few studies investigate the effects of this microdeletion on interneuron development. Using ventral telencephalic organoids derived from human induced pluripotent stem cells, we have investigated the effect of this microdeletion on organoid size, progenitor proliferation and organisation into neural rosettes, ganglionic eminence marker expression at early developmental timepoints, and expression of the neuronal marker NEUN at later stages. At early stages, deletion organoids exhibited greater variations in size with concomitant increases in relative neural rosette area and the expression of the ventral telencephalic marker COUPTFII, with increased variability in these properties. Cell cycle analysis revealed an increase in total cell cycle length caused primarily by an elongated G1 phase, the duration of which also varied more than normal. At later stages, deletion organoids increased their NEUN expression. We propose that 16p11.2 microdeletions increase developmental variability and may contribute to ASD aetiology by lengthening the cell cycle of ventral progenitors, promoting premature differentiation into interneurons.
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Affiliation(s)
- Rana Fetit
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Michela Ilaria Barbato
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Theil
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Pratt
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - David J. Price
- Simons Initiative for the Developing Brain, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, Hugh Robson Building, Edinburgh Medical School Biomedical Sciences, The University of Edinburgh, Edinburgh EH8 9XD, UK
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14
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Dong Z, He W, Lin G, Chen X, Cao S, Guan T, Sun Y, Zhang Y, Qi M, Guo B, Zhou Z, Zhuo R, Wu R, Liu M, Liu Y. Histone acetyltransferase KAT2A modulates neural stem cell differentiation and proliferation by inducing degradation of the transcription factor PAX6. J Biol Chem 2023; 299:103020. [PMID: 36791914 PMCID: PMC10011063 DOI: 10.1016/j.jbc.2023.103020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Neural stem cells (NSCs) proliferation and differentiation rely on proper expression and post-translational modification of transcription factors involved in the determination of cell fate. Further characterization is needed to connect modifying enzymes with their transcription factor substrates in the regulation of these processes. Here, we demonstrated that the inhibition of KAT2A, a histone acetyltransferase, leads to a phenotype of small eyes in the developing embryo of zebrafish, which is associated with enhanced proliferation and apoptosis of NSCs in zebrafish eyes. We confirmed that this phenotype is mediated by the evaluated level of PAX6 protein. We further verified that KAT2A negatively regulates PAX6 at the protein level in cultured neural stem cells of rat cerebral cortex. We revealed that PAX6 is a novel acetylation substrate of KAT2A, and the acetylation of PAX6 promotes its ubiquitination mediated by the E3 ligase RNF8 that facilitated PAX6 degradation. Our study proposes that KAT2A inhibition results in accelerated proliferation, delayed differentiation, or apoptosis, depending on the context of PAX6 dosage. Thus, the KAT2A/PAX6 axis plays an essential role to keep a balance between the self-renewal and differentiation of NSCs.
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Affiliation(s)
- Zhangji Dong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Wei He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ge Lin
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Xu Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Sixian Cao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Tuchen Guan
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ying Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Yufang Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Mengwei Qi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Beibei Guo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Zhihao Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Run Zhuo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China.
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China.
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15
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Radoszkiewicz K, Jezierska-Woźniak K, Waśniewski T, Sarnowska A. Understanding Intra- and Inter-Species Variability in Neural Stem Cells' Biology Is Key to Their Successful Cryopreservation, Culture, and Propagation. Cells 2023; 12:cells12030488. [PMID: 36766833 PMCID: PMC9914787 DOI: 10.3390/cells12030488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Although clinical trials on human neural stem cells (hNSCs) have already been implemented in the treatment of neurological diseases and they have demonstrated their therapeutic effects, many questions remain in the field of preclinical research regarding the biology of these cells, their therapeutic properties, and their neurorestorative potential. Unfortunately, scientific reports are inconsistent and much of the NSCs research has been conducted on rodents rather than human cells for ethical reasons or due to insufficient cell material. Therefore, a question arises as to whether or which conclusions drawn on the isolation, cell survival, proliferation, or cell fate observed in vitro in rodent NSCs can be introduced into clinical applications. This paper presents the effects of different spatial, nutritional, and dissociation conditions on NSCs' functional properties, which are highly species-dependent. Our study confirmed that the discrepancies in the available literature on NSCs survival, proliferation, and fate did not only depend on intra-species factors and applied environmental conditions, but they were also affected by significant inter-species variability. Human and rodent NSCs share one feature, i.e., the necessity to be cultured immediately after isolation, which significantly maintains their survival. Additionally, in the absence of experiments on human cells, rat NSCs biology (neurosphere formation potential and neural differentiation stage) seems closer to that of humans rather than mice in response to environmental factors.
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Affiliation(s)
- Klaudia Radoszkiewicz
- Translational Platform for Regenerative Medicine, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Katarzyna Jezierska-Woźniak
- Department of Neurosurgery, Laboratory for Regenerative Medicine, Stem Cells Bank, University of Warmia and Mazury in Olsztyn, 10-720 Olsztyn, Poland
| | - Tomasz Waśniewski
- Department of Obstetrics and Gynaecology, School of Medicine, Collegium Medicum, University of Warmia and Mazury, 10-561 Olsztyn, Poland
| | - Anna Sarnowska
- Translational Platform for Regenerative Medicine, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-608-6598
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16
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Wang X, Fan W, Xu Z, Zhang Q, Li N, Li R, Wang G, He S, Li W, Liao D, Zhang Z, Shu N, Huang J, Zhao C, Hou S. SOX2-positive retinal stem cells are identified in adult human pars plicata by single-cell transcriptomic analyses. MedComm (Beijing) 2023; 4:e198. [PMID: 36582303 PMCID: PMC9790047 DOI: 10.1002/mco2.198] [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: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/26/2022] Open
Abstract
Stem cell therapy is a promising strategy to rescue visual impairment caused by retinal degeneration. Previous studies have proposed controversial theories about whether in situ retinal stem cells (RSCs) are present in adult human eye tissue. Single-cell RNA sequencing (scRNA-seq) has emerged as one of the most powerful tools to reveal the heterogeneity of tissue cells. By using scRNA-seq, we explored the cell heterogeneity of different subregions of adult human eyes, including pars plicata, pars plana, retinal pigment epithelium (RPE), iris, and neural retina (NR). We identified one subpopulation expressing SRY-box transcription factor 2 (SOX2) as RSCs, which were present in the pars plicata of the adult human eye. Further analysis showed the identified subpopulation of RSCs expressed specific markers aquaporin 1 (AQP1) and tetraspanin 12 (TSPAN12). We, therefore, isolated this subpopulation using these two markers by flow sorting and found that the isolated RSCs could proliferate and differentiate into some retinal cell types, including photoreceptors, neurons, RPE cells, microglia, astrocytes, horizontal cells, bipolar cells, and ganglion cells; whereas, AQP1- TSPAN12- cells did not have this differentiation potential. In conclusion, our results showed that SOX2-positive RSCs are present in the pars plicata and may be valuable for treating human retinal diseases due to their proliferation and differentiation potential.
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17
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Hooked Up from a Distance: Charting Genome-Wide Long-Range Interaction Maps in Neural Cells Chromatin to Identify Novel Candidate Genes for Neurodevelopmental Disorders. Int J Mol Sci 2023; 24:ijms24021164. [PMID: 36674677 PMCID: PMC9863356 DOI: 10.3390/ijms24021164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/10/2023] Open
Abstract
DNA sequence variants (single nucleotide polymorphisms or variants, SNPs/SNVs; copy number variants, CNVs) associated to neurodevelopmental disorders (NDD) and traits often map on putative transcriptional regulatory elements, including, in particular, enhancers. However, the genes controlled by these enhancers remain poorly defined. Traditionally, the activity of a given enhancer, and the effect of its possible alteration associated to the sequence variants, has been thought to influence the nearest gene promoter. However, the obtainment of genome-wide long-range interaction maps in neural cells chromatin challenged this view, showing that a given enhancer is very frequently not connected to the nearest promoter, but to a more distant one, skipping genes in between. In this Perspective, we review some recent papers, who generated long-range interaction maps (by HiC, RNApolII ChIA-PET, Capture-HiC, or PLACseq), and overlapped the identified long-range interacting DNA segments with DNA sequence variants associated to NDD (such as schizophrenia, bipolar disorder and autism) and traits (intelligence). This strategy allowed to attribute the function of enhancers, hosting the NDD-related sequence variants, to a connected gene promoter lying far away on the linear chromosome map. Some of these enhancer-connected genes had indeed been already identified as contributive to the diseases, by the identification of mutations within the gene's protein-coding regions (exons), validating the approach. Significantly, however, the connected genes also include many genes that were not previously found mutated in their exons, pointing to novel candidate contributors to NDD and traits. Thus, long-range interaction maps, in combination with DNA variants detected in association with NDD, can be used as "pointers" to identify novel candidate disease-relevant genes. Functional manipulation of the long-range interaction network involving enhancers and promoters by CRISPR-Cas9-based approaches is beginning to probe for the functional significance of the identified interactions, and the enhancers and the genes involved, improving our understanding of neural development and its pathology.
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18
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Chang FC, Zhou Y, James MM, Zareie HM, Ando Y, Yang J, Zhang M. Effect of Degree of Deacetylation of Chitosan/Chitin on Human Neural Stem Cell Culture. Macromol Biosci 2023; 23:e2200389. [PMID: 36281904 DOI: 10.1002/mabi.202200389] [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: 10/04/2022] [Indexed: 01/19/2023]
Abstract
Stem cell therapy and research for neural diseases depends on reliable reproduction of neural stem cells. Chitosan-based materials have been proposed as a substrate for culturing human neural stem cells (hNSCs) in the pursuit of clinically compatible culture conditions that are chemically defined and compliant with good manufacturing practices. The physical and biochemical properties of chitosan and chitin are strongly regulated by the degree of deacetylation (DD). However, the effect of DD on hNSC behavior has not been systematically investigated. In this study, films with DD ranging from 93% to 14% are fabricated with chitosan and chitin. Under xeno-free conditions, hNSCs proliferate preferentially on films with a higher DD, exhibiting adherent morphology and retaining multipotency. Lowering the DD leads to formation of neural stem cell spheroids due to unsteady adhesion. The neural spheroids present NSC multipotency protein expression reduction and cytoplasmic translocation. This study provides an insight into the influence of the DD on hNSCs behavior and may serve as a guideline for hNSC research using chitosan-based biomaterials. It demonstrates the capability of controlling hNSC fate by simply tailoring the DD of chitosan.
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Affiliation(s)
- Fei-Chien Chang
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yang Zhou
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Matthew Michael James
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Hadi M Zareie
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA.,School of Mathematical and Physical Science, University of Technology, Ultimo, Sydney, NSW, 2007, Australia
| | - Yoshiki Ando
- Materials Department, Medical R&D Center, Corporate R&D Group, KYOCERA Corporation, Yasu, Shiga, 520-2362, Japan
| | - Jihui Yang
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Miqin Zhang
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
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Ehnes DD, Alghadeer A, Hanson-Drury S, Zhao YT, Tilmes G, Mathieu J, Ruohola-Baker H. Sci-Seq of Human Fetal Salivary Tissue Introduces Human Transcriptional Paradigms and a Novel Cell Population. FRONTIERS IN DENTAL MEDICINE 2022; 3:887057. [PMID: 36540608 PMCID: PMC9762771 DOI: 10.3389/fdmed.2022.887057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Multiple pathologies and non-pathological factors can disrupt the function of the non-regenerative human salivary gland including cancer and cancer therapeutics, autoimmune diseases, infections, pharmaceutical side effects, and traumatic injury. Despite the wide range of pathologies, no therapeutic or regenerative approaches exist to address salivary gland loss, likely due to significant gaps in our understanding of salivary gland development. Moreover, identifying the tissue of origin when diagnosing salivary carcinomas requires an understanding of human fetal development. Using computational tools, we identify developmental branchpoints, a novel stem cell-like population, and key signaling pathways in the human developing salivary glands by analyzing our human fetal single-cell sequencing data. Trajectory and transcriptional analysis suggest that the earliest progenitors yield excretory duct and myoepithelial cells and a transitional population that will yield later ductal cell types. Importantly, this single-cell analysis revealed a previously undescribed population of stem cell-like cells that are derived from SD and expresses high levels of genes associated with stem cell-like function. We have observed these rare cells, not in a single niche location but dispersed within the developing duct at later developmental stages. Our studies introduce new human-specific developmental paradigms for the salivary gland and lay the groundwork for the development of translational human therapeutics.
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Affiliation(s)
- Devon Duron Ehnes
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Ammar Alghadeer
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Sesha Hanson-Drury
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Yan Ting Zhao
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Gwen Tilmes
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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20
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Hernández-Pérez OR, Juárez-Navarro KJ, Diaz NF, Padilla-Camberos E, Beltran-Garcia MJ, Cardenas-Castrejon D, Corona-Perez H, Hernández-Jiménez C, Díaz-Martínez NE. Biomolecules resveratrol + coenzyme Q10 recover the cell state of human mesenchymal stem cells after 1-methyl-4-phenylpyridinium-induced damage and improve proliferation and neural differentiation. Front Neurosci 2022; 16:929590. [PMID: 36117620 PMCID: PMC9471188 DOI: 10.3389/fnins.2022.929590] [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: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/20/2022] Open
Abstract
Neurodegenerative disorders are a critical affection with a high incidence around the world. Currently, there are no effective treatments to solve this problem. However, the application of mesenchymal stem cells (MSCs) and antioxidants in neurodegenerative diseases has shown to be a promising tool due to their multiple therapeutic effects. This work aimed to evaluate the effects of a combination of resveratrol (RSV) and coenzyme Q10 (CoQ10) on the proliferation and differentiation of MSC and the protector effects in induced damage. To characterize the MSCs, we performed flow cytometry, protocols of cellular differentiation, and immunocytochemistry analysis. The impact of RSV + CoQ10 in proliferation was evaluated by supplementing 2.5 and 10 μM of RSV + CoQ10 in a cellular kinetic for 14 days. Cell viability and lactate dehydrogenase levels (LDH) were also analyzed. The protective effect of RSV + CoQ10 was assessed by supplementing the treatment to damaged MSCs by 1-methyl-4-phenylpyridinium (MPP+); cellular viability, LDH, and reactive oxygen species (ROS) were evaluated.. MSCs expressed the surface markers CD44, CD73, CD90, and CD105 and showed multipotential ability. The combination of RSV + CoQ10 increased the proliferation potential and cell viability and decreased LDH levels. In addition, it reverted the effect of MPP+-induced damage in MSCs to enhance cell viability and decrease LDH and ROS. Finally, RSV + CoQ10 promoted the differentiation of neural progenitors. The combination of RSV + CoQ10 represents a potential treatment to improve MSCs capacities and protect against neurodegenerative damage.
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Affiliation(s)
- Oscar R. Hernández-Pérez
- Laboratorio de Reprogramación Celular y Bioingeniería de Tejidos, Biotecnología Médica y Farmacéutica, CONACYT Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | - Karen J. Juárez-Navarro
- Laboratorio de Reprogramación Celular y Bioingeniería de Tejidos, Biotecnología Médica y Farmacéutica, CONACYT Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | - Nestor F. Diaz
- Instituto Nacional de Perinatología (INPER), Mexico City, Mexico
| | - Eduardo Padilla-Camberos
- Biotecnología Médica y Farmacéutica, CONACYT Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
| | - Miguel J. Beltran-Garcia
- Departamento de Biotecnológicas y Ambientales, Universidad Autónoma de Guadalajara, Zapopan, Mexico
| | | | | | | | - Néstor E. Díaz-Martínez
- Laboratorio de Reprogramación Celular y Bioingeniería de Tejidos, Biotecnología Médica y Farmacéutica, CONACYT Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Mexico
- *Correspondence: Néstor E. Díaz-Martínez,
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21
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D’Aurizio R, Catona O, Pitasi M, Li YE, Ren B, Nicolis SK. Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease. Int J Mol Sci 2022; 23:ijms23147964. [PMID: 35887306 PMCID: PMC9322198 DOI: 10.3390/ijms23147964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding variation in complex human disease has been well established by genome-wide association studies, and is thought to involve regulatory elements, such as enhancers, whose variation affects the expression of the gene responsible for the disease. The regulatory elements often lie far from the gene they regulate, or within introns of genes differing from the regulated gene, making it difficult to identify the gene whose function is affected by a given enhancer variation. Enhancers are connected to their target gene promoters via long-range physical interactions (loops). In our study, we re-mapped, onto the human genome, more than 10,000 enhancers connected to promoters via long-range interactions, that we had previously identified in mouse brain-derived neural stem cells by RNApolII-ChIA-PET analysis, coupled to ChIP-seq mapping of DNA/chromatin regions carrying epigenetic enhancer marks. These interactions are thought to be functionally relevant. We discovered, in the human genome, thousands of DNA regions syntenic with the interacting mouse DNA regions (enhancers and connected promoters). We further annotated these human regions regarding their overlap with sequence variants (single nucleotide polymorphisms, SNPs; copy number variants, CNVs), that were previously associated with neurodevelopmental disease in humans. We document various cases in which the genetic variant, associated in humans to neurodevelopmental disease, affects an enhancer involved in long-range interactions: SNPs, previously identified by genome-wide association studies to be associated with schizophrenia, bipolar disorder, and intelligence, are located within our human syntenic enhancers, and alter transcription factor recognition sites. Similarly, CNVs associated to autism spectrum disease and other neurodevelopmental disorders overlap with our human syntenic enhancers. Some of these enhancers are connected (in mice) to homologs of genes already associated to the human disease, strengthening the hypothesis that the gene is indeed involved in the disease. Other enhancers are connected to genes not previously associated with the disease, pointing to their possible pathogenetic involvement. Our observations provide a resource for further exploration of neural disease, in parallel with the now widespread genome-wide identification of DNA variants in patients with neural disease.
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Affiliation(s)
- Romina D’Aurizio
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), 56124 Pisa, Italy;
- Correspondence:
| | - Orazio Catona
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), 56124 Pisa, Italy;
| | - Mattia Pitasi
- Dipartimento di Biotecnologie e Bioscienze, University of Milano-Bicocca, 20126 Milano, Italy; (M.P.); (S.K.N.)
| | - Yang Eric Li
- University of California San Diego, La Jolla, CA 92093, USA; (Y.E.L.); (B.R.)
| | - Bing Ren
- University of California San Diego, La Jolla, CA 92093, USA; (Y.E.L.); (B.R.)
| | - Silvia Kirsten Nicolis
- Dipartimento di Biotecnologie e Bioscienze, University of Milano-Bicocca, 20126 Milano, Italy; (M.P.); (S.K.N.)
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22
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Patients' Stem Cells Differentiation in a 3D Environment as a Promising Experimental Tool for the Study of Amyotrophic Lateral Sclerosis. Int J Mol Sci 2022; 23:ijms23105344. [PMID: 35628156 PMCID: PMC9141644 DOI: 10.3390/ijms23105344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease (NDD) that affects motor neurons, causing weakness, muscle atrophy and spasticity. Unfortunately, there are only symptomatic treatments available. Two important innovations in recent years are three-dimensional (3D) bioprinting and induced pluripotent stem cells (iPSCs). The aim of this work was to demonstrate the robustness of 3D cultures for the differentiation of stem cells for the study of ALS. We reprogrammed healthy and sALS peripheral blood mononuclear cells (PBMCs) in iPSCs and differentiated them in neural stem cells (NSCs) in 2D. NSCs were printed in 3D hydrogel-based constructs and subsequently differentiated first in motor neuron progenitors and finally in motor neurons. Every step of differentiation was tested for cell viability and characterized by confocal microscopy and RT-qPCR. Finally, we tested the electrophysiological characteristics of included NSC34. We found that NSCs maintained good viability during the 3D differentiation. Our results suggest that the hydrogel does not interfere with the correct differentiation process or with the electrophysiological features of the included cells. Such evidence confirmed that 3D bioprinting can be considered a good model for the study of ALS pathogenesis.
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23
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Mercurio S, Serra L, Pagin M, Nicolis SK. Deconstructing Sox2 Function in Brain Development and Disease. Cells 2022; 11:cells11101604. [PMID: 35626641 PMCID: PMC9139651 DOI: 10.3390/cells11101604] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
SOX2 is a transcription factor conserved throughout vertebrate evolution, whose expression marks the central nervous system from the earliest developmental stages. In humans, SOX2 mutation leads to a spectrum of CNS defects, including vision and hippocampus impairments, intellectual disability, and motor control problems. Here, we review how conditional Sox2 knockout (cKO) in mouse with different Cre recombinases leads to very diverse phenotypes in different regions of the developing and postnatal brain. Surprisingly, despite the widespread expression of Sox2 in neural stem/progenitor cells of the developing neural tube, some regions (hippocampus, ventral forebrain) appear much more vulnerable than others to Sox2 deletion. Furthermore, the stage of Sox2 deletion is also a critical determinant of the resulting defects, pointing to a stage-specificity of SOX2 function. Finally, cKOs illuminate the importance of SOX2 function in different cell types according to the different affected brain regions (neural precursors, GABAergic interneurons, glutamatergic projection neurons, Bergmann glia). We also review human genetics data regarding the brain defects identified in patients carrying mutations within human SOX2 and examine the parallels with mouse mutants. Functional genomics approaches have started to identify SOX2 molecular targets, and their relevance for SOX2 function in brain development and disease will be discussed.
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24
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Zhang Z, Zamojski M, Smith GR, Willis TL, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper MAS, Vasoya M, Cheng WS, Zaslavsky E, Nair VD, Turgeon JL, Bernard DJ, Troyanskaya OG, Andoniadou CL, Sealfon SC, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell Rep 2022; 38:110467. [PMID: 35263594 PMCID: PMC8957708 DOI: 10.1016/j.celrep.2022.110467] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/23/2021] [Accepted: 02/09/2022] [Indexed: 01/07/2023] Open
Abstract
Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource from pediatric, adult, and aged postmortem pituitaries (snpituitaryatlas.princeton.edu) and characterize cell-type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early-life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors that are significantly associated with gene expression in PSCs compared with other cell types and within PSCs. We identify distinct deterministic mechanisms that contribute to heterogeneous marker expression within PSCs. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes and cell type identity. This study profiles the gene expression and chromatin accessibility landscapes in postmortem male and female pituitaries of different ages using single nucleus multiomics technologies. Zhang et al. characterize the pituitary stem cell population and develop computational methods, which allow us to elucidate regulatory mechanisms underlying pituitary stem cell identity.
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Affiliation(s)
- Zidong Zhang
- Lewis-Sigler Institute for Integrative Genomics and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Thea L Willis
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Val Yianni
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Natalia Mendelev
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Nitish Seenarine
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mary Anne S Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Wan Sze Cheng
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Judith L Turgeon
- Department of Internal Medicine, University of California, Davis, Davis, CA, USA
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Cynthia L Andoniadou
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK; Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
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25
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Noack F, Vangelisti S, Raffl G, Carido M, Diwakar J, Chong F, Bonev B. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. Nat Neurosci 2022; 25:154-167. [PMID: 35132236 PMCID: PMC8825286 DOI: 10.1038/s41593-021-01002-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022]
Abstract
How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex. By profiling multiple epigenetic layers and enhancer activity in vivo, the authors show a widespread remodeling of the regulatory landscape during mouse cortical development and identify Neurog2 as a key transcription factor driving this process.
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Affiliation(s)
- Florian Noack
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Silvia Vangelisti
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gerald Raffl
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Madalena Carido
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jeisimhan Diwakar
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Faye Chong
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany. .,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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26
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Editing SOX Genes by CRISPR-Cas: Current Insights and Future Perspectives. Int J Mol Sci 2021; 22:ijms222111321. [PMID: 34768751 PMCID: PMC8583549 DOI: 10.3390/ijms222111321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 01/16/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent years, CRISPR-Cas technology was rapidly developed and different types of DNA or RNA sequence editors, gene activator or repressor, and epigenome modulators established. The versatility and feasibility of CRISPR-Cas technology has introduced this system as the most suitable tool for discovering and studying the mechanism of specific genes and also for generating appropriate cell and animal models. SOX genes play crucial roles in development processes and stemness. To elucidate the exact roles of SOX factors and their partners in tissue hemostasis and cell regeneration, generating appropriate in vitro and in vivo models is crucial. In line with these premises, CRISPR-Cas technology is a promising tool for studying different family members of SOX transcription factors. In this review, we aim to highlight the importance of CRISPR-Cas and summarize the applications of this novel, promising technology in studying and decoding the function of different members of the SOX gene family.
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27
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Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG. Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag. Dev Dyn 2021; 251:729-742. [PMID: 34647658 DOI: 10.1002/dvdy.430] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis. RESULTS To overcome these challenges, we adapted the chromatin profiling methods Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and CUT&Tag for use in zebrafish and applied these methods to generate high-resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences. CONCLUSIONS Our results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
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Affiliation(s)
| | | | - Fanju W Meng
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, Georgia, USA
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28
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Pagin M, Pernebrink M, Giubbolini S, Barone C, Sambruni G, Zhu Y, Chiara M, Ottolenghi S, Pavesi G, Wei CL, Cantù C, Nicolis SK. Sox2 controls neural stem cell self-renewal through a Fos-centered gene regulatory network. Stem Cells 2021; 39:1107-1119. [PMID: 33739574 DOI: 10.1002/stem.3373] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
The Sox2 transcription factor is necessary for the long-term self-renewal of neural stem cells (NSCs). Its mechanism of action is still poorly defined. To identify molecules regulated by Sox2, and acting in mouse NSC maintenance, we transduced, into Sox2-deleted NSC, genes whose expression is strongly downregulated following Sox2 loss (Fos, Jun, Egr2), individually or in combination. Fos alone rescued long-term proliferation, as shown by in vitro cell growth and clonal analysis. Furthermore, pharmacological inhibition by T-5224 of FOS/JUN AP1 complex binding to its targets decreased cell proliferation and expression of the putative target Suppressor of cytokine signaling 3 (Socs3). Additionally, Fos requirement for efficient long-term proliferation was demonstrated by the reduction of NSC clones capable of long-term expansion following CRISPR/Cas9-mediated Fos inactivation. Previous work showed that the Socs3 gene is strongly downregulated following Sox2 deletion, and its re-expression by lentiviral transduction rescues long-term NSC proliferation. Fos appears to be an upstream regulator of Socs3, possibly together with Jun and Egr2; indeed, Sox2 re-expression in Sox2-deleted NSC progressively activates both Fos and Socs3 expression; in turn, Fos transduction activates Socs3 expression. Based on available SOX2 ChIPseq and ChIA-PET data, we propose a model whereby Sox2 is a direct activator of both Socs3 and Fos, as well as possibly Jun and Egr2; furthermore, we provide direct evidence for FOS and JUN binding on Socs3 promoter, suggesting direct transcriptional regulation. These results provide the basis for developing a model of a network of interactions, regulating critical effectors of NSC proliferation and long-term maintenance.
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Affiliation(s)
- Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Mattias Pernebrink
- Wallenberg Centre for Molecular Medicine (WCMM) and Department of Biomedical and Clinical Sciences, Faculty of Health Science, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science, Linköping University, Linköping, Sweden
| | - Simone Giubbolini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Cristiana Barone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Gaia Sambruni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Matteo Chiara
- Department of Biosciences, University of Milano, Milan, Italy
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, Milan, Italy
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine (WCMM) and Department of Biomedical and Clinical Sciences, Faculty of Health Science, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science, Linköping University, Linköping, Sweden
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Pagin M, Pernebrink M, Pitasi M, Malighetti F, Ngan CY, Ottolenghi S, Pavesi G, Cantù C, Nicolis SK. FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes. Cells 2021; 10:cells10071757. [PMID: 34359927 PMCID: PMC8303191 DOI: 10.3390/cells10071757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
The transcription factor SOX2 is important for brain development and for neural stem cells (NSC) maintenance. Sox2-deleted (Sox2-del) NSC from neonatal mouse brain are lost after few passages in culture. Two highly expressed genes, Fos and Socs3, are strongly downregulated in Sox2-del NSC; we previously showed that Fos or Socs3 overexpression by lentiviral transduction fully rescues NSC's long-term maintenance in culture. Sox2-del NSC are severely defective in neuronal production when induced to differentiate. NSC rescued by Sox2 reintroduction correctly differentiate into neurons. Similarly, Fos transduction rescues normal or even increased numbers of immature neurons expressing beta-tubulinIII, but not more differentiated markers (MAP2). Additionally, many cells with both beta-tubulinIII and GFAP expression appear, indicating that FOS stimulates the initial differentiation of a "mixed" neuronal/glial progenitor. The unexpected rescue by FOS suggested that FOS, a SOX2 transcriptional target, might act on neuronal genes, together with SOX2. CUT&RUN analysis to detect genome-wide binding of SOX2, FOS, and JUN (the AP1 complex) revealed that a high proportion of genes expressed in NSC are bound by both SOX2 and AP1. Downregulated genes in Sox2-del NSC are highly enriched in genes that are also expressed in neurons, and a high proportion of the "neuronal" genes are bound by both SOX2 and AP1.
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Affiliation(s)
- Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (M.P.); (M.P.); (F.M.); (S.O.)
| | - Mattias Pernebrink
- Wallenberg Centre for Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden;
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Mattia Pitasi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (M.P.); (M.P.); (F.M.); (S.O.)
| | - Federica Malighetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (M.P.); (M.P.); (F.M.); (S.O.)
| | - Chew-Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (M.P.); (M.P.); (F.M.); (S.O.)
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20134 Milano, Italy;
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden;
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
- Correspondence: (C.C.); (S.K.N.)
| | - Silvia K. Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (M.P.); (M.P.); (F.M.); (S.O.)
- Correspondence: (C.C.); (S.K.N.)
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