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Islam M, Behura SK. Role of caveolin-1 in metabolic programming of fetal brain. iScience 2023; 26:107710. [PMID: 37720105 PMCID: PMC10500482 DOI: 10.1016/j.isci.2023.107710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/10/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Mice lacking caveolin-1 (Cav1), a key protein of plasma membrane, exhibit brain aging at an early adult stage. Here, integrative analyses of metabolomics, transcriptomics, epigenetics, and single-cell data were performed to test the hypothesis that metabolic deregulation of fetal brain due to the ablation of Cav1 is linked to brain aging in these mice. The results of this study show that lack of Cav1 caused deregulation in the lipid and amino acid metabolism in the fetal brain, and genes associated with these deregulated metabolites were significantly altered in the brain upon aging. Moreover, ablation of Cav1 deregulated several metabolic genes in specific cell types of the fetal brain and impacted DNA methylation of those genes in coordination with mouse epigenetic clock. The findings of this study suggest that the aging program of brain is confounded by metabolic abnormalities in the fetal stage due to the absence of Cav1.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, 920 East Campus Drive, University of Missouri, Columbia, MO 65211, USA
| | - Susanta K. Behura
- Division of Animal Sciences, 920 East Campus Drive, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, USA
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2
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Xu Y, Kusuyama J, Osana S, Matsuhashi S, Li L, Takada H, Inada H, Nagatomi R. Lactate promotes neuronal differentiation of SH-SY5Y cells by lactate-responsive gene sets through NDRG3-dependent and -independent manners. J Biol Chem 2023:104802. [PMID: 37172727 DOI: 10.1016/j.jbc.2023.104802] [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: 10/22/2022] [Revised: 04/23/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Lactate serves as the major glucose alternative to an energy substrate in the brain. Lactate level is increased in the fetal brain from the middle stage of gestation, indicating the involvement of lactate in brain development and neuronal differentiation. Recent reports show that lactate functions as a signaling molecule to regulate gene expression and protein stability. However, the roles of lactate signaling in neuronal cells remain unknown. Here, we showed that lactate promotes the all stages of neuronal differentiation of SH-SY5Y and Neuro2A, human and mouse neuroblastoma cell lines, characterized by increased neuronal marker expression and the rates of neurites extension. Transcriptomics revealed many lactate-responsive genes sets such as SPARCL1 in SH-SY5Y, Neuro2A, and primary embryonic mouse neuronal cells. The effects of lactate on neuronal function were mainly mediated through monocarboxylate transporters 1 (MCT1). We found that NDRG family member 3 (NDRG3), a lactate-binding protein, was highly expressed and stabilized by lactate treatment during neuronal differentiation. Combinative RNA-seq of SH-SY5Y with lactate treatment and NDRG3 knockdown shows that the promotive effects of lactate on neural differentiation are regulated through NDRG3-dependent and independent manners. Moreover, we identified TEA domain family member 1 (TEAD1) and ETS-related transcription factor 4 (ELF4) are the specific transcription factors that are regulated by both lactate and NDRG3 in neuronal differentiation. TEAD1 and ELF4 differently affect the expression of neuronal marker genes in SH-SY5Y cells. These results highlight the biological roles of extracellular and intracellular lactate as a critical signaling molecule that modifies neuronal differentiation.
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Affiliation(s)
- Yidan Xu
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Joji Kusuyama
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan; Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan; Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan; Department of Biosignals and Inheritance, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Shion Osana
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan; Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan; Graduate School of Informatics and Engineering, University of Electro-Communications
| | - Satayuki Matsuhashi
- Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Longfei Li
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroaki Takada
- Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Hitoshi Inada
- Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan; Department of Developmental Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryoichi Nagatomi
- Department of Medicine and Science in Sports and Exercise, Tohoku University Graduate School of Medicine, Sendai, Japan; Division of Biomedical Engineering for Health and Welfare, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.
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Chen Z, King WC, Hwang A, Gerstein M, Zhang J. DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. SCIENCE ADVANCES 2022; 8:eabq3745. [PMID: 36449617 PMCID: PMC9710871 DOI: 10.1126/sciadv.abq3745] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Recent advances in single-cell sequencing technologies have provided unprecedented opportunities to measure the gene expression profile and RNA velocity of individual cells. However, modeling transcriptional dynamics is computationally challenging because of the high-dimensional, sparse nature of the single-cell gene expression measurements and the nonlinear regulatory relationships. Here, we present DeepVelo, a neural network-based ordinary differential equation that can model complex transcriptome dynamics by describing continuous-time gene expression changes within individual cells. We apply DeepVelo to public datasets from different sequencing platforms to (i) formulate transcriptome dynamics on different time scales, (ii) measure the instability of cell states, and (iii) identify developmental driver genes via perturbation analysis. Benchmarking against the state-of-the-art methods shows that DeepVelo can learn a more accurate representation of the velocity field. Furthermore, our perturbation studies reveal that single-cell dynamical systems could exhibit chaotic properties. In summary, DeepVelo allows data-driven discoveries of differential equations that delineate single-cell transcriptome dynamics.
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Affiliation(s)
- Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - William C. King
- Healthcare and Life Sciences, Microsoft, Redmond, WA 98052, USA
| | - Aheyon Hwang
- Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mark Gerstein
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Corresponding author. (M.G.); (J.Z.)
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (M.G.); (J.Z.)
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Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Handfield LF, Asenjo-Martinez A, Lisa-Vargas I, Seemann SE, Lee JTH, Patikas N, Kornum BR, Denham M, Hyttel P, Witter MP, Gorodkin J, Pers TH, Hemberg M, Khodosevich K, Hall VJ. Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming. Front Cell Dev Biol 2022; 10:976549. [PMID: 36046338 PMCID: PMC9420913 DOI: 10.3389/fcell.2022.976549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Stellate cells are principal neurons in the entorhinal cortex that contribute to spatial processing. They also play a role in the context of Alzheimer's disease as they accumulate Amyloid beta early in the disease. Producing human stellate cells from pluripotent stem cells would allow researchers to study early mechanisms of Alzheimer's disease, however, no protocols currently exist for producing such cells. In order to develop novel stem cell protocols, we characterize at high resolution the development of the porcine medial entorhinal cortex by tracing neuronal and glial subtypes from mid-gestation to the adult brain to identify the transcriptomic profile of progenitor and adult stellate cells. Importantly, we could confirm the robustness of our data by extracting developmental factors from the identified intermediate stellate cell cluster and implemented these factors to generate putative intermediate stellate cells from human induced pluripotent stem cells. Six transcription factors identified from the stellate cell cluster including RUNX1T1, SOX5, FOXP1, MEF2C, TCF4, EYA2 were overexpressed using a forward programming approach to produce neurons expressing a unique combination of RELN, SATB2, LEF1 and BCL11B observed in stellate cells. Further analyses of the individual transcription factors led to the discovery that FOXP1 is critical in the reprogramming process and omission of RUNX1T1 and EYA2 enhances neuron conversion. Our findings contribute not only to the profiling of cell types within the developing and adult brain's medial entorhinal cortex but also provides proof-of-concept for using scRNAseq data to produce entorhinal intermediate stellate cells from human pluripotent stem cells in-vitro.
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Affiliation(s)
- Tobias Bergmann
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yong Liu
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jonathan Skov
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leo Mogus
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Julie Lee
- Novo Nordisk Foundation Center for Stem Cell Research, DanStem University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrea Asenjo-Martinez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lisa-Vargas
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stefan E. Seemann
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nikolaos Patikas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Birgitte Rahbek Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Denham
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Poul Hyttel
- Disease, Stem Cells and Embryology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Menno P. Witter
- Kavli Institute for Systems Neuroscience, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tune H. Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa Jane Hall
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Mogenet A, Barlesi F, Besse B, Michiels S, Karimi M, Tran-Dien A, Girard N, Mazieres J, Audigier-Valette C, Locatelli-Sanchez M, Kamal M, Gestraud P, Hamza A, Jacquet A, Jimenez M, Yara S, Greillier L, Bertucci F, Planchard D, Soria JC, Bieche I, Tomasini P. Molecular profiling of non-small-cell lung cancer patients with or without brain metastases included in the randomized SAFIR02-LUNG trial and association with intracranial outcome. Lung Cancer 2022; 169:31-39. [DOI: 10.1016/j.lungcan.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/13/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]
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Fraguas S, Cárcel S, Vivancos C, Molina MD, Ginés J, Mazariegos J, Sekaran T, Bartscherer K, Romero R, Cebrià F. CREB-binding protein (CBP) gene family regulates planarian survival and stem cell differentiation. Dev Biol 2021; 476:53-67. [PMID: 33774010 DOI: 10.1016/j.ydbio.2021.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022]
Abstract
In developmental biology, the regulation of stem cell plasticity and differentiation remains an open question. CBP(CREB-binding protein)/p300 is a conserved gene family that functions as a transcriptional co-activator and plays important roles in a wide range of cellular processes, including cell death, the DNA damage response, and tumorigenesis. The acetyl transferase activity of CBPs is particularly important, as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affect gene expression. Many studies have described the conserved functions of CBP/p300 in stem cell proliferation and differentiation. The planarian Schmidtea mediterranea is an excellent model for the in vivo study of the molecular mechanisms underlying stem cell differentiation during regeneration. However, how this process is regulated genetically and epigenetically is not well-understood yet. We identified 5 distinct Smed-cbp genes in S. mediterranea that show different expression patterns. Functional analyses revealed that Smed-cbp-2 appears to be essential for stem cell maintenance. On the other hand, the silencing of Smed-cbp-3 resulted in the growth of blastemas that were apparently normal, but remained largely unpigmented and undifferentiated. Smed-cbp-3 silencing also affected the differentiation of several cell lineages including neural, epidermal, digestive, and excretory cell types. Finally, we analysed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their functions in planarian stem cell biology. Our results indicate that planarian cbp genes play key roles in stem cell maintenance and differentiation.
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Affiliation(s)
- Susanna Fraguas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain
| | - Sheila Cárcel
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Coral Vivancos
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Ma Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain
| | - Jordi Ginés
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Judith Mazariegos
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | | | | | - Rafael Romero
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain.
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