1
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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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2
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Maleszewska M, Wojnicki K, Mieczkowski J, Król SK, Jacek K, Śmiech M, Kocyk M, Ciechomska IA, Bujko M, Siedlecki J, Kotulska K, Grajkowska W, Zawadzka M, Kaminska B. DMRTA2 supports glioma stem-cell mediated neovascularization in glioblastoma. Cell Death Dis 2024; 15:228. [PMID: 38509074 PMCID: PMC10954651 DOI: 10.1038/s41419-024-06603-y] [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: 09/26/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Glioblastoma (GBM) is the most common and lethal brain tumor in adults. Due to its fast proliferation, diffusive growth and therapy resistance survival times are less than two years for patients with IDH-wildtype GBM. GBM is noted for the considerable cellular heterogeneity, high stemness indices and abundance of the glioma stem-like cells known to support tumor progression, therapeutic resistance and recurrence. Doublesex- and mab-3-related transcription factor a2 (DMRTA2) is involved in maintaining neural progenitor cells (NPC) in the cell cycle and its overexpression suppresses NPC differentiation. Despite the reports showing that primary GBM originates from transformed neural stem/progenitors cells, the role of DMRTA2 in gliomagenesis has not been elucidated so far. Here we show the upregulation of DMRTA2 expression in malignant gliomas. Immunohistochemical staining showed the protein concentrated in small cells with high proliferative potential and cells localized around blood vessels, where it colocalizes with pericyte-specific markers. Knock-down of DMRTA2 in human glioma cells impairs proliferation but not viability of the cells, and affects the formation of the tumor spheres, as evidenced by strong decrease in the number and size of spheres in in vitro cultures. Moreover, the knockdown of DMRTA2 in glioma spheres affects the stabilization of the glioma stem-like cell-dependent tube formation in an in vitro angiogenesis assay. We conclude that DMRTA2 is a new player in gliomagenesis and tumor neovascularization and due to its high expression in malignant gliomas could be a biomarker and potential target for new therapeutic strategies in glioblastoma.
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Affiliation(s)
- Marta Maleszewska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Sylwia K Król
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karol Jacek
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Śmiech
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Kocyk
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Janusz Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Małgorzata Zawadzka
- Laboratory of Neuromuscular Plasticity, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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3
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Li M, Guo H, Carey M, Huang C. Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging. NATURE AGING 2024; 4:62-79. [PMID: 38177329 PMCID: PMC10947366 DOI: 10.1038/s43587-023-00549-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
The decline in stem cell function during aging may affect the regenerative capacity of mammalian organisms; however, the gene regulatory mechanism underlying this decline remains unclear. Here we show that the aging of neural stem and progenitor cells (NSPCs) in the male mouse brain is characterized by a decrease in the generation efficacy of proliferative NSPCs rather than the changes in lineage specificity of NSPCs. We reveal that the downregulation of age-dependent genes in NSPCs drives cell aging by decreasing the population of actively proliferating NSPCs while increasing the expression of quiescence markers. We found that epigenetic deregulation of the MLL complex at promoters leads to transcriptional inactivation of age-dependent genes, highlighting the importance of the dynamic interaction between histone modifiers and gene regulatory elements in regulating transcriptional program of aging cells. Our study sheds light on the key intrinsic mechanisms driving stem cell aging through epigenetic regulators and identifies potential rejuvenation targets that could restore the function of aging stem cells.
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Affiliation(s)
- Meiyang Li
- Center for Neurobiology, Shantou University Medical College, Shantou, China
| | - Hongzhi Guo
- Center for Neurobiology, Shantou University Medical College, Shantou, China
| | - Michael Carey
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA.
| | - Chengyang Huang
- Center for Neurobiology, Shantou University Medical College, Shantou, China.
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA.
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4
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O'Brien BS, Mokry RL, Schumacher ML, Rosas-Rogers S, Terhune SS, Ebert AD. Neutralizing antibodies with neurotropic factor treatment maintain neurodevelopmental gene expression upon exposure to human cytomegalovirus. J Virol 2023; 97:e0069623. [PMID: 37796129 PMCID: PMC10653813 DOI: 10.1128/jvi.00696-23] [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: 05/10/2023] [Accepted: 08/23/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Human cytomegalovirus (HCMV) infection is the leading cause of non-heritable birth defects worldwide. HCMV readily infects the early progenitor cell population of the developing brain, and we have found that infection leads to significantly downregulated expression of key neurodevelopmental transcripts. Currently, there are no approved therapies to prevent or mitigate the effects of congenital HCMV infection. Therefore, we used human-induced pluripotent stem cell-derived organoids and neural progenitor cells to elucidate the glycoproteins and receptors used in the viral entry process and whether antibody neutralization was sufficient to block viral entry and prevent disruption of neurodevelopmental gene expression. We found that blocking viral entry alone was insufficient to maintain the expression of key neurodevelopmental genes, but neutralization combined with neurotrophic factor treatment provided robust protection. Together, these studies offer novel insight into mechanisms of HCMV infection in neural tissues, which may aid future therapeutic development.
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Affiliation(s)
- Benjamin S. O'Brien
- Department of Cell Biology, Neurobiology, and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L. Mokry
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan L. Schumacher
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Suzette Rosas-Rogers
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Scott S. Terhune
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Marquette University and Medical College of Wisconsin Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Allison D. Ebert
- Department of Cell Biology, Neurobiology, and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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5
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The Intricate Epigenetic and Transcriptional Alterations in Pediatric High-Grade Gliomas: Targeting the Crosstalk as the Oncogenic Achilles’ Heel. Biomedicines 2022; 10:biomedicines10061311. [PMID: 35740334 PMCID: PMC9219798 DOI: 10.3390/biomedicines10061311] [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: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are a deadly and heterogenous subgroup of gliomas for which the development of innovative treatments is urgent. Advances in high-throughput molecular techniques have shed light on key epigenetic components of these diseases, such as K27M and G34R/V mutations on histone 3. However, modification of DNA compaction is not sufficient by itself to drive those tumors. Here, we review molecular specificities of pHGGs subcategories in the context of epigenomic rewiring caused by H3 mutations and the subsequent oncogenic interplay with transcriptional signaling pathways co-opted from developmental programs that ultimately leads to gliomagenesis. Understanding how transcriptional and epigenetic alterations synergize in each cellular context in these tumors could allow the identification of new Achilles’ heels, thereby highlighting new levers to improve their therapeutic management.
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6
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O’Brien BS, Mokry RL, Schumacher ML, Pulakanti K, Rao S, Terhune SS, Ebert AD. Downregulation of neurodevelopmental gene expression in iPSC-derived cerebral organoids upon infection by human cytomegalovirus. iScience 2022; 25:104098. [PMID: 35391828 PMCID: PMC8980761 DOI: 10.1016/j.isci.2022.104098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/18/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a betaherpesvirus that can cause severe birth defects including vision and hearing loss, microcephaly, and seizures. Currently, no approved treatment options exist for in utero infections. Here, we aimed to determine the impact of HCMV infection on the transcriptome of developing neurons in an organoid model system. Cell populations isolated from organoids based on a marker for infection and transcriptomes were defined. We uncovered downregulation in key cortical, neurodevelopmental, and functional gene pathways which occurred regardless of the degree of infection. To test the contributions of specific HCMV immediate early proteins known to disrupt neural differentiation, we infected NPCs using a recombinant virus harboring a destabilization domain. Despite suppressing their expression, HCMV-mediated transcriptional downregulation still occurred. Together, our studies have revealed that HCMV infection causes a profound downregulation of neurodevelopmental genes and suggest a role for other viral factors in this process.
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Affiliation(s)
- Benjamin S. O’Brien
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L. Mokry
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Megan L. Schumacher
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Sridhar Rao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Blood Research Institute, Versiti, Milwaukee, WI 53226, USA
| | - Scott S. Terhune
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Allison D. Ebert
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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7
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Kwak HJ, Lee SG, Park SC, Kim JH, Weisblat DA, Park C, Cho SJ. Head transcriptome profiling of glossiphoniid leech ( Helobdella austinensis) reveals clues about proboscis development. Open Biol 2022; 12:210298. [PMID: 35232253 PMCID: PMC8889196 DOI: 10.1098/rsob.210298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cephalization refers to the evolutionary trend towards the concentration of neural tissues, sensory organs, mouth and associated structures at the front end of bilaterian animals. Comprehensive studies on gene expression related to the anterior formation in invertebrate models are currently lacking. In this study, we performed de novo transcriptional profiling on a proboscis-bearing leech (Helobdella austinensis) to identify differentially expressed genes (DEGs) in the anterior versus other parts of the body, in particular to find clues as to the development of the proboscis. Between the head and the body, 132 head-specific DEGs were identified, of which we chose 11 to investigate their developmental function during embryogenesis. Analysis of the spatial expression of these genes using in situ hybridization showed that they were characteristically expressed in the anterior region of the developing embryo, including the proboscis. Our results provide information on the genes related to head formation and insights into the function of proboscis-related genes during organogenesis with the potential roles of genes not yet characterized.
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Affiliation(s)
- Hee-Jin Kwak
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon Cheol Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung-Hyeuk Kim
- Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention, Incheon 22689, Republic of Korea
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
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8
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Unraveling unique and common cell type-specific mechanisms in glioblastoma multiforme. Comput Struct Biotechnol J 2022; 20:90-106. [PMID: 34976314 PMCID: PMC8688884 DOI: 10.1016/j.csbj.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Glioblastoma multiforme persists to be an enigmatic distress in neuro-oncology. Its untethering capacity to thrive in a confined microenvironment, metastasize intracranially, and remain resistant to the systemic treatments, renders this tumour incurable. The glial cell type specificity in GBM remains exploratory. In our study, we aimed to address this problem by studying the GBM at the cell type level in the brain. The cellular makeup of this tumour is composed of genetically altered glial cells which include astrocyte, microglia, oligodendrocyte precursor cell, newly formed oligodendrocyte and myelinating oligodendrocyte. We extracted cell type-specific solid tumour as well as recurrent solid tumour glioma genes, and studied their functional networks and contribution towards gliomagenesis. We identified the principal transcription factors that are found to be regulating vital tumorigenic processes. We also assessed the protein-protein interaction networks at their domain level to get a more microscopic view of the structural and functional operations that transpire in these cells. This yielded the eminent protein regulators exhibiting their regulation in signaling pathways. Overall, our study unveiled regulatory mechanisms in glioma cell types that can be targeted for a more efficient glioma therapy.
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Key Words
- CAMs, Cell adhesion molecules
- CNS, Cental nervous system
- DEG, Differentially expressed genes
- EMT, Epithelial-mesenchymal transistion
- GBM, Glioblastoma multiforme
- GSC, Glioblastoma Stem Cell
- Glial cell types
- Glioblastoma multiforme
- INstruct, a database of structurally resolved protein interactome
- MO, Myelinating oligodendrocyte
- NCBI, National Centre for Biotechnology Information
- NFO, Newly formed oligodendrocyte
- NPC, Neural progenitor cell
- OPC, Oligodendrocyte precursor cell
- PDI, Protein domain interactions
- PDIN, Protein domain interaction network
- PPI, Protein-protein interactions
- Primary solid tumour
- Protein domains
- Protein interaction networks
- RSEM, RNA-seq by Expectation-Maximization
- Recurrent solid tumour transcription factors
- SIGNOR, Signaling Network Open Resource
- TCGA, The Cancer Genome Atlas
- TF, Transcription factor
- TP, Primary solid tumour
- TR, Recurrent solid tumour
- WHO, World health organization
- iDEP, Integrated Differential Expression and Pathway analysis
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9
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Kikkawa T, Osumi N. Multiple Functions of the Dmrt Genes in the Development of the Central Nervous System. Front Neurosci 2021; 15:789583. [PMID: 34955736 PMCID: PMC8695973 DOI: 10.3389/fnins.2021.789583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The Dmrt genes encode the transcription factor containing the DM (doublesex and mab-3) domain, an intertwined zinc finger-like DNA binding module. While Dmrt genes are mainly involved in the sexual development of various species, recent studies have revealed that Dmrt genes, which belong to the DmrtA subfamily, are differentially expressed in the embryonic brain and spinal cord and are essential for the development of the central nervous system. Herein, we summarize recent studies that reveal the multiple functions of the Dmrt genes in various aspects of vertebrate neural development, including brain patterning, neurogenesis, and the specification of neurons.
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Affiliation(s)
- Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
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10
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Bressan RB, Southgate B, Ferguson KM, Blin C, Grant V, Alfazema N, Wills JC, Marques-Torrejon MA, Morrison GM, Ashmore J, Robertson F, Williams CAC, Bradley L, von Kriegsheim A, Anderson RA, Tomlinson SR, Pollard SM. Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants. Cell Stem Cell 2021; 28:877-893.e9. [PMID: 33631116 PMCID: PMC8110245 DOI: 10.1016/j.stem.2021.01.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/22/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023]
Abstract
Point mutations within the histone H3.3 are frequent in aggressive childhood brain tumors known as pediatric high-grade gliomas (pHGGs). Intriguingly, distinct mutations arise in discrete anatomical regions: H3.3-G34R within the forebrain and H3.3-K27M preferentially within the hindbrain. The reasons for this contrasting etiology are unknown. By engineering human fetal neural stem cell cultures from distinct brain regions, we demonstrate here that cell-intrinsic regional identity provides differential responsiveness to each mutant that mirrors the origins of pHGGs. Focusing on H3.3-G34R, we find that the oncohistone supports proliferation of forebrain cells while inducing a cytostatic response in the hindbrain. Mechanistically, H3.3-G34R does not impose widespread transcriptional or epigenetic changes but instead impairs recruitment of ZMYND11, a transcriptional repressor of highly expressed genes. We therefore propose that H3.3-G34R promotes tumorigenesis by focally stabilizing the expression of key progenitor genes, thereby locking initiating forebrain cells into their pre-existing immature state.
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Affiliation(s)
- Raul Bardini Bressan
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Kirsty M Ferguson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Carla Blin
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Vivien Grant
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Neza Alfazema
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Jimi C Wills
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Maria Angeles Marques-Torrejon
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Gillian M Morrison
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - James Ashmore
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Faye Robertson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Charles A C Williams
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Leanne Bradley
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Tomlinson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK.
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11
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Kasahara R, Yuzawa T, Fujii T, Aoki F, Suzuki MG. dmrt11E ortholog is a crucial factor for oogenesis of the domesticated silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 129:103517. [PMID: 33422636 DOI: 10.1016/j.ibmb.2020.103517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 05/26/2023]
Abstract
DMRT (Doublesex and Mab-3-related transcription factor) is a highly conserved transcription factor family involved in sex determination in numerous animal species. One DMRT, dmrt2/dmrt11E, has entirely different functions in invertebrate and vertebrate species, indicating unpredicted functions. Here, we performed functional analysis of the dmrt11E gene in the domesticated silkworm, Bombyx mori. This gene was preferentially expressed in ovarioles at the last larval instar stage. Its mRNA accumulated in ovarian eggs during the adult stage. CRISPR/Cas9-mediated knockout of Bombyx dmrt11E (Bmdmrt11E) caused defects in oogenesis, resulting in the production of abnormal eggs with transparent liquids. These eggs had significantly reduced fertility and lipid levels. Transcriptomic comparisons between ovaries of control and mutant insects at two developmental stages identified six genes that may be under the control of Bmdmrt11E. Finally, we provide a possible model for lipid uptake and storage in eggs of Bombyx mori.
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Affiliation(s)
- Ryota Kasahara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Tomohisa Yuzawa
- Japan Water Systems Corporation, 4-9-4 Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Takehsi Fujii
- Department of Agricultural Science and Technology, Faculty of Agriculture, Setsunan University, 45-1 Nagao-Togecho, Hirakata-shi, Osaka, 573-0101, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562, Japan.
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12
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Fallah HP, Rodrigues MS, Zanardini M, Nóbrega RH, Habibi HR. Effects of gonadotropin-inhibitory hormone on early and late stages of spermatogenesis in ex-vivo culture of zebrafish testis. Mol Cell Endocrinol 2021; 520:111087. [PMID: 33249103 DOI: 10.1016/j.mce.2020.111087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022]
Abstract
Gonadotropin-inhibitory hormone (Gnih) is known to play a role in the regulation of reproduction in vertebrates by influencing gonadotropin release and synthesis. While the endocrine actions of Gnih have been identified in several species, its paracrine/autocrine effects in the control of spermatogenesis are less defined. We have used ex vivo culture of zebrafish testis to investigate the role of gonadal zebrafish Gnih (zGnih) in the regulation of the spermatogenic process. We used FACScan cell cycle analysis, morphometric quantifications, BrdU incorporation and caspase-3 activity assays as well as measuring 11-Ketotestosterone (11-KT) level in the culture media. FACScan analysis and morphometric quantification results demonstrated direct action of zGnih on basal and gonadotropin (Lh and Fsh)-induced spermatogenesis. Treatment with zGnih (10 nM) significantly decreased the number of G0/G1 cells after 7-days of culture while no significant changes were found in the proportion area of spermatogonia cell types. Investigation of DNA synthesis using BrdU (5-Bromo-2'-Deoxyuridine) labeling showed that treatment with zGnih (10 nM) significantly decreased proliferative activity of type A spermatogonia, while increased the mitotic activity of type B spermatogonia. We also showed that treatment with zGnih (100 nM) completely eliminated 11-KT release induced by 100 ng/ml Fsh. Treatment with zGnih (10 and 100 nM) also inhibited both hCG and Fsh-induced spermatogenesis. These results, plus our previous findings, demonstrate that zGnih produced locally in the testis is a component of a complex multifactorial system that regulates testicular function in zebrafish.
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Affiliation(s)
- Hamideh P Fallah
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Maira S Rodrigues
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada; Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Maya Zanardini
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Rafael H Nóbrega
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Hamid R Habibi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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13
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Jin Y, Qin X. Significance of TP53 mutation in treatment and prognosis in head and neck squamous cell carcinoma. Biomark Med 2021; 15:15-28. [PMID: 33427498 DOI: 10.2217/bmm-2020-0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background: TP53 is ranked as the most common mutated gene in head and neck squamous cell carcinoma (HNSCC). Results: The status of TP53 mutation was investigated on International Cancer Genome Consortium and The Cancer Genome Atlas database and TP53-related differentially expressed genes were screened out from transcriptome data and mutation information. A TP53-related prognostic gene signature (TIMP4, ONECUT2, CGNL1, DMRTA2 and NKX2.3) was constructed based on Cox regression analysis and LASSO algorithm. Univariate and multivariate analyses were carried out to identify promising prognosticators for HNSCC. Conclusion: Our findings provide a well-rounded landscape of TP53 mutation in HNSCC and pave the groundwork for developing innovative and effective cancer treatment methods for HNSCC.
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Affiliation(s)
- Yu Jin
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
| | - Xing Qin
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
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14
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Single-cell RNA-seq analysis revealed long-lasting adverse effects of tamoxifen on neurogenesis in prenatal and adult brains. Proc Natl Acad Sci U S A 2020; 117:19578-19589. [PMID: 32727894 DOI: 10.1073/pnas.1918883117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The CreER/LoxP system is widely accepted to track neural lineages and study gene functions upon tamoxifen (TAM) administration. We have observed that prenatal TAM treatment caused high rates of delayed delivery and fetal mortality. This substance could produce undesired results, leading to data misinterpretation. Here, we report that administration of TAM during early stages of cortical neurogenesis promoted precocious neural differentiation, while it inhibited neural progenitor cell (NPC) proliferation. The TAM-induced inhibition of NPC proliferation led to deficits in cortical neurogenesis, dendritic morphogenesis, synaptic formation, and cortical patterning in neonatal and postnatal offspring. Mechanistically, by employing single-cell RNA-sequencing (scRNA-seq) analysis combined with in vivo and in vitro assays, we show TAM could exert these drastic effects mainly through dysregulating the Wnt-Dmrta2 signaling pathway. In adult mice, administration of TAM significantly attenuated NPC proliferation in both the subventricular zone and the dentate gyrus. This study revealed the cellular and molecular mechanisms for the adverse effects of TAM on corticogenesis, suggesting that care must be taken when using the TAM-induced CreER/LoxP system for neural lineage tracing and genetic manipulation studies in both embryonic and adult brains.
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15
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Kikkawa T, Sakayori N, Yuuki H, Katsuyama Y, Matsuzaki F, Konno D, Abe T, Kiyonari H, Osumi N. Dmrt
genes participate in the development of Cajal‐Retzius cells derived from the cortical hem in the telencephalon. Dev Dyn 2020; 249:698-710. [DOI: 10.1002/dvdy.156] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 01/11/2023] Open
Affiliation(s)
- Takako Kikkawa
- Department of Developmental NeuroscienceUnited Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine Sendai Miyagi Japan
| | - Nobuyuki Sakayori
- Department of Molecular GeneticsInstitute of Biomedical Sciences, Fukushima Medical University Fukushima Japan
| | - Hayato Yuuki
- Department of Developmental NeuroscienceUnited Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine Sendai Miyagi Japan
| | - Yu Katsuyama
- Department of AnatomyShiga University of Medical Science Otsu Shiga Japan
| | - Fumio Matsuzaki
- Laboratory for Cell AsymmetryRIKEN Center for Biosystems Dynamics Research Kobe Japan
| | - Daijiro Konno
- Laboratory for Cell AsymmetryRIKEN Center for Biosystems Dynamics Research Kobe Japan
- Department of PathophysiologyMedical Institute of Bioregulation, Kyushu University Fukuoka Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Kobe Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Kobe Japan
| | - Noriko Osumi
- Department of Developmental NeuroscienceUnited Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine Sendai Miyagi Japan
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16
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Fallah HP, Rodrigues MS, Corchuelo S, Nóbrega RH, Habibi HR. Role of GnRH Isoforms in Paracrine/Autocrine Control of Zebrafish (Danio rerio) Spermatogenesis. Endocrinology 2020; 161:5701481. [PMID: 31930304 DOI: 10.1210/endocr/bqaa004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/10/2020] [Indexed: 12/25/2022]
Abstract
Abstract
It is well established that hypothalamic GnRH (gonadotropin-releasing hormone) is one of the key peptides involved in the neuroendocrine control of testicular development and spermatogenesis. However, the role of GnRH as a paracrine regulator of testicular function has not been fully investigated. The present study demonstrates the presence of GnRH and its receptors in the zebrafish (Danio rerio) testis, and provides information on direct action of native GnRH isoforms (GnRH2 and GnRH3) on different stages of spermatogenesis in this model. Both GnRH2 and GnRH3 stimulated basal spermatogenesis by increasing numbers of type Aund spermatogonia, spermatozoa, and testosterone release, and in this study GnRH2 exerted higher relative activity than GnRH3. Next, we evaluated the effects of GnRH isoforms on human chorionic gonadotropin (hCG)- and follicle-stimulating hormone (Fsh)-induced spermatogenesis. The 2 GnRH isoforms were found to have different effects on Fsh- and hCG-induced response depending on the stage of spermatogenesis and concentration of the peptides. The results provide strong support for the hypothesis that locally produced GnRH2 and GnRH3 are important components of the complex multifactorial system that regulates testicular germinal cell development and function in adult zebrafish.
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Affiliation(s)
- Hamideh P Fallah
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Maira S Rodrigues
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Sheryll Corchuelo
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Rafael H Nóbrega
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Hamid R Habibi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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17
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Gruzin M, Mekheal M, Ruhlman K, Winkowski M, Petko J. Developmental expression of doublesex-related transcripts in the common house spider, Parasteatoda tepidariorum. Gene Expr Patterns 2020; 35:119101. [DOI: 10.1016/j.gep.2020.119101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 01/28/2023]
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18
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Ratié L, Desmaris E, García-Moreno F, Hoerder-Suabedissen A, Kelman A, Theil T, Bellefroid EJ, Molnár Z. Loss of Dmrt5 Affects the Formation of the Subplate and Early Corticogenesis. Cereb Cortex 2019; 30:3296-3312. [PMID: 31845734 PMCID: PMC7197206 DOI: 10.1093/cercor/bhz310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dmrt5 (Dmrta2) and Dmrt3 are key regulators of cortical patterning and progenitor proliferation and differentiation. In this study, we show an altered apical to intermediate progenitor transition, with a delay in SP neurogenesis and premature birth of Ctip2+ cortical neurons in Dmrt5−/− mice. In addition to the cortical progenitors, DMRT5 protein appears present in postmitotic subplate (SP) and marginal zone neurons together with some migrating cortical neurons. We observed the altered split of preplate and the reduced SP and disturbed radial migration of cortical neurons into cortical plate in Dmrt5−/− brains and demonstrated an increase in the proportion of multipolar cells in primary neuronal cultures from Dmrt5−/− embryonic brains. Dmrt5 affects cortical development with specific time sensitivity that we described in two conditional mice with slightly different deletion time. We only observed a transient SP phenotype at E15.5, but not by E18.5 after early (Dmrt5lox/lox;Emx1Cre), but not late (Dmrt5lox/lox;NestinCre) deletion of Dmrt5. SP was less disturbed in Dmrt5lox/lox;Emx1Cre and Dmrt3−/− brains than in Dmrt5−/− and affects dorsomedial cortex more than lateral and caudal cortex. Our study demonstrates a novel function of Dmrt5 in the regulation of early SP formation and radial cortical neuron migration. Summary Statement Our study demonstrates a novel function of Dmrt5 in regulating marginal zone and subplate formation and migration of cortical neurons to cortical plate.
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Affiliation(s)
- Leslie Ratié
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Elodie Desmaris
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
| | - Fernando García-Moreno
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK.,Achucarro Basque Center for Neuroscience, Parque Científico UPV/EHU Edif. Sede, E-48940 Leioa, Spain.,IKERBASQUE Foundation, 48013 Bilbao, Spain
| | | | - Alexandra Kelman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Theil
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Eric J Bellefroid
- ULB Neuroscience Institute, Université Libre de Bruxelles, B-6041 Gosselies, Belgium
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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19
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Paracrine/autocrine control of spermatogenesis by gonadotropin-inhibitory hormone. Mol Cell Endocrinol 2019; 492:110440. [DOI: 10.1016/j.mce.2019.04.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 11/17/2022]
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20
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Costa RL, Boroni M, Soares MA. Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. Sci Rep 2018; 8:15254. [PMID: 30323202 PMCID: PMC6189122 DOI: 10.1038/s41598-018-33498-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/19/2018] [Indexed: 12/25/2022] Open
Abstract
The human papillomavirus (HPV) is present in a significant fraction of head-and-neck squamous cell cancer (HNSCC). The main goal of this study was to identify distinct co-expression patterns between HPV+ and HPV- HNSCC and to provide insights into potential regulatory mechanisms/effects within the analyzed networks. We selected cases deposited in The Cancer Genome Atlas database comprising data of gene expression, methylation profiles and mutational patterns, in addition to clinical information. The intersection among differentially expressed and differentially methylated genes showed the negative correlations between the levels of methylation and expression, suggesting that these genes have their expression levels regulated by methylation alteration patterns in their promoter. Weighted correlation network analysis was used to identify co-expression modules and a systematic approach was applied to refine them and identify key regulatory elements integrating results from the other omics. Three distinct co-expression modules were associated with HPV status and molecular signatures. Validation using independent studies reporting biological experimental data converged for the most significant genes in all modules. This study provides insights into complex genetic and epigenetic particularities in the development and progression of HNSCC according to HPV status, and contribute to unveiling specific genes/pathways as novel therapeutic targets in HNSCC.
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Affiliation(s)
- Raquel L Costa
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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21
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DMRT5, DMRT3, and EMX2 Cooperatively Repress Gsx2 at the Pallium-Subpallium Boundary to Maintain Cortical Identity in Dorsal Telencephalic Progenitors. J Neurosci 2018; 38:9105-9121. [PMID: 30143575 DOI: 10.1523/jneurosci.0375-18.2018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/23/2018] [Accepted: 08/15/2018] [Indexed: 11/21/2022] Open
Abstract
Specification of dorsoventral regional identity in progenitors of the developing telencephalon is a first pivotal step in the development of the cerebral cortex and basal ganglia. Previously, we demonstrated that the two zinc finger doublesex and mab-3 related (Dmrt) genes, Dmrt5 (Dmrta2) and Dmrt3, which are coexpressed in high caudomedial to low rostrolateral gradients in the cerebral cortical primordium, are separately needed for normal formation of the cortical hem, hippocampus, and caudomedial neocortex. We have now addressed the role of Dmrt3 and Dmrt5 in controlling dorsoventral division of the telencephalon in mice of either sex by comparing the phenotypes of single knock-out (KO) with double KO embryos and by misexpressing Dmrt5 in the ventral telencephalon. We find that DMRT3 and DMRT5 act as critical regulators of progenitor cell dorsoventral identity by repressing ventralizing regulators. Early ventral fate transcriptional regulators expressed in the dorsal lateral ganglionic eminence, such as Gsx2, are upregulated in the dorsal telencephalon of Dmrt3;Dmrt5 double KO embryos and downregulated when ventral telencephalic progenitors express ectopic Dmrt5 Conditional overexpression of Dmrt5 throughout the telencephalon produces gene expression and structural defects that are highly consistent with reduced GSX2 activity. Further, Emx2;Dmrt5 double KO embryos show a phenotype similar to Dmrt3;Dmrt5 double KO embryos, and both DMRT3, DMRT5 and the homeobox transcription factor EMX2 bind to a ventral telencephalon-specific enhancer in the Gsx2 locus. Together, our findings uncover cooperative functions of DMRT3, DMRT5, and EMX2 in dividing dorsal from ventral in the telencephalon.SIGNIFICANCE STATEMENT We identified the DMRT3 and DMRT5 zinc finger transcription factors as novel regulators of dorsoventral patterning in the telencephalon. Our data indicate that they have overlapping functions and compensate for one another. The double, but not the single, knock-out produces a dorsal telencephalon that is ventralized, and olfactory bulb tissue takes over most remaining cortex. Conversely, overexpressing Dmrt5 throughout the telencephalon causes expanded expression of dorsal gene determinants and smaller olfactory bulbs. Furthermore, we show that the homeobox transcription factor EMX2 that is coexpressed with DMRT3 and DMRT5 in cortical progenitors cooperates with them to maintain dorsoventral patterning in the telencephalon. Our study suggests that DMRT3/5 function with EMX2 in positioning the pallial-subpallial boundary by antagonizing the ventral homeobox transcription factor GSX2.
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22
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Abstract
Sex differences in the brain are prominent features across the animal kingdom. Understanding the anatomical and regulatory mechanisms behind these differences is critical for both explaining sexually dimorphic behaviors and developing sex-targeted treatments for neurological disorders. Clinical studies considering sex biases and basic research on animal models have provided much evidence for the existence of sex differences in the brain and, in a larger sense, sexual dimorphisms in the nervous system. However, due to the complexity of structure and dimorphic behaviors, it is yet unclear precisely how neuronal sexual dimorphisms are regulated on a molecular or cellular level. This commentary reviews available tools for investigating sexual dimorphisms using a simple model organism, the roundworm Caenorhabditis elegans ( C. elegans), which enables one to study gene regulation at single-cell resolution with a number of cutting-edge molecular and genetic technologies. I highlight the doublesex/mab-3 family of transcription factors, first discovered in invertebrates, and their roles in a potentially universal regulatory mechanism underlying neuronal sexual dimorphisms. Studies of these transcription factors using C. elegans, fruit flies, and vertebrates will promote our understanding of fundamental mechanisms behind sex differences in the brain.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
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23
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Wei Y, Pandian GN, Yu Z, Zou T, Li Y, Darokar J, Hashiya K, Bando T, Sugiyama H. Synthetic DNA-Binding Inhibitor of HES1 Alters the Notch Signaling Pathway and Induces Neuronal Differentiation. ACS OMEGA 2018; 3:3608-3616. [PMID: 30023873 PMCID: PMC6045482 DOI: 10.1021/acsomega.8b00220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/12/2018] [Indexed: 05/02/2023]
Abstract
Synthetic DNA-binding inhibitors capable of gaining precise control over neurogenesis factors could obviate the current clinical barriers associated with the use of small molecules in regenerative medicine. Here, we report the design and bioefficacy of the synthetic ligand PIP-RBPJ-1, which caused promoter-specific suppression of neurogenesis-associated HES1 and its downstream genes. Furthermore, PIP-RBPJ-1 alone altered the neural-system-associated Notch-signaling factors and remarkably induced neurogenesis with an efficiency that was comparable to that of a conventional approach.
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Affiliation(s)
- Yulei Wei
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Ganesh N. Pandian
- World
Premier International Research Center, Institute for Integrated Cell-Material
Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiyacho, 606-8501 Kyoto, Japan
- E-mail: . Phone: +81-075-753-4002 (G.N.P.)
| | - Zutao Yu
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Tingting Zou
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Yue Li
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Jayant Darokar
- Department
of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, 110-016 New Delhi, India
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, 606-8502 Kyoto, Japan
- World
Premier International Research Center, Institute for Integrated Cell-Material
Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiyacho, 606-8501 Kyoto, Japan
- E-mail: . Phone: +81-075-753-4002 (H.S.)
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24
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Popovitchenko T, Rasin MR. Transcriptional and Post-Transcriptional Mechanisms of the Development of Neocortical Lamination. Front Neuroanat 2017; 11:102. [PMID: 29170632 PMCID: PMC5684109 DOI: 10.3389/fnana.2017.00102] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022] Open
Abstract
The neocortex is a laminated brain structure that is the seat of higher cognitive capacity and responses, long-term memory, sensory and emotional functions, and voluntary motor behavior. Proper lamination requires that progenitor cells give rise to a neuron, that the immature neuron can migrate away from its mother cell and past other cells, and finally that the immature neuron can take its place and adopt a mature identity characterized by connectivity and gene expression; thus lamination proceeds through three steps: genesis, migration, and maturation. Each neocortical layer contains pyramidal neurons that share specific morphological and molecular characteristics that stem from their prenatal birth date. Transcription factors are dynamic proteins because of the cohort of downstream factors that they regulate. RNA-binding proteins are no less dynamic, and play important roles in every step of mRNA processing. Indeed, recent screens have uncovered post-transcriptional mechanisms as being integral regulatory mechanisms to neocortical development. Here, we summarize major aspects of neocortical laminar development, emphasizing transcriptional and post-transcriptional mechanisms, with the aim of spurring increased understanding and study of its intricacies.
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Affiliation(s)
- Tatiana Popovitchenko
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Mladen-Roko Rasin
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
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25
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Dmrt5, a Novel Neurogenic Factor, Reciprocally Regulates Lhx2 to Control the Neuron-Glia Cell-Fate Switch in the Developing Hippocampus. J Neurosci 2017; 37:11245-11254. [PMID: 29025924 PMCID: PMC5688529 DOI: 10.1523/jneurosci.1535-17.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/18/2017] [Accepted: 09/23/2017] [Indexed: 11/21/2022] Open
Abstract
Regulation of the neuron-glia cell-fate switch is a critical step in the development of the CNS. Previously, we demonstrated that Lhx2 is a necessary and sufficient regulator of this process in the mouse hippocampal primordium, such that Lhx2 overexpression promotes neurogenesis and suppresses gliogenesis, whereas loss of Lhx2 has the opposite effect. We tested a series of transcription factors for their ability to mimic Lhx2 overexpression and suppress baseline gliogenesis, and also to compensate for loss of Lhx2 and suppress the resulting enhanced level of gliogenesis in the hippocampus. Here, we demonstrate a novel function of Dmrt5/Dmrta2 as a neurogenic factor in the developing hippocampus. We show that Dmrt5, as well as known neurogenic factors Neurog2 and Pax6, can each not only mimic Lhx2 overexpression, but also can compensate for loss of Lhx2 to different extents. We further uncover a reciprocal regulatory relationship between Dmrt5 and Lhx2, such that each can compensate for loss of the other. Dmrt5 and Lhx2 also have opposing regulatory control on Pax6 and Neurog2, indicating a complex bidirectionally regulated network that controls the neuron-glia cell-fate switch.SIGNIFICANCE STATEMENT We identify Dmrt5 as a novel regulator of the neuron-glia cell-fate switch in the developing hippocampus. We demonstrate Dmrt5 to be neurogenic, and reciprocally regulated by Lhx2: loss of either factor promotes gliogenesis; overexpression of either factor suppresses gliogenesis and promotes neurogenesis; each can substitute for loss of the other. Furthermore, each factor has opposing effects on established neurogenic genes Neurog2 and Pax6 Dmrt5 is known to suppress their expression, and we show that Lhx2 is required to maintain it. Our study reveals a complex regulatory network with bidirectional control of a fundamental feature of CNS development, the control of the production of neurons versus astroglia in the developing hippocampus.Finally, we confirm that Lhx2 binds a highly conserved putative enhancer of Dmrt5, suggesting an evolutionarily conserved regulatory relationship between these factors. Our findings uncover a complex network that involves Lhx2, Dmrt5, Neurog2, and Pax6, and that ensures the appropriate amount and timing of neurogenesis and gliogenesis in the developing hippocampus.
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