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Griñán-Ferré C, Bellver-Sanchis A, Guerrero A, Pallàs M. Advancing personalized medicine in neurodegenerative diseases: The role of epigenetics and pharmacoepigenomics in pharmacotherapy. Pharmacol Res 2024; 205:107247. [PMID: 38834164 DOI: 10.1016/j.phrs.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
About 80 % of brain disorders have a genetic basis. The pathogenesis of most neurodegenerative diseases is associated with a myriad of genetic defects, epigenetic alterations (DNA methylation, histone/chromatin remodeling, miRNA dysregulation), and environmental factors. The emergence of new sequencing technologies and tools to study the epigenome has led to identifying predictive biomarkers for earlier diagnosis, opening up the possibility of prophylactical interventions. As a result, advances in pharmacogenetics and pharmacoepigenomics now allow for personalized treatments based on the profile of each patient and the specific genetic and epigenetic mechanisms involved. This Review highlights the complexity of neurodegenerative diseases and the variability in patient responses to pharmacotherapy, emphasizing the influence of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of drugs used to treat those conditions. We specifically discuss the potential modulatory effect of several genetic polymorphisms associated with an increased risk of developing different neurodegenerative diseases. We explore genetic and genomic technologies and the potential of analyzing individual-specific drug metabolism to predict and influence drug response and associated clinical outcomes. We also provide insights into the mechanism of action of the drugs under investigation and their potential impact on disease-modifying pathways. Finally, the Review underscores the great potential of this field to enhance the effectiveness and safety of drug treatments through personalized medicine.
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Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Aina Bellver-Sanchis
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Ana Guerrero
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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Gan L, Zheng L, Zou J, Luo P, Chen T, Zou J, Li W, Chen Q, Cheng L, Zhang F, Qian B. Critical roles of lncRNA-mediated autophagy in urologic malignancies. Front Pharmacol 2024; 15:1405199. [PMID: 38939836 PMCID: PMC11208713 DOI: 10.3389/fphar.2024.1405199] [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: 03/22/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Urologic oncology is a significant public health concern on a global scale. Recent research indicates that long chain non-coding RNAs (lncRNAs) and autophagy play crucial roles in various cancers, including urologic malignancies. This article provides a summary of the latest research findings, suggesting that lncRNA-mediated autophagy could either suppress or promote tumors in prostate, kidney, and bladder cancers. The intricate network involving different lncRNAs, target genes, and mediated signaling pathways plays a crucial role in urological malignancies by modulating the autophagic process. Dysregulated expression of lncRNAs can disrupt autophagy, leading to tumorigenesis, progression, and enhanced resistance to therapy. Consequently, targeting particular lncRNAs that control autophagy could serve as a dependable diagnostic tool and a promising prognostic biomarker in urologic oncology, while also holding potential as an effective therapeutic approach.
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Affiliation(s)
- Lifeng Gan
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Tao Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Jun Zou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Le Cheng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Fangtao Zhang
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
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Vitale C, Natali G, Cerullo MS, Floss T, Michetti C, Grasselli G, Benfenati F. The homeostatic effects of the RE-1 silencing transcription factor on cortical networks are altered under ictogenic conditions in the mouse. Acta Physiol (Oxf) 2024; 240:e14146. [PMID: 38606882 DOI: 10.1111/apha.14146] [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: 10/21/2023] [Revised: 02/22/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
AIM The Repressor Element-1 Silencing Transcription Factor (REST) is an epigenetic master regulator playing a crucial role in the nervous system. In early developmental stages, REST downregulation promotes neuronal differentiation and the acquisition of the neuronal phenotype. In addition, postnatal fluctuations in REST expression contribute to shaping neuronal networks and maintaining network homeostasis. Here we investigate the role of the early postnatal deletion of neuronal REST in the assembly and strength of excitatory and inhibitory synaptic connections. METHODS We investigated excitatory and inhibitory synaptic transmission by patch-clamp recordings in acute neocortical slices in a conditional knockout mouse model (RestGTi) in which Rest was deleted by delivering PHP.eB adeno-associated viruses encoding CRE recombinase under the control of the human synapsin I promoter in the lateral ventricles of P0-P1 pups. RESULTS We show that, under physiological conditions, Rest deletion increased the intrinsic excitability of principal cortical neurons in the primary visual cortex and the density and strength of excitatory synaptic connections impinging on them, without affecting inhibitory transmission. Conversely, in the presence of a pathological excitation/inhibition imbalance induced by pentylenetetrazol, Rest deletion prevented the increase in synaptic excitation and decreased seizure severity. CONCLUSION The data indicate that REST exerts distinct effects on the excitability of cortical circuits depending on whether it acts under physiological conditions or in the presence of pathologic network hyperexcitability. In the former case, REST preserves a correct excitatory/inhibitory balance in cortical circuits, while in the latter REST loses its homeostatic activity and may become pro-epileptogenic.
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Affiliation(s)
- Carmela Vitale
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Giulia Natali
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Maria Sabina Cerullo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Thomas Floss
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Caterina Michetti
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Giorgio Grasselli
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Pharmacy, University of Genova, Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
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Shmal D, Mantero G, Floss T, Benfenati F, Maya-Vetencourt JF. Restoring vision in adult amblyopia by enhancing plasticity through deletion of the transcriptional repressor REST. iScience 2024; 27:109507. [PMID: 38591011 PMCID: PMC11000024 DOI: 10.1016/j.isci.2024.109507] [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: 09/27/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Visual cortical plasticity is high during early life, but gradually decreases with development. This is due to the Otx2-driven maturation of intracortical inhibition that parallels the condensation of extracellular matrix components into perineuronal nets mainly around parvalbumin-positive GABAergic neurons. Repressor Element 1 Silencing Transcription (REST) epigenetically controls the expression of a plethora of neuron-specific genes. We demonstrate that the conditional knockout of REST in the primary visual cortex of adult mice induces a shift of ocular dominance after short-term monocular deprivation and promotes the recovery of vision in long-term deprived animals after reverse suture. These phenomena paralleled a reduction of perineuronal net density and increased expression of REST target genes, but not of the homeoprotein Otx2 in the visual cortex contralateral to the deprived eye. This shows that REST regulates adult visual cortical plasticity and is a potential therapeutic target to restore vision in adult amblyopia by enhancing V1 plasticity.
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Affiliation(s)
- Dmytro Shmal
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Giulia Mantero
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Thomas Floss
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - José Fernando Maya-Vetencourt
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Biology, University of Pisa, Pisa, Italy
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Mu C, Gao M, Xu W, Sun X, Chen T, Xu H, Qiu H. Mechanisms of microRNA-132 in central neurodegenerative diseases: A comprehensive review. Biomed Pharmacother 2024; 170:116029. [PMID: 38128185 DOI: 10.1016/j.biopha.2023.116029] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
MicroRNA-132 (miR-132) is a highly conserved molecule that plays a crucial regulatory role in central nervous system (CNS) disorders. The expression levels of miR-132 exhibit variability in various neurological disorders and have been closely linked to disease onset and progression. The expression level of miR-132 in the CNS is regulated by a diverse range of stimuli and signaling pathways, including neuronal migration and integration, dendritic outgrowth, and complexity, synaptogenesis, synaptic plasticity, as well as inflammation and apoptosis activation. The aberrant expression of miR-132 in various central neurodegenerative diseases has garnered widespread attention. Clinical studies have revealed altered miR-132 expression levels in both chronic and acute CNS diseases, positioning miR-132 as a potential biomarker or therapeutic target. An in-depth exploration of miR-132 holds the promise of enhancing our understanding of the mechanisms underlying CNS diseases, thereby offering novel insights and strategies for disease diagnosis and treatment. It is anticipated that this review will assist researchers in recognizing the potential value of miR-132 and in generating innovative ideas for clinical trials related to CNS degenerative diseases.
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Affiliation(s)
- Chenxi Mu
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Meng Gao
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Weijing Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China; School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China
| | - Xun Sun
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Tianhao Chen
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Hui Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China.
| | - Hongbin Qiu
- School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China.
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Lee SCES, Pyo AHA, Koritzinsky M. Longitudinal dynamics of the tumor hypoxia response: From enzyme activity to biological phenotype. SCIENCE ADVANCES 2023; 9:eadj6409. [PMID: 37992163 PMCID: PMC10664991 DOI: 10.1126/sciadv.adj6409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023]
Abstract
Poor oxygenation (hypoxia) is a common spatially heterogeneous feature of human tumors. Biological responses to tumor hypoxia are orchestrated by the decreased activity of oxygen-dependent enzymes. The affinity of these enzymes for oxygen positions them along a continuum of oxygen sensing that defines their roles in launching reactive and adaptive cellular responses. These responses encompass regulation of all steps in the central dogma, with rapid perturbation of the metabolome and proteome followed by more persistent reprogramming of the transcriptome and epigenome. Core hypoxia response genes and pathways are commonly regulated at multiple inflection points, fine-tuning the dependencies on oxygen concentration and hypoxia duration. Ultimately, shifts in the activity of oxygen-sensing enzymes directly or indirectly endow cells with intrinsic hypoxia tolerance and drive processes that are associated with aggressive phenotypes in cancer including angiogenesis, migration, invasion, immune evasion, epithelial mesenchymal transition, and stemness.
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Affiliation(s)
- Sandy Che-Eun S. Lee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Hye An Pyo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Marianne Koritzinsky
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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7
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Natali G, Michetti C, Krawczun-Rygmaczewska A, Floss T, Cesca F, Benfenati F. Conditional knockout of REST/NRSF in excitatory neurons reduces seizure susceptibility to chemical kindling. Front Cell Neurosci 2023; 17:1267609. [PMID: 38034589 PMCID: PMC10687554 DOI: 10.3389/fncel.2023.1267609] [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: 07/26/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
The repressor element-1 silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) is an epigenetic master regulator that plays a crucial role during nervous system development and maturation. REST function was originally described during development, where it determines neuronal phenotype. However, recent studies showed that REST participates in several processes in the adult brain, including neuronal plasticity and epileptogenesis. In this regard, the relationships between REST and epilepsy are still controversial and need further investigation. As forebrain excitatory neurons are the common final pathway of seizure susceptibility, we investigated the role of REST in epilepsy by inducing REST conditional knockout (REST-cKO) specifically in excitatory neurons of the hippocampus. To target the excitatory neuronal population, we cloned the calcium/calmodulin-dependent protein kinase IIα minimal promoter upstream of Cre recombinase. After assessing the specificity of the promoter's expression, the transgenes were packaged in an engineered adeno-associated virus able to cross the blood-brain and blood-cerebrospinal fluid barriers and delivered in the lateral ventricles of 2-month-old RESTflox/flox mice to characterize, after 1 month, the cognitive phenotype and the seizure propensity. We show that REST-cKO mice display lower levels of anxiety in the light-dark test with respect to control mice but have unaltered motor, social, and cognitive profiles. The evaluation of the susceptibility to epileptic seizures showed that REST-cKO mice are more resistant to pentylenetetrazole-induced kindling but not to seizures induced by a single administration of the convulsant and show higher survival rates. Overall, these data suggest that the absence of REST in forebrain excitatory neurons decreases seizure susceptibility, pointing to a pro-epileptogenic role of the transcriptional repressor under conditions of pathological excitation/inhibition imbalance.
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Affiliation(s)
- Giulia Natali
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Caterina Michetti
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Alicja Krawczun-Rygmaczewska
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Thomas Floss
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
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Moyers BA, Partridge EC, Mackiewicz M, Betti MJ, Darji R, Meadows SK, Newberry KM, Brandsmeier LA, Wold BJ, Mendenhall EM, Myers RM. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res 2023; 33:gr.278205.123. [PMID: 37852782 PMCID: PMC10760452 DOI: 10.1101/gr.278205.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.
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Affiliation(s)
- Belle A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michael J Betti
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Barbara J Wold
- Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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10
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Nassar A, Satarker S, Gurram PC, Upadhya D, Fayaz SM, Nampoothiri M. Repressor Element-1 Binding Transcription Factor (REST) as a Possible Epigenetic Regulator of Neurodegeneration and MicroRNA-Based Therapeutic Strategies. Mol Neurobiol 2023; 60:5557-5577. [PMID: 37326903 PMCID: PMC10471693 DOI: 10.1007/s12035-023-03437-1] [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: 03/14/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
Neurodegenerative disorders (NDD) have grabbed significant scientific consideration due to their fast increase in prevalence worldwide. The specific pathophysiology of the disease and the amazing changes in the brain that take place as it advances are still the top issues of contemporary research. Transcription factors play a decisive role in integrating various signal transduction pathways to ensure homeostasis. Disruptions in the regulation of transcription can result in various pathologies, including NDD. Numerous microRNAs and epigenetic transcription factors have emerged as candidates for determining the precise etiology of NDD. Consequently, understanding by what means transcription factors are regulated and how the deregulation of transcription factors contributes to neurological dysfunction is important to the therapeutic targeting of pathways that they modulate. RE1-silencing transcription factor (REST) also named neuron-restrictive silencer factor (NRSF) has been studied in the pathophysiology of NDD. REST was realized to be a part of a neuroprotective element with the ability to be tuned and influenced by numerous microRNAs, such as microRNAs 124, 132, and 9 implicated in NDD. This article looks at the role of REST and the influence of various microRNAs in controlling REST function in the progression of Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD) disease. Furthermore, to therapeutically exploit the possibility of targeting various microRNAs, we bring forth an overview of drug-delivery systems to modulate the microRNAs regulating REST in NDD.
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Affiliation(s)
- Ajmal Nassar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Prasada Chowdari Gurram
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dinesh Upadhya
- Centre for Molecular Neurosciences, Kasturba Medical College Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - S M Fayaz
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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11
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Carvalho LB, Dos Santos Sanna PL, Dos Santos Afonso CC, Bondan EF, da Silva Feltran G, Ferreira MR, Birbrair A, Andia DC, Latini A, Foganholi da Silva RA. MicroRNA biogenesis machinery activation and lncRNA and REST overexpression as neuroprotective responses to fight inflammation in the hippocampus. J Neuroimmunol 2023; 382:578149. [PMID: 37481910 DOI: 10.1016/j.jneuroim.2023.578149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Brain Long non-coding RNA (lncRNA) and microRNAs (miRs) play essential roles in the regulation of several important biological processes, including neuronal activity, cognitive processes, neurogenesis, angiogenesis, and neuroinflammation. In this context, the transcriptional repressor, RE1 silencing transcription factor (Rest), acts regulating the expression of neuronal genes as well as of lncRNAs and multiple miRNAs in the central nervous system. Nevertheless, its role in neuroinflammation was less explored. Here, we demonstrate, using an in vivo model of neuroinflammation induced by i.p. injection of LPS (0.33 mg/kg), that neuroinflammation increases gene expression of pro-inflammatory cytokines concomitant with the native and truncated forms of Rest and of non-coding RNAs. Additionally, the increased expression of enzymes Drosha ribonuclease III) (Drosha), Exportin 5 (Xpo5) and Endoribonuclease dicer (Dicer), associated with high expression of neuroprotective miRs 22 and 132 are indicative that the activation of biogenesis of miRs in the hippocampal region is a Central Nervous System (CNS) protective mechanism for the deleterious effects of neuroinflammation. Our results indicate that positive regulation of Rest gene expression in the hippocampal region by neuroinflammation correlates directly with the expression of miRs 22 and 132 and inversely with miR 335. In parallel, the confirmation of the possible alignment between the lncRNAs with miR 335 by bioinformatics corroborates with the sponge effect of Hottip and Hotair hybridizing and inhibiting the pro-inflammatory action of miR 335. This suggests the existence of a possible correlation between the activation of miR biogenesis machinery with increased expression of the transcription factor Rest, contributing to neuroprotection.
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Affiliation(s)
| | | | | | - Eduardo F Bondan
- CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, SP, Brazil
| | - Marcel Rodrigues Ferreira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unity, Botucatu Medical School, São Paulo State University, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA; Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Denise Carleto Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | - Alexandra Latini
- Laboratory of Bioenergetics and Oxidative Stress, LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rodrigo A Foganholi da Silva
- Dentistry, University of Taubaté, Taubaté, São Paulo, SP, Brazil; CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil.
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12
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [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: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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13
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Gong S, Zhang A, Yao M, Xin W, Guan X, Qin S, Liu Y, Xiong J, Yang K, Xiong L, He T, Huang Y, Zhao J. REST contributes to AKI-to-CKD transition through inducing ferroptosis in renal tubular epithelial cells. JCI Insight 2023; 8:166001. [PMID: 37288660 PMCID: PMC10393228 DOI: 10.1172/jci.insight.166001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/20/2023] [Indexed: 06/09/2023] Open
Abstract
Ischemic-reperfusion injury (IRI) is a major pathogenic factor in acute kidney injury (AKI), which directly leads to the hypoxic injury of renal tubular epithelial cells (RTECs). Although emerging studies suggest repressor element 1-silencing transcription factor (REST) as a master regulator of gene repression under hypoxia, its role in AKI remains elusive. Here, we found that REST was upregulated in AKI patients, mice, and RTECs, which was positively associated with the degree of kidney injury, while renal tubule-specific knockout of Rest significantly alleviated AKI and its progression to chronic kidney disease (CKD). Subsequent mechanistic studies indicated that suppression of ferroptosis was responsible for REST-knockdown-induced amelioration of hypoxia-reoxygenation injury, during which process Cre-expressing adenovirus-mediated REST downregulation attenuated ferroptosis through upregulating glutamate-cysteine ligase modifier subunit (GCLM) in primary RTECs. Further, REST transcriptionally repressed GCLM expression via directly binding to its promoter region. In conclusion, our findings revealed the involvement of REST, a hypoxia regulatory factor, in AKI-to-CKD transition and identified the ferroptosis-inducing effect of REST, which may serve as a promising therapeutic target for ameliorating AKI and its progression to CKD.
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14
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Yamato E. Aberrant Expression of Rest4 Gene in Low-Functioning Pancreatic Beta Cell Line. Horm Metab Res 2023. [PMID: 36758614 DOI: 10.1055/a-2031-9803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Repressor element-1 silencing transcription factor (Rest) is not expressed in pancreatic beta cells and neuronal cells. However, Rest4, a truncated form of Rest, is expressed in high passaged MIN6 (HP-MIN6) cells, a pancreatic beta cell line that lost glucose-responsive insulin secretion. Rest4 is also expressed in injured MIN6 cells and isolated islets. Herein, the forced expression of dominant negative form of Rest in HP-MIN6 cells was subjected to microarray analysis of gene expression to investigate the role of Rest4 gene in MIN6 cells. Furthermore, the forced expression of Rest4 gene in MIN6 cells was subjected to microarray analysis of gene expression to investigate the function of Rest4 in normal insulin-producing cells. The results showed that Rest4 inhibits cell proliferation and DNA and RNA metabolism and stimulates secretory mechanisms and nervous system gene expression. These findings suggest that Rest4 may act defensively against cellular injury in pancreatic beta cells.
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Affiliation(s)
- Eiji Yamato
- Nutrition and Food Science, Mukogawa Woman's University, Nishinomiya, Japan
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15
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Sreekumar A, Saini S. Role of transcription factors and chromatin modifiers in driving lineage reprogramming in treatment-induced neuroendocrine prostate cancer. Front Cell Dev Biol 2023; 11:1075707. [PMID: 36711033 PMCID: PMC9879360 DOI: 10.3389/fcell.2023.1075707] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Therapy-induced neuroendocrine prostate cancer (NEPC) is a highly lethal variant of prostate cancer that is increasing in incidence with the increased use of next-generation of androgen receptor (AR) pathway inhibitors. It arises via a reversible trans-differentiation process, referred to as neuroendocrine differentiation (NED), wherein prostate cancer cells show decreased expression of AR and increased expression of neuroendocrine (NE) lineage markers including enolase 2 (ENO2), chromogranin A (CHGA) and synaptophysin (SYP). NEPC is associated with poor survival rates as these tumors are aggressive and often metastasize to soft tissues such as liver, lung and central nervous system despite low serum PSA levels relative to disease burden. It has been recognized that therapy-induced NED involves a series of genetic and epigenetic alterations that act in a highly concerted manner in orchestrating lineage switching. In the recent years, we have seen a spurt in research in this area that has implicated a host of transcription factors and epigenetic modifiers that play a role in driving this lineage switching. In this article, we review the role of important transcription factors and chromatin modifiers that are instrumental in lineage reprogramming of prostate adenocarcinomas to NEPC under the selective pressure of various AR-targeted therapies. With an increased understanding of the temporal and spatial interplay of transcription factors and chromatin modifiers and their associated gene expression programs in NEPC, better therapeutic strategies are being tested for targeting NEPC effectively.
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16
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Nayak M, Das D, Pradhan J, Ahmed R, Laureano-Melo R, Dandapat J. Epigenetic signature in neural plasticity: the journey so far and journey ahead. Heliyon 2022; 8:e12292. [PMID: 36590572 PMCID: PMC9798197 DOI: 10.1016/j.heliyon.2022.e12292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Neural plasticity is a remarkable characteristic of the brain which allows neurons to rewire their structure in response to internal and external stimuli. Many external stimuli collectively referred to as 'epigenetic factors' strongly influence structural and functional reorganization of the brain, thereby acting as a potential driver of neural plasticity. DNA methylation and demethylation, histone acetylation, and deacetylation are some of the frontline epigenetic mechanisms behind neural plasticity. Epigenetic signature molecules (mostly proteins) play a pivotal role in epigenetic reprogramming. Though neuro-epigenetics is an incredibly important field of emerging research, the critical role of signature proteins associated with epigenetic alteration and their involvement in neural plasticity needs further attention. This study gives an integrated and systematic overview of the current state of knowledge with a clear idea of types of neural plasticity and the context-dependent role of epigenetic signature molecules and their modulation by some natural bioactive compounds.
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Affiliation(s)
- Madhusmita Nayak
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Diptimayee Das
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Faculty of Allied Health Science, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Chennai India
| | - Jyotsnarani Pradhan
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Corresponding author.
| | - R.G. Ahmed
- Division of Anatomy and Embryology, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Roberto Laureano-Melo
- Barra Mansa University Center, R. Ver. Pinho de Carvalho, 267, 27330-550, Barra Mansa, Rio de Janeiro, Brazil
| | - Jagneshwar Dandapat
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India,Corresponding author.
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17
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Zhang H, Li H, Lu M, Wang S, Ma X, Wang F, Liu J, Li X, Yang H, Zhang F, Shen H, Buckley NJ, Gamper N, Yamoah EN, Lv P. Repressor element 1-silencing transcription factor deficiency yields profound hearing loss through K v7.4 channel upsurge in auditory neurons and hair cells. eLife 2022; 11:76754. [PMID: 36125121 PMCID: PMC9525063 DOI: 10.7554/elife.76754] [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: 01/04/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Repressor element 1-silencing transcription factor (REST) is a transcriptional repressor that recognizes neuron-restrictive silencer elements in the mammalian genomes in a tissue- and cell-specific manner. The identity of REST target genes and molecular details of how REST regulates them are emerging. We performed conditional null deletion of Rest (cKO), mainly restricted to murine hair cells (HCs) and auditory neurons (aka spiral ganglion neurons [SGNs]). Null inactivation of full-length REST did not affect the development of normal HCs and SGNs but manifested as progressive hearing loss in adult mice. We found that the inactivation of REST resulted in an increased abundance of Kv7.4 channels at the transcript, protein, and functional levels. Specifically, we found that SGNs and HCs from Rest cKO mice displayed increased Kv7.4 expression and augmented Kv7 currents; SGN’s excitability was also significantly reduced. Administration of a compound with Kv7.4 channel activator activity, fasudil, recapitulated progressive hearing loss in mice. In contrast, inhibition of the Kv7 channels by XE991 rescued the auditory phenotype of Rest cKO mice. Previous studies identified some loss-of-function mutations within the Kv7.4-coding gene, Kcnq4, as a causative factor for progressive hearing loss in mice and humans. Thus, the findings reveal that a critical homeostatic Kv7.4 channel level is required for proper auditory functions.
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Affiliation(s)
- Haiwei Zhang
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Hongchen Li
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Mingshun Lu
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Shengnan Wang
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Xueya Ma
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Fei Wang
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Jiaxi Liu
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Xinyu Li
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Haichao Yang
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Fan Zhang
- Department of Pharmacology, Hebei Medical University, Hebei, China
| | - Haitao Shen
- Laboratory of Pathology, Hebei Medical University, Hebei, China
| | - Noel J Buckley
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Nikita Gamper
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Ebenezer N Yamoah
- Department of Physiology and Cell Biology, University of Nevada Reno, Reno, United States
| | - Ping Lv
- Department of Pharmacology, Hebei Medical University, Hebei, China
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18
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Saint Just Ribeiro M, Tripathi P, Namjou B, Harley JB, Chepelev I. Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1. Front Genet 2022; 13:1008582. [PMID: 36160011 PMCID: PMC9490475 DOI: 10.3389/fgene.2022.1008582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
A major goal of genetics research is to elucidate mechanisms explaining how genetic variation contributes to phenotypic variation. The genetic variants identified in genome-wide association studies (GWASs) generally explain only a small proportion of heritability of phenotypic traits, the so-called missing heritability problem. Recent evidence suggests that additional common variants beyond lead GWAS variants contribute to phenotypic variation; however, their mechanistic underpinnings generally remain unexplored. Herein, we undertake a study of haplotype-specific mechanisms of gene regulation at 8p23.1 in the human genome, a region associated with a number of complex diseases. The FAM167A-BLK locus in this region has been consistently found in the genome-wide association studies (GWASs) of systemic lupus erythematosus (SLE) in all major ancestries. Our haplotype-specific chromatin interaction (Hi-C) experiments, allele-specific enhancer activity measurements, genetic analyses, and epigenome editing experiments revealed that: 1) haplotype-specific long-range chromatin interactions are prevalent in 8p23.1; 2) BLK promoter and cis-regulatory elements cooperatively interact with haplotype-specificity; 3) genetic variants at distal regulatory elements are allele-specific modifiers of the promoter variants at FAM167A-BLK; 4) the BLK promoter interacts with and, as an enhancer-like promoter, regulates FAM167A expression and 5) local allele-specific enhancer activities are influenced by global haplotype structure due to chromatin looping. Although systemic lupus erythematosus causal variants at the FAM167A-BLK locus are thought to reside in the BLK promoter region, our results reveal that genetic variants at distal regulatory elements modulate promoter activity, changing BLK and FAM167A gene expression and disease risk. Our results suggest that global haplotype-specific 3-dimensional chromatin looping architecture has a strong influence on local allelic BLK and FAM167A gene expression, providing mechanistic details for how regional variants controlling the BLK promoter may influence disease risk.
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Affiliation(s)
- Mariana Saint Just Ribeiro
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Pulak Tripathi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - John B. Harley
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
| | - Iouri Chepelev
- Research Service, US Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
- Cincinnati Education and Research for Veterans Foundation, Cincinnati, OH, United States
- *Correspondence: Iouri Chepelev, ; John B. Harley,
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19
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Inazumi H, Kuwahara K. NRSF/REST-Mediated Epigenomic Regulation in the Heart: Transcriptional Control of Natriuretic Peptides and Beyond. BIOLOGY 2022; 11:biology11081197. [PMID: 36009824 PMCID: PMC9405064 DOI: 10.3390/biology11081197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Reactivation of the fetal cardiac gene program, such as those encoding atrial and brain natriuretic peptides (ANP and BNP, respectively), is a characteristic feature of failing hearts. We previously revealed that a transcriptional repressor, neuron-restrictive silencer factor (NRSF), also called repressor element-1-silencing transcription factor (REST), plays a crucial role in the transcriptional control of ANP, BNP and other fetal cardiac genes through collaboration with various other transcription factors to maintain physiological cardiac function and electrical stability. Increased production of ANP and BNP prevents the progression of heart failure, but reactivation of Gαo and fetal-type cardiac ion channels (T-type Ca2+ and HCN channels) leads to deteriorated cardiac function and lethal arrhythmias observed in mice with disturbed NRSF function. Epigenetic regulators with which NRSF forms a complex modify histone acetylation and methylation, thereby participating in NRSF-mediated transcriptional regulation. Further comprehensive studies will lead to clarification of the molecular mechanisms underlying the development of cardiac dysfunction and heart failure. Abstract Reactivation of fetal cardiac genes, including those encoding atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), is a key feature of pathological cardiac remodeling and heart failure. Intensive studies on the regulation of ANP and BNP have revealed the involvement of numerous transcriptional factors in the regulation of the fetal cardiac gene program. Among these, we identified that a transcriptional repressor, neuron-restrictive silencer factor (NRSF), also named repressor element-1-silencing transcription factor (REST), which was initially detected as a transcriptional repressor of neuron-specific genes in non-neuronal cells, plays a pivotal role in the transcriptional regulation of ANP, BNP and other fetal cardiac genes. Here we review the transcriptional regulation of ANP and BNP gene expression and the role of the NRSF repressor complex in the regulation of cardiac gene expression and the maintenance of cardiac homeostasis.
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Affiliation(s)
- Hideaki Inazumi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Koichiro Kuwahara
- Department of Cardiovascular Medicine, School of Medicine, Shinshu University, 3-1-1 Asahi, Nagano 390-8621, Japan
- Correspondence: ; Tel.: +81-263-37-3191; Fax: +81-263-37-3195
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20
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Kim I, Choi S, Yoo S, Lee M, Park JW. AURKB, in concert with REST, acts as an oxygen-sensitive epigenetic regulator of the hypoxic induction of MDM2. BMB Rep 2022. [PMID: 35410638 PMCID: PMC9252896 DOI: 10.5483/bmbrep.2022.55.6.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The acute response to hypoxia is mainly driven by hypoxia-inducible factors, but their effects gradually subside with time. Hypoxia-specific histone modifications may be important for the stable maintenance of long-term adaptation to hypoxia. However, little is known about the molecular mechanisms underlying the dynamic alterations of histones under hypoxic conditions. We found that the phosphorylation of histone H3 at Ser-10 (H3S10) was noticeably attenuated after hypoxic challenge, which was mediated by the inhibition of aurora kinase B (AURKB). To understand the role of AURKB in epigenetic regulation, DNA microarray and transcription factor binding site analyses combined with proteomics analysis were performed. Under normoxia, phosphorylated AURKB, in concert with the repressor element-1 silencing transcription factor (REST), phosphorylates H3S10, which allows the AURKB–REST complex to access the MDM2 proto-oncogene. REST then acts as a transcriptional repressor of MDM2 and downregulates its expression. Under hypoxia, AURKB is dephosphorylated and the AURKB–REST complex fails to access MDM2, leading to the upregulation of its expression. In this study, we present a case of hypoxia-specific epigenetic regulation of the oxygen-sensitive AURKB signaling pathway. To better understand the cellular adaptation to hypoxia, it is worthwhile to further investigate the epigenetic regulation of genes under hypoxic conditions.
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Affiliation(s)
- Iljin Kim
- Department of Pharmacology, Inha University College of Medicine, Incheon 22212, Korea
| | - Sanga Choi
- Department of Pharmacology, Inha University College of Medicine, Incheon 22212, Korea
| | - Seongkyeong Yoo
- Department of Pharmacology, Inha University College of Medicine, Incheon 22212, Korea
| | - Mingyu Lee
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, MA, USA
| | - Jong-Wan Park
- Department of Pharmacology, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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21
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Swaminathan J, Maegawa S, Shaik S, Sharma A, Bravo-Alegria J, Guo L, Xu L, Harmanci A, Gopalakrishnan V. Cross-Talk Between Histone Methyltransferases and Demethylases Regulate REST Transcription During Neurogenesis. Front Oncol 2022; 12:855167. [PMID: 35600406 PMCID: PMC9120943 DOI: 10.3389/fonc.2022.855167] [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: 01/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The RE1 Silencing Transcription Factor (REST) is a major regulator of neurogenesis and brain development. Medulloblastoma (MB) is a pediatric brain cancer characterized by a blockade of neuronal specification. REST gene expression is aberrantly elevated in a subset of MBs that are driven by constitutive activation of sonic hedgehog (SHH) signaling in cerebellar granular progenitor cells (CGNPs), the cells of origin of this subgroup of tumors. To understand its transcriptional deregulation in MBs, we first studied control of Rest gene expression during neuronal differentiation of normal mouse CGNPs. Higher Rest expression was observed in proliferating CGNPs compared to differentiating neurons. Interestingly, two Rest isoforms were expressed in CGNPs, of which only one showed a significant reduction in expression during neurogenesis. In proliferating CGNPs, higher MLL4 and KDM7A activities opposed by the repressive polycomb repressive complex 2 (PRC2) and the G9A/G9A-like protein (GLP) complex function allowed Rest homeostasis. During differentiation, reduction in MLL4 enrichment on chromatin, in conjunction with an increase in PRC2/G9A/GLP/KDM7A activities promoted a decline in Rest expression. These findings suggest a lineage-context specific paradoxical role for KDM7A in the regulation of Rest expression in CGNPs. In human SHH-MBs (SHH-α and SHH-β) where elevated REST gene expression is associated with poor prognosis, up- or downregulation of KDM7A caused a significant worsening in patient survival. Our studies are the first to implicate KDM7A in REST regulation and in MB biology.
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Affiliation(s)
- Jyothishmathi Swaminathan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shinji Maegawa
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Shavali Shaik
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Ajay Sharma
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Javiera Bravo-Alegria
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, United States
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Department of Molecular and Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Brain Tumor Center - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Center for Cancer Epigenetics - University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- MD Anderson-UTHealth Science Center Graduate School of Biomedical Sciences, Houston, TX, United States
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22
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Duly AMP, Kao FCL, Teo WS, Kavallaris M. βIII-Tubulin Gene Regulation in Health and Disease. Front Cell Dev Biol 2022; 10:851542. [PMID: 35573698 PMCID: PMC9096907 DOI: 10.3389/fcell.2022.851542] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Microtubule proteins form a dynamic component of the cytoskeleton, and play key roles in cellular processes, such as vesicular transport, cell motility and mitosis. Expression of microtubule proteins are often dysregulated in cancer. In particular, the microtubule protein βIII-tubulin, encoded by the TUBB3 gene, is aberrantly expressed in a range of epithelial tumours and is associated with drug resistance and aggressive disease. In normal cells, TUBB3 expression is tightly restricted, and is found almost exclusively in neuronal and testicular tissues. Understanding the mechanisms that control TUBB3 expression, both in cancer, mature and developing tissues will help to unravel the basic biology of the protein, its role in cancer, and may ultimately lead to the development of new therapeutic approaches to target this protein. This review is devoted to the transcriptional and posttranscriptional regulation of TUBB3 in normal and cancerous tissue.
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Affiliation(s)
- Alastair M. P. Duly
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
| | - Felicity C. L. Kao
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
- School of Women and Children’s Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wee Siang Teo
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
| | - Maria Kavallaris
- Children’s Cancer Institute, Lowy Cancer Research Center, UNSW Sydney, Randwick, NSW, Australia
- Australian Center for NanoMedicine, UNSW Sydney, Sydney, NSW, Australia
- School of Women and Children’s Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW, Australia
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23
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Su XJ, Shen BD, Wang K, Song QX, Yang X, Wu DS, Shen HX, Zhu C. Roles of the Neuron-Restrictive Silencer Factor in the Pathophysiological Process of the Central Nervous System. Front Cell Dev Biol 2022; 10:834620. [PMID: 35300407 PMCID: PMC8921553 DOI: 10.3389/fcell.2022.834620] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The neuron-restrictive silencer factor (NRSF), also known as repressor element 1 (RE-1) silencing transcription factor (REST) or X2 box repressor (XBR), is a zinc finger transcription factor that is widely expressed in neuronal and non-neuronal cells. It is a master regulator of the nervous system, and the function of NRSF is the basis of neuronal differentiation, diversity, plasticity, and survival. NRSF can bind to the neuron-restrictive silencer element (NRSE), recruit some co-repressors, and then inhibit transcription of NRSE downstream genes through epigenetic mechanisms. In neurogenesis, NRSF functions not only as a transcriptional silencer that can mediate the transcriptional inhibition of neuron-specific genes in non-neuronal cells and thus give neuron cells specificity, but also as a transcriptional activator to induce neuronal differentiation. Many studies have confirmed the association between NRSF and brain disorders, such as brain injury and neurodegenerative diseases. Overexpression, underexpression, or mutation may lead to neurological disorders. In tumorigenesis, NRSF functions as an oncogene in neuronal tumors, such as neuroblastomas, medulloblastomas, and pheochromocytomas, stimulating their proliferation, which results in poor prognosis. Additionally, NRSF-mediated selective targets gene repression plays an important role in the development and maintenance of neuropathic pain caused by nerve injury, cancer, and diabetes. At present, several compounds that target NRSF or its co-repressors, such as REST-VP16 and X5050, have been shown to be clinically effective against many brain diseases, such as seizures, implying that NRSF and its co-repressors may be potential and promising therapeutic targets for neural disorders. In the present review, we introduced the biological characteristics of NRSF; reviewed the progress to date in understanding the roles of NRSF in the pathophysiological processes of the nervous system, such as neurogenesis, brain disorders, neural tumorigenesis, and neuropathic pain; and suggested new therapeutic approaches to such brain diseases.
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Affiliation(s)
- Xin-Jin Su
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bei-Duo Shen
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Kun Wang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Xin Song
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xue Yang
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - De-Sheng Wu
- Department of Spine Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Hong-Xing Shen
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhu
- Department of Spine Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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24
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Alles SRA, Smith PA. Peripheral Voltage-Gated Cation Channels in Neuropathic Pain and Their Potential as Therapeutic Targets. FRONTIERS IN PAIN RESEARCH 2022; 2:750583. [PMID: 35295464 PMCID: PMC8915663 DOI: 10.3389/fpain.2021.750583] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
The persistence of increased excitability and spontaneous activity in injured peripheral neurons is imperative for the development and persistence of many forms of neuropathic pain. This aberrant activity involves increased activity and/or expression of voltage-gated Na+ and Ca2+ channels and hyperpolarization activated cyclic nucleotide gated (HCN) channels as well as decreased function of K+ channels. Because they display limited central side effects, peripherally restricted Na+ and Ca2+ channel blockers and K+ channel activators offer potential therapeutic approaches to pain management. This review outlines the current status and future therapeutic promise of peripherally acting channel modulators. Selective blockers of Nav1.3, Nav1.7, Nav1.8, Cav3.2, and HCN2 and activators of Kv7.2 abrogate signs of neuropathic pain in animal models. Unfortunately, their performance in the clinic has been disappointing; some substances fail to meet therapeutic end points whereas others produce dose-limiting side effects. Despite this, peripheral voltage-gated cation channels retain their promise as therapeutic targets. The way forward may include (i) further structural refinement of K+ channel activators such as retigabine and ASP0819 to improve selectivity and limit toxicity; use or modification of Na+ channel blockers such as vixotrigine, PF-05089771, A803467, PF-01247324, VX-150 or arachnid toxins such as Tap1a; the use of Ca2+ channel blockers such as TTA-P2, TTA-A2, Z 944, ACT709478, and CNCB-2; (ii) improving methods for assessing “pain” as opposed to nociception in rodent models; (iii) recognizing sex differences in pain etiology; (iv) tailoring of therapeutic approaches to meet the symptoms and etiology of pain in individual patients via quantitative sensory testing and other personalized medicine approaches; (v) targeting genetic and biochemical mechanisms controlling channel expression using anti-NGF antibodies such as tanezumab or re-purposed drugs such as vorinostat, a histone methyltransferase inhibitor used in the management of T-cell lymphoma, or cercosporamide a MNK 1/2 inhibitor used in treatment of rheumatoid arthritis; (vi) combination therapy using drugs that are selective for different channel types or regulatory processes; (vii) directing preclinical validation work toward the use of human or human-derived tissue samples; and (viii) application of molecular biological approaches such as clustered regularly interspaced short palindromic repeats (CRISPR) technology.
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Affiliation(s)
- Sascha R A Alles
- Department of Anesthesiology and Critical Care Medicine, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Peter A Smith
- Department of Pharmacology, Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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25
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Epigenetic mechanisms in paediatric brain tumours: regulators lose control. Biochem Soc Trans 2022; 50:167-185. [PMID: 35076654 DOI: 10.1042/bst20201227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms are essential to regulate gene expression during normal development. However, they are often disrupted in pathological conditions including tumours, where they contribute to their formation and maintenance through altered gene expression. In recent years, next generation genomic techniques has allowed a remarkable advancement of our knowledge of the genetic and molecular landscape of paediatric brain tumours and have highlighted epigenetic deregulation as a common hallmark in their pathogenesis. This review describes the main epigenetic dysregulations found in paediatric brain tumours, including at DNA methylation and histone modifications level, in the activity of chromatin-modifying enzymes and in the expression of non-coding RNAs. How these altered processes influence tumour biology and how they can be leveraged to dissect the molecular heterogeneity of these tumours and contribute to their classification is also addressed. Finally, the availability and value of preclinical models as well as the current clinical trials exploring targeting key epigenetic mediators in paediatric brain tumours are discussed.
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26
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Roy B, Lee E, Li T, Rampersaud M. Role of miRNAs in Neurodegeneration: From Disease Cause to Tools of Biomarker Discovery and Therapeutics. Genes (Basel) 2022; 13:genes13030425. [PMID: 35327979 PMCID: PMC8951370 DOI: 10.3390/genes13030425] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans are living with Alzheimer’s disease, and there is a possibility that there will be 1.2 million Parkinson’s disease patients in the USA by 2030. There is no clear-cut universal mechanism for identifying neurodegenerative diseases, and therefore, they pose a challenge for neurobiology scientists. Genetic and environmental factors modulate these diseases leading to familial or sporadic forms. Prior studies have shown that miRNA levels are altered during the course of the disease, thereby suggesting that these noncoding RNAs may be the contributing factor in neurodegeneration. In this review, we highlight the role of miRNAs in the pathogenesis of neurodegenerative diseases. Through this review, we aim to achieve four main objectives: First, we highlight how dysregulation of miRNA biogenesis led to these diseases. Second, we highlight the computational or bioinformatics tools required to identify the putative molecular targets of miRNAs, leading to biological molecular pathways or mechanisms involved in these diseases. Third, we focus on the dysregulation of miRNAs and their target genes leading to several neurodegenerative diseases. In the final section, we highlight the use of miRNAs as potential diagnostic biomarkers in the early asymptomatic preclinical diagnosis of these age-dependent debilitating diseases. Additionally, we discuss the challenges and advances in the development of miRNA therapeutics for brain targeting. We list some of the innovative strategies employed to deliver miRNA into target cells and the relevance of these viral and non-viral carrier systems in RNA therapy for neurodegenerative diseases. In summary, this review highlights the relevance of studying brain-enriched miRNAs, the mechanisms underlying their regulation of target gene expression, their dysregulation leading to progressive neurodegeneration, and their potential for biomarker marker and therapeutic intervention. This review thereby highlights ways for the effective diagnosis and prevention of these neurodegenerative disorders in the near future.
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Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07012, USA
- Correspondence:
| | - Erica Lee
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Teresa Li
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Maria Rampersaud
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
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27
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Krauß L, Urban BC, Hastreiter S, Schneider C, Wenzel P, Hassan Z, Wirth M, Lankes K, Terrasi A, Klement C, Cernilogar FM, Öllinger R, de Andrade Krätzig N, Engleitner T, Schmid RM, Steiger K, Rad R, Krämer OH, Reichert M, Schotta G, Saur D, Schneider G. HDAC2 Facilitates Pancreatic Cancer Metastasis. Cancer Res 2022; 82:695-707. [PMID: 34903606 PMCID: PMC9359718 DOI: 10.1158/0008-5472.can-20-3209] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023]
Abstract
The mortality of patients with pancreatic ductal adenocarcinoma (PDAC) is strongly associated with metastasis, a multistep process that is incompletely understood in this disease. Although genetic drivers of PDAC metastasis have not been defined, transcriptional and epigenetic rewiring can contribute to the metastatic process. The epigenetic eraser histone deacetylase 2 (HDAC2) has been connected to less differentiated PDAC, but the function of HDAC2 in PDAC has not been comprehensively evaluated. Using genetically defined models, we show that HDAC2 is a cellular fitness factor that controls cell cycle in vitro and metastasis in vivo, particularly in undifferentiated, mesenchymal PDAC cells. Unbiased expression profiling detected a core set of HDAC2-regulated genes. HDAC2 controlled expression of several prosurvival receptor tyrosine kinases connected to mesenchymal PDAC, including PDGFRα, PDGFRβ, and EGFR. The HDAC2-maintained program disabled the tumor-suppressive arm of the TGFβ pathway, explaining impaired metastasis formation of HDAC2-deficient PDAC. These data identify HDAC2 as a tractable player in the PDAC metastatic cascade. The complexity of the function of epigenetic regulators like HDAC2 implicates that an increased understanding of these proteins is needed for implementation of effective epigenetic therapies. SIGNIFICANCE HDAC2 has a context-specific role in undifferentiated PDAC and the capacity to disseminate systemically, implicating HDAC2 as targetable protein to prevent metastasis.
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Affiliation(s)
- Lukas Krauß
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Bettina C. Urban
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Sieglinde Hastreiter
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Carolin Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Patrick Wenzel
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, German
| | - Katharina Lankes
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Andrea Terrasi
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Christine Klement
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Filippo M. Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Roland M. Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University of Mainz Medical Center, Mainz, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, München, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
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28
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:ijms23031072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Correspondence: ; Tel.: +49-(0)381-494-5879; Fax: +49-(0)381-494-5882
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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29
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Rizavi HS, Chase KA, Liu C, Gavin H, Rosen C, Xia C, Guidotti A, Sharma RP. Differential H3K9me2 heterochromatin levels and concordant mRNA expression in postmortem brain tissue of individuals with schizophrenia, bipolar, and controls. Front Psychiatry 2022; 13:1006109. [PMID: 36386965 PMCID: PMC9644155 DOI: 10.3389/fpsyt.2022.1006109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
The existence of repressive and durable chromatin assemblies along gene promoters or networks, especially in the brain, is of theoretical and therapeutic relevance in a subset of individuals diagnosed with schizophrenia who experience a chronic, persistent, and treatment-resistant trajectory. We used chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) to generate an epigenomic map that includes differential sites occupied by di-methylated lysine 9 of histone 3 (H3K9me2), a repressive modification that is yet unexplored in human postmortem brain tissue. We have discovered over 150 significantly differential promoter sites in the postmortem prefrontal cortex tissue of individuals diagnosed with schizophrenia (n = 15) when compared to controls (n = 15). Potentially dysregulated gene categories include postsynaptic proteins, processing enzymes (for proproteins, lipids, and oxidative stress), cadherin family genes, the complement system, and peptide hormones. Ten genes with significantly increased or decreased H3K9me2 promoter occupation were selected through statistical analysis, function, or previous GWAS association, and Quantitative RT-PCR (qRT-PCR) was performed on an extended sample of postmortem brain tissue, adding an additional 17 controls, 7 individuals with schizophrenia, and 19 individuals with bipolar samples (n = 32 control, 22 schizophrenia, 19 bipolar). This approach revealed that mRNA expression levels correlated with chromatin modification levels in eight of 10 selected genes, and mRNA expression in the total sample could be predicted by the occupancy of H3K9me2. Utilization of this method and replication in a larger sample open a pathway to durable and restrictive epigenomic assemblies whose accumulation across the lifespan of individuals diagnosed with schizophrenia may explain treatment resistance, and advance therapeutic options.
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Affiliation(s)
- Hooriyah S Rizavi
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| | - Kayla A Chase
- Department of Biochemistry and Molecular Biology, University of Illinois at Chicago, Chicago, IL, United States
| | - Chunyu Liu
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Hannah Gavin
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Cherise Rosen
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Cuihua Xia
- School of Life Sciences, Central South University, Changsha, China
| | - Alessandro Guidotti
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Rajiv P Sharma
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
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30
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Yang T, Guo R, Ofengeim D, Hwang JY, Zukin RS, Chen J, Zhang F. Molecular and Cellular Mechanisms of Ischemia-Induced Neuronal Death. Stroke 2022. [DOI: 10.1016/b978-0-323-69424-7.00005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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31
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Prestigio C, Ferrante D, Marte A, Romei A, Lignani G, Onofri F, Valente P, Benfenati F, Baldelli P. REST/NRSF drives homeostatic plasticity of inhibitory synapses in a target-dependent fashion. eLife 2021; 10:e69058. [PMID: 34855580 PMCID: PMC8639147 DOI: 10.7554/elife.69058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
The repressor-element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF) controls hundreds of neuron-specific genes. We showed that REST/NRSF downregulates glutamatergic transmission in response to hyperactivity, thus contributing to neuronal homeostasis. However, whether GABAergic transmission is also implicated in the homeostatic action of REST/NRSF is unknown. Here, we show that hyperactivity-induced REST/NRSF activation, triggers a homeostatic rearrangement of GABAergic inhibition, with increased frequency of miniature inhibitory postsynaptic currents (IPSCs) and amplitude of evoked IPSCs in mouse cultured hippocampal neurons. Notably, this effect is limited to inhibitory-onto-excitatory neuron synapses, whose density increases at somatic level and decreases in dendritic regions, demonstrating a complex target- and area-selectivity. The upscaling of perisomatic inhibition was occluded by TrkB receptor inhibition and resulted from a coordinated and sequential activation of the Npas4 and Bdnf gene programs. On the opposite, the downscaling of dendritic inhibition was REST-dependent, but BDNF-independent. The findings highlight the central role of REST/NRSF in the complex transcriptional responses aimed at rescuing physiological levels of network activity in front of the ever-changing environment.
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Affiliation(s)
- Cosimo Prestigio
- Department of Experimental Medicine, University of GenovaGenovaItaly
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Daniele Ferrante
- Department of Experimental Medicine, University of GenovaGenovaItaly
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Antonella Marte
- Department of Experimental Medicine, University of GenovaGenovaItaly
| | - Alessandra Romei
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square HouseLondonUnited Kingdom
| | - Franco Onofri
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Pierluigi Valente
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di TecnologiaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
| | - Pietro Baldelli
- Department of Experimental Medicine, University of GenovaGenovaItaly
- IRCCS, Ospedale Policlinico San MartinoGenovaItaly
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Schreiter T, Gieseler RK, Vílchez-Vargas R, Jauregui R, Sowa JP, Klein-Scory S, Broering R, Croner RS, Treckmann JW, Link A, Canbay A. Transcriptome-Wide Analysis of Human Liver Reveals Age-Related Differences in the Expression of Select Functional Gene Clusters and Evidence for a PPP1R10-Governed 'Aging Cascade'. Pharmaceutics 2021; 13:pharmaceutics13122009. [PMID: 34959291 PMCID: PMC8709089 DOI: 10.3390/pharmaceutics13122009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 12/27/2022] Open
Abstract
A transcriptome-wide analysis of human liver for demonstrating differences between young and old humans has not yet been performed. However, identifying major age-related alterations in hepatic gene expression may pinpoint ontogenetic shifts with important hepatic and systemic consequences, provide novel pharmacogenetic information, offer clues to efficiently counteract symptoms of old age, and improve the overarching understanding of individual decline. Next-generation sequencing (NGS) data analyzed by the Mann-Whitney nonparametric test and Ensemble Feature Selection (EFS) bioinformatics identified 44 transcripts among 60,617 total and 19,986 protein-encoding transcripts that significantly (p = 0.0003 to 0.0464) and strikingly (EFS score > 0.3:16 transcripts; EFS score > 0.2:28 transcripts) differ between young and old livers. Most of these age-related transcripts were assigned to the categories 'regulome', 'inflammaging', 'regeneration', and 'pharmacogenes'. NGS results were confirmed by quantitative real-time polymerase chain reaction. Our results have important implications for the areas of ontogeny/aging and the age-dependent increase in major liver diseases. Finally, we present a broadly substantiated and testable hypothesis on a genetically governed 'aging cascade', wherein PPP1R10 acts as a putative ontogenetic master regulator, prominently flanked by IGFALS and DUSP1. This transcriptome-wide analysis of human liver offers potential clues towards developing safer and improved therapeutic interventions against major liver diseases and increased insights into key mechanisms underlying aging.
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Affiliation(s)
- Thomas Schreiter
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Robert K. Gieseler
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ramiro Vílchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ruy Jauregui
- Data Science Grasslands, Grasslands Research Centre, AgResearch, Palmerston North 4410, New Zealand;
| | - Jan-Peter Sowa
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Susanne Klein-Scory
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Laboratory of Immunology & Molecular Biology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
| | - Ruth Broering
- Department of Gastroenterology and Hepatology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Roland S. Croner
- Department of General, Visceral, Vascular and Transplantation Surgery, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Jürgen W. Treckmann
- Department of General, Visceral and Transplantation Surgery, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Ali Canbay
- Department of Medicine, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany; (T.S.); (R.K.G.); (J.-P.S.); (S.K.-S.)
- Section of Hepatology and Gastroenterology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, 44892 Bochum, Germany
- Correspondence: ; Tel.: +49-234-299-3401
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Martinez B, Peplow PV. Altered microRNA expression in animal models of Huntington's disease and potential therapeutic strategies. Neural Regen Res 2021; 16:2159-2169. [PMID: 33818488 PMCID: PMC8354140 DOI: 10.4103/1673-5374.310673] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A review of recent animal models of Huntington's disease showed many microRNAs had altered expression levels in the striatum and cerebral cortex, and which were mostly downregulated. Among the altered microRNAs were miR-9/9*, miR-29b, miR-124a, miR-132, miR-128, miR-139, miR-122, miR-138, miR-23b, miR-135b, miR-181 (all downregulated) and miR-448 (upregulated), and similar changes had been previously found in Huntington's disease patients. In the animal cell studies, the altered microRNAs included miR-9, miR-9*, miR-135b, miR-222 (all downregulated) and miR-214 (upregulated). In the animal models, overexpression of miR-155 and miR-196a caused a decrease in mutant huntingtin mRNA and protein level, lowered the mutant huntingtin aggregates in striatum and cortex, and improved performance in behavioral tests. Improved performance in behavioral tests also occurred with overexpression of miR-132 and miR-124. In the animal cell models, overexpression of miR-22 increased the viability of rat primary cortical and striatal neurons infected with mutant huntingtin and decreased huntingtin -enriched foci of ≥ 2 µm. Also, overexpression of miR-22 enhanced the survival of rat primary striatal neurons treated with 3-nitropropionic acid. Exogenous expression of miR-214, miR-146a, miR-150, and miR-125b decreased endogenous expression of huntingtin mRNA and protein in HdhQ111/HdhQ111 cells. Further studies with animal models of Huntington's disease are warranted to validate these findings and identify specific microRNAs whose overexpression inhibits the production of mutant huntingtin protein and other harmful processes and may provide a more effective means of treating Huntington's disease in patients and slowing its progression.
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Affiliation(s)
- Bridget Martinez
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Medicine, St. Georges University School of Medicine, Grenada
| | - Philip V. Peplow
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Correspondence to: Philip V. Peplow, .
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Fonseca-Barriendos D, Frías-Soria CL, Pérez-Pérez D, Gómez-López R, Borroto Escuela DO, Rocha L. Drug-resistant epilepsy: Drug target hypothesis and beyond the receptors. Epilepsia Open 2021; 7 Suppl 1:S23-S33. [PMID: 34542940 PMCID: PMC9340308 DOI: 10.1002/epi4.12539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a chronic neurological disorder that affects more than 50 million people worldwide. Despite a recent introduction of antiseizure drugs for the treatment of epileptic seizures, one-third of these patients suffer from drug-resistant epilepsy (DRE). The therapeutic target hypothesis is a cited theory to explain DRE. According to the target hypothesis, the failure to achieve seizure freedom leads to alteration of the structure and/or function of the antiseizure medication (ASM) target. However, this hypothesis fails to explain why patients with DRE do not respond to antiseizure medications of different targets. This review presents different conditions, such as epigenetic mechanisms and protein-protein interactions that may result in alterations of diverse drug targets using different mechanisms. These novel conditions represent new targets to control DRE.
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Affiliation(s)
| | | | - Daniel Pérez-Pérez
- Plan of Combined Studies in Medicine (PECEM), Faculty of Medicine, UNAM, México City, Mexico
| | - Rosenda Gómez-López
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City, México
| | | | - Luisa Rocha
- Pharmacobiology Department, Center for Research and Advanced Studies, México City, México
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He R, Zhang X, Ding L. DBX2 promotes glioblastoma cell proliferation by regulating REST expression. Curr Pharm Biotechnol 2021; 23:1101-1108. [PMID: 34463226 DOI: 10.2174/1389201022666210830142827] [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: 03/06/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glioblastoma (GBM) is the most common but lethal brain cancer with poor prognosis. The developing brain homeobox 2 (DBX2) has been reported to play important roles in tumor growth. However, the mechanisms of DBX2 in GBM are still unknown. OBJECTIVE This study aims to investigate the function and mechanisms of DBX2 in GBM. METHODS The expressions of DBX2 and REST in GBM were measured by analyzing data from databases, and the results were checked by qPCR and/or western blot of GBM cell lines. Cell proliferation was determined by CCK8 assay, immunohistochemistry and colony formation assay. ChIP-qPCR was used to determine the binding sites of DBX2 on REST. RESULTS In this study, we found that the expression of DBX2 was upregulated in the GBM cell lines. The cell proliferation was damaged after blocking DBX2 expression in U87 and U251 GBM cell lines. The expression level of DBX2 had a positive relationship with that of REST. Our ChIP-qPCR results showed that DBX2 is directly bound to the promoter region of REST. Additionally, the increased GBM cell proliferation caused by DBX2 overexpression can be rescued by REST loss of function. CONCLUSION DBX2 could promote cell proliferation of GBM by binding to the promoter region of REST gene and increasing REST expression.
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Affiliation(s)
- Ruixing He
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
| | - Xiaotian Zhang
- Neurosurgery Department, Hongze Huai'an District People's Hospital, Jiangsu. China
| | - Lianshu Ding
- Neurosurgery Department, the Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Jiangsu. China
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Maciaszek JL, Oak N, Nichols KE. Recent advances in Wilms' tumor predisposition. Hum Mol Genet 2021; 29:R138-R149. [PMID: 32412586 DOI: 10.1093/hmg/ddaa091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Wilms' tumor (WT), the most common childhood kidney cancer, develops in association with an underlying germline predisposition in up to 15% of cases. Germline alterations affecting the WT1 gene and epigenetic alterations affecting the 11p15 locus are associated with a selective increase in WT risk. Nevertheless, WT also occurs in the context of more pleiotropic cancer predispositions, such as DICER1, Li-Fraumeni and Bloom syndrome, as well as Fanconi anemia. Recent germline genomic investigations have increased our understanding of the host genetic factors that influence WT risk, with sequencing of rare familial cases and large WT cohorts revealing an expanding array of predisposition genes and associated genetic conditions. Here, we describe evidence implicating WT1, the 11p15 locus, and the recently identified genes CTR9, REST and TRIM28 in WT predisposition. We discuss the clinical features, mode of inheritance and biological aspects of tumorigenesis, when known. Despite these described associations, many cases of familial WT remain unexplained. Continued investigations are needed to fully elucidate the landscape of germline genetic alterations in children with WT. Establishing a genetic diagnosis is imperative for WT families so that individuals harboring a predisposing germline variant can undergo surveillance, which should enable the early detection of tumors and use of less intensive treatments, thereby leading to improved overall outcomes.
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Affiliation(s)
- Jamie L Maciaszek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ninad Oak
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Dong X, Cong S. MicroRNAs in Huntington's Disease: Diagnostic Biomarkers or Therapeutic Agents? Front Cell Neurosci 2021; 15:705348. [PMID: 34421543 PMCID: PMC8377808 DOI: 10.3389/fncel.2021.705348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/20/2021] [Indexed: 01/01/2023] Open
Abstract
MicroRNA (miRNA) is a non-coding single-stranded small molecule of approximately 21 nucleotides. It degrades or inhibits the translation of RNA by targeting the 3′-UTR. The miRNA plays an important role in the growth, development, differentiation, and functional execution of the nervous system. Dysregulated miRNA expression has been associated with several pathological processes of neurodegenerative disorders, including Huntington’s disease (HD). Recent studies have suggested promising roles of miRNAs as biomarkers and potential therapeutic targets for HD. Here, we review the emerging role of dysregulated miRNAs in HD and describe general biology of miRNAs, their pathophysiological implications, and their potential roles as biomarkers and therapeutic agents.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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Butler-Ryan R, Wood IC. The functions of repressor element 1-silencing transcription factor in models of epileptogenesis and post-ischemia. Metab Brain Dis 2021; 36:1135-1150. [PMID: 33813634 PMCID: PMC8272694 DOI: 10.1007/s11011-021-00719-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
Epilepsy is a debilitating neurological disorder characterised by recurrent seizures for which 30% of patients are refractory to current treatments. The genetic and molecular aetiologies behind epilepsy are under investigation with the goal of developing new epilepsy medications. The transcriptional repressor REST (Repressor Element 1-Silencing Transcription factor) is a focus of interest as it is consistently upregulated in epilepsy patients and following brain insult in animal models of epilepsy and ischemia. This review analyses data from different epilepsy models and discusses the contribution of REST to epileptogenesis. We propose that in healthy brains REST acts in a protective manner to homeostatically downregulate increases in excitability, to protect against seizure through downregulation of BDNF (Brain-Derived Neurotrophic Factor) and its receptor, TrkB (Tropomyosin receptor kinase B). However, in epilepsy patients and post-seizure, REST may increase to a larger degree, which allows downregulation of the glutamate receptor subunit GluR2. This leads to AMPA glutamate receptors lacking GluR2 subunits, which have increased permeability to Ca2+, causing excitotoxicity, cell death and seizure. This concept highlights therapeutic potential of REST modulation through gene therapy in epilepsy patients.
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Affiliation(s)
- Ruth Butler-Ryan
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
| | - Ian C. Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
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Pereira V, Lamoine S, Cuménal M, Lolignier S, Aissouni Y, Pizzoccaro A, Prival L, Balayssac D, Eschalier A, Bourinet E, Busserolles J. Epigenetics Involvement in Oxaliplatin-Induced Potassium Channel Transcriptional Downregulation and Hypersensitivity. Mol Neurobiol 2021; 58:3575-3587. [PMID: 33772465 DOI: 10.1007/s12035-021-02361-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/15/2021] [Indexed: 01/10/2023]
Abstract
Peripheral neuropathy is the most frequent dose-limiting adverse effect of oxaliplatin. Acute pain symptoms that are induced or exacerbated by cold occur in almost all patients immediately following the first infusions. Evidence has shown that oxaliplatin causes ion channel expression modulations in dorsal root ganglia neurons, which are thought to contribute to peripheral hypersensitivity. Most dysregulated genes encode ion channels involved in cold and mechanical perception, noteworthy members of a sub-group of potassium channels of the K2P family, TREK and TRAAK. Downregulation of these K2P channels has been identified as an important tuner of acute oxaliplatin-induced hypersensitivity. We investigated the molecular mechanisms underlying this peripheral dysregulation in a murine model of neuropathic pain triggered by a single oxaliplatin administration. We found that oxaliplatin-mediated TREK-TRAAK downregulation, as well as downregulation of other K+ channels of the K2P and Kv families, involves a transcription factor known as the neuron-restrictive silencer factor (NRSF) and its epigenetic co-repressors histone deacetylases (HDACs). NRSF knockdown was able to prevent most of these K+ channel mRNA downregulation in mice dorsal root ganglion neurons as well as oxaliplatin-induced acute cold and mechanical hypersensitivity. Interestingly, pharmacological inhibition of class I HDAC reproduces the antinociceptive effects of NRSF knockdown and leads to an increased K+ channel expression in oxaliplatin-treated mice.
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Affiliation(s)
- Vanessa Pereira
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Sylvain Lamoine
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Mélissa Cuménal
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Stéphane Lolignier
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Youssef Aissouni
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Anne Pizzoccaro
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS UMR-5203, INSERM U1091, F-34094, Montpellier, France
| | - Laetitia Prival
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - David Balayssac
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Alain Eschalier
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France
| | - Emmanuel Bourinet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS UMR-5203, INSERM U1091, F-34094, Montpellier, France
| | - Jérôme Busserolles
- Université Clermont Auvergne, Inserm UMR-U1107, Neuro-Dol, 28, pl. H.Dunant, F-63000, Clermont-Ferrand, France.
- Institut Analgesia, Faculté de Médecine, BP38, F-63001, Clermont-Ferrand, France.
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REST Inhibits Direct Reprogramming of Pancreatic Exocrine to Endocrine Cells by Preventing PDX1-Mediated Activation of Endocrine Genes. Cell Rep 2021; 31:107591. [PMID: 32375045 DOI: 10.1016/j.celrep.2020.107591] [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: 07/30/2019] [Revised: 01/29/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The emerging appreciation of plasticity among pancreatic lineages has created interest in harnessing cellular reprogramming for β cell replacement therapy of diabetes. Current reprogramming methodologies are inefficient, largely because of a limited understanding of the underlying mechanisms. Using an in vitro reprogramming system, we reveal the transcriptional repressor RE-1 silencing transcription factor (REST) as a barrier for β cell gene expression in the reprogramming of pancreatic exocrine cells. We observe that REST-bound loci lie adjacent to the binding sites of multiple key β cell transcription factors, including PDX1. Accordingly, a loss of REST function combined with PDX1 expression results in the synergistic activation of endocrine genes. This is accompanied by increased histone acetylation and PDX1 binding at endocrine gene loci. Collectively, our data identify a mechanism for REST activity involving the prevention of PDX1-mediated activation of endocrine genes and uncover REST downregulation and the resulting chromatin alterations as key events in β cell reprogramming.
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Tang Y, Jia Z, Xu H, Da LT, Wu Q. Mechanism of REST/NRSF regulation of clustered protocadherin α genes. Nucleic Acids Res 2021; 49:4506-4521. [PMID: 33849071 PMCID: PMC8096226 DOI: 10.1093/nar/gkab248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022] Open
Abstract
Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDHα genes. Thus, REST/NRSF represses PCDHα gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.
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Affiliation(s)
- Yuanxiao Tang
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhilian Jia
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Honglin Xu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-tai Da
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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Low REST Expression Indicates a Biomarker of Poor Prognosis in Patients with Renal Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6682758. [PMID: 33834072 PMCID: PMC8012131 DOI: 10.1155/2021/6682758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 11/25/2022]
Abstract
It was initially found that neural-restrictive silencer factor/repressor 1-silencing transcription factor (REST) is a transcriptional repressor of neuronal genes in nonneuronal cells. However, it is reported to be abundantly expressed in various types of aggressive cancer cells. In this study, we evaluated the expression patterns of REST in renal cell carcinoma and found that its expression is lower in tumor tissues compared to normal tissues. The chi-square test showed that the low REST expression was closely related to patients' clinicopathologic parameters, including the pathologic stage and survival status. ROC curve showed that REST had excellent clinical diagnostic prospect. In addition, patients with low REST expression had poor over survival (OS) and relapse-free survival (RFS). Univariate and multivariate Cox regression analysis confirmed that the low REST expression was an independent predictor of poor prognosis in renal cell carcinoma. Gene set enrichment analysis identified P53 pathway, reactive oxygen species pathway, glycolysis, DNA repair, cholesterol homeostasis, and MYC targets V2 enriched with low REST expression phenotype. These results suggested that REST may be a novel biomarker for the diagnosis and prognosis of renal cell carcinoma in clinical applications.
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Butler-Ryan R, Wood IC. Efficient infection of organotypic hippocampal slice cultures with adenovirus carrying the transgene REST/NRSF. J Neurosci Methods 2021; 356:109147. [PMID: 33771654 DOI: 10.1016/j.jneumeth.2021.109147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
Organotypic hippocampal slice cultures provide a useful platform maintaining hippocampal structure and synaptic connections of the brain over weeks in culture with ease of in vitro manipulations. Gene transfer is a particularly desirable tool for using with them but current difficulties with transformation of transgenes into these cultures is a barrier to their use in research. Previous quantifications of viral infections have shown low transformation rates and have relied upon invasive microinjections. In this paper we present an efficient way of infecting organotypic cultures with adenovirus at the acute slice stage that does not require injection. We use the adenoviral delivery system to introduce the transcription factor REST and a GFP marker, providing around 41 % cellular infection spread throughout the entire slice culture and promoting transgene expression for weeks in vitro. GFP expression was observed most intensely in the slices when they were infected just a few hours after plating and was shown to infect neurons and microglia. We decided to use the transcription factor REST/NRSF as an example transgene which was delivered into cells via the adenoviral construct, conferring overexpression of REST in addition to the GFP marker. This outlines a technique whereby adenoviral infection of organotypic cultures can infect neurons with good efficiency and confer successful manipulation of genetic factors within the cell.
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Affiliation(s)
- Ruth Butler-Ryan
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Ian C Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities. Sci Rep 2021; 11:6178. [PMID: 33731831 PMCID: PMC7971087 DOI: 10.1038/s41598-021-85612-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/19/2021] [Indexed: 11/08/2022] Open
Abstract
A preceding experiment suggested that a compound, which inhibits binding of the REST/NRSF segment to the cleft of a receptor protein mSin3B, can be a potential drug candidate to ameliorate many neuropathies. We have recently developed an enhanced conformational sampling method, genetic-algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics, and in the present study, applied it to three systems consisting of mSin3B and one of three compounds, sertraline, YN3, and acitretin. Other preceding experiments showed that only sertraline inhibits the binding of REST/NRSF to mSin3B. The current simulation study produced the spatial distribution of the compounds around mSin3B, and showed that sertraline and YN3 bound to the cleft of mSin3B with a high propensity, although acitretin did not. Further analyses of the simulation data indicated that only the sertraline-mSin3B complex produced a hydrophobic core similar to that observed in the molecular interface of the REST/NRSF-mSin3B complex: An aromatic ring of sertraline sunk deeply in the mSin3B's cleft forming a hydrophobic core contacting to hydrophobic amino-acid residues located at the bottom of the cleft. The present study proposes a step to design a compound that inhibits competitively the binding of a ligand to its receptor.
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Neuroendocrine-Related Circulating Transcripts in Small-Cell Lung Cancers: Detection Methods and Future Perspectives. Cancers (Basel) 2021; 13:cancers13061339. [PMID: 33809582 PMCID: PMC8061767 DOI: 10.3390/cancers13061339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The recent implementation of techniques to study circulating tumor cells allowed a rapid increase in knowledge about the molecular basis of Small-Cell Lung Cancer (SCLC), which appears to be more heterogeneous and dynamic than expected. Here, we present a summary of current knowledge and new findings about some of the neuroendocrine-related transcripts expressed in SCLC patients that could offer a great opportunity in distinguishing and managing different SCLC phenotypes. Abstract No well-established prognostic or predictive molecular markers of small-cell lung cancer (SCLC) are currently available; therefore, all patients receive standard treatment. Adequate quantities and quality of tissue samples are frequently unavailable to perform a molecular analysis of SCLC, which appears more heterogeneous and dynamic than expected. The implementation of techniques to study circulating tumor cells could offer a suitable alternative to expand the knowledge of the molecular basis of a tumor. In this context, the advantage of SCLC circulating cells to express some specific markers to be explored in blood as circulating transcripts could offer a great opportunity in distinguishing and managing different SCLC phenotypes. Here, we present a summary of published data and new findings about the detection methods and potential application of a group of neuroendocrine related transcripts in the peripheral blood of SCLC patients. In the era of new treatments, easy and rapid detection of informative biomarkers in blood warrants further investigation, since it represents an important option to obtain essential information for disease monitoring and/or better treatment choices.
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Zhu HE, Li T, Shi S, Chen DX, Chen W, Chen H. ESCO2 promotes lung adenocarcinoma progression by regulating hnRNPA1 acetylation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:64. [PMID: 33573689 PMCID: PMC7876794 DOI: 10.1186/s13046-021-01858-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Emerging evidence indicates that metabolism reprogramming and abnormal acetylation modification play an important role in lung adenocarcinoma (LUAD) progression, although the mechanism is largely unknown. METHODS Here, we used three public databases (Oncomine, Gene Expression Omnibus [GEO], The Cancer Genome Atlas [TCGA]) to analyze ESCO2 (establishment of cohesion 1 homolog 2) expression in LUAD. The biological function of ESCO2 was studiedusing cell proliferation, colony formation, cell migration, and invasion assays in vitro, and mouse xenograft models in vivo. ESCO2 interacting proteins were searched using gene set enrichment analysis (GSEA) and mass spectrometry. Pyruvate kinase M1/2 (PKM) mRNA splicing assay was performed using RT-PCR together with restriction digestion. LUAD cell metabolism was studied using glucose uptake assays and lactate production. ESCO2 expression was significantly upregulated in LUAD tissues, and higher ESCO2 expression indicated worse prognosis for patients with LUAD. RESULTS We found that ESCO2 promoted LUAD cell proliferation and metastasis metabolic reprogramming in vitro and in vivo. Mechanistically, ESCO2 increased hnRNPA1 (heterogeneous nuclear ribonucleoprotein A1) binding to the intronic sequences flanking exon 9 (EI9) of PKM mRNA by inhibiting hnRNPA1 nuclear translocation, eventually inhibiting PKM1 isoform formation and inducing PKM2 isoform formation. CONCLUSIONS Our findings confirm that ESCO2 is a key factor in promoting LUAD malignant progression and suggest that it is a new target for treating LUAD.
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Affiliation(s)
- Hui-Er Zhu
- Department of General Practice, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Tao Li
- Department of Anesthesiology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Shengnan Shi
- State Key Laboratory of Animal Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, South China Key Laboratory of Animal Nutrition and Feed, Ministry of Agriculture, Guangzhou, 510640, P. R. China
| | - De-Xiong Chen
- Department of General Practice, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China
| | - Weiping Chen
- Department of Respiratory, The People's Hospital of Qingyuan, Sixth Affiliate Hospital of Guangzhou Medical University, Qingyuan, 511518, P. R. China.
| | - Hui Chen
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, P.R. China.
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Szemes M, Melegh Z, Bellamy J, Park JH, Chen B, Greenhough A, Catchpoole D, Malik K. Transcriptomic Analyses of MYCN-Regulated Genes in Anaplastic Wilms' Tumour Cell Lines Reveals Oncogenic Pathways and Potential Therapeutic Vulnerabilities. Cancers (Basel) 2021; 13:656. [PMID: 33562123 PMCID: PMC7915280 DOI: 10.3390/cancers13040656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
The MYCN proto-oncogene is deregulated in many cancers, most notably in neuroblastoma, where MYCN gene amplification identifies a clinical subset with very poor prognosis. Gene expression and DNA analyses have also demonstrated overexpression of MYCN mRNA, as well as focal amplifications, copy number gains and presumptive change of function mutations of MYCN in Wilms' tumours with poorer outcomes, including tumours with diffuse anaplasia. Surprisingly, however, the expression and functions of the MYCN protein in Wilms' tumours still remain obscure. In this study, we assessed MYCN protein expression in primary Wilms' tumours using immunohistochemistry of tissue microarrays. We found MYCN protein to be expressed in tumour blastemal cells, and absent in stromal and epithelial components. For functional studies, we used two anaplastic Wilms' tumour cell-lines, WiT49 and 17.94, to study the biological and transcriptomic effects of MYCN depletion. We found that MYCN knockdown consistently led to growth suppression but not cell death. RNA sequencing identified 561 MYCN-regulated genes shared by WiT49 and 17.94 cell-lines. As expected, numerous cellular processes were downstream of MYCN. MYCN positively regulated the miRNA regulator and known Wilms' tumour oncogene LIN28B, the genes encoding methylosome proteins PRMT1, PRMT5 and WDR77, and the mitochondrial translocase genes TOMM20 and TIMM50. MYCN repressed genes including the developmental signalling receptor ROBO1 and the stromal marker COL1A1. Importantly, we found that MYCN also repressed the presumptive Wilms' tumour suppressor gene REST, with MYCN knockdown resulting in increased REST protein and concomitant repression of RE1-Silencing Transcription factor (REST) target genes. Together, our study identifies regulatory axes that interact with MYCN, providing novel pathways for potential targeted therapeutics for poor-prognosis Wilms' tumour.
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Affiliation(s)
- Marianna Szemes
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
| | - Zsombor Melegh
- Department of Cellular Pathology, Southmead Hospital, Bristol BS10 5NB, UK;
| | - Jacob Bellamy
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
| | - Ji Hyun Park
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
| | - Biyao Chen
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
| | - Alexander Greenhough
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
| | - Daniel Catchpoole
- The Kids Research Institute, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia;
| | - Karim Malik
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.B.); (J.H.P.); (B.C.); (A.G.)
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Abstract
PURPOSE OF REVIEW Neuroendocrine prostate cancer (NEPC) is an aggressive histologic subtype of prostate cancer that most commonly arises in later stages of prostate cancer as a mechanism of treatment resistance. The poor prognosis of NEPC is attributed in part to late diagnosis and a lack of effective therapeutic agents. Here, we review the clinical and molecular features of NEPC based on recent studies and outline future strategies and directions. RECENT FINDINGS NEPC can arise "de novo" but most commonly develops as a result of lineage plasticity whereby prostate cancer cells adopt alternative lineage programs as a means to bypass therapy. Dependence on androgen receptor (AR) signaling is lost as tumors progress from a prostate adenocarcinoma to a NEPC histology, typically manifested by the downregulation of AR, PSA, and PSMA expression in tumors. Genomic analyses from patient biopsies combined with preclinical modeling have pointed to loss of tumor suppressors RB1 and TP53 as key facilitators of lineage plasticity. Activation of oncogenic drivers combined with significant epigenetic changes (e.g., EZH2 overexpression, DNA methylation) further drives tumor proliferation and expression of downstream neuronal and neuroendocrine lineage pathways controlled in part by pioneer and lineage determinant transcription factors (e.g., SOX2, ASCL1, BRN2). These biologic insights have provided a framework for the study of this subgroup of advanced prostate cancers and have started to provide rationale for the development of biomarker-driven therapeutic strategies. Further study of the dynamic process that leads to NEPC is required for the development of effective strategies to identify and treat patients developing lineage plasticity as a mechanism of treatment resistance.
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The role of E3 ubiquitin ligases in the development and progression of glioblastoma. Cell Death Differ 2021; 28:522-537. [PMID: 33432111 PMCID: PMC7862665 DOI: 10.1038/s41418-020-00696-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Abstract
Despite recent advances in our understanding of the disease, glioblastoma (GB) continues to have limited treatment options and carries a dismal prognosis for patients. Efforts to stratify this heterogeneous malignancy using molecular classifiers identified frequent alterations in targetable proteins belonging to several pathways including the receptor tyrosine kinase (RTK) and mitogen-activated protein kinase (MAPK) signalling pathways. However, these findings have failed to improve clinical outcomes for patients. In almost all cases, GB becomes refractory to standard-of-care therapy, and recent evidence suggests that disease recurrence may be associated with a subpopulation of cells known as glioma stem cells (GSCs). Therefore, there remains a significant unmet need for novel therapeutic strategies. E3 ubiquitin ligases are a family of >700 proteins that conjugate ubiquitin to target proteins, resulting in an array of cellular responses, including DNA repair, pro-survival signalling and protein degradation. Ubiquitin modifications on target proteins are diverse, ranging from mono-ubiquitination through to the formation of polyubiquitin chains and mixed chains. The specificity in substrate tagging and chain elongation is dictated by E3 ubiquitin ligases, which have essential regulatory roles in multiple aspects of brain cancer pathogenesis. In this review, we begin by briefly summarising the histological and molecular classification of GB. We comprehensively describe the roles of E3 ubiquitin ligases in RTK and MAPK, as well as other, commonly altered, oncogenic and tumour suppressive signalling pathways in GB. We also describe the role of E3 ligases in maintaining glioma stem cell populations and their function in promoting resistance to ionizing radiation (IR) and chemotherapy. Finally, we consider how our knowledge of E3 ligase biology may be used for future therapeutic interventions in GB, including the use of blood-brain barrier permeable proteolysis targeting chimeras (PROTACs).
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Jeyaraj SE, Sivasangari K, García-Colunga J, Rajan KE. Environmental enrichment enhances sociability by regulating glutamate signaling pathway through GR by epigenetic mechanisms in amygdala of Indian field mice Mus booduga. Gen Comp Endocrinol 2021; 300:113641. [PMID: 33017584 DOI: 10.1016/j.ygcen.2020.113641] [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: 06/15/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Environmental enrichment (EE) dynamically regulates gene expression and synaptic plasticity with positive consequences on behavior. The present study was performed on field-mice to explore the effects of EE on both captive-condition inducing social stress and epigenetic changes of molecules resilience stress. For this purpose, field-mice were caught and allowed to habituate in standard laboratory conditions for 7 days. The next day animals were randomly assigned to three groups: i) mice at short-term standard condition (STSC); which were subjected to social interaction test (SIT) on day 9, ii) mice continuously maintainedfor additional 30 days, with these long-term standard conditions (LTSC), and iii) mice maintained in an EE cage for additional 30 days. After achieving SIT, we examined epigenetic changes of a repertory of molecules associated with resilience stress, by determining their levels by Western blot. Thus, the main findings were that during SIT, EE exerted more social interaction of field-mice with the strangers compared with STSC and LTSC mice. Related with social behavior results, we found that in mice subjected to EE the levels of histone 3 lysine 9 di-methylation (H3K9me2), glucocorticoid receptor (GR), N-methyl-D asparate (NMDA) receptor subunits NR2A and NR2B, postsynaptic density protein-95 (PSD-95), and mature brain-derived neurotrophic factor (mBDNF) were significantly elevated; whereas the levels of DNA methyltransferase-3A (DNMT3A), methyl-CpG-binding protein-2 (MeCP2), repressor element-1 silencing transcription factor (REST), H3K4me2 and lysine demethylase-1A (KDM1A) decreased. These results suggest that enhanced sociability of EE mice could be mediated, in part, by altered expression of molecules regulating glutamate signaling pathway through GR by epigenetic mechanisms.
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Affiliation(s)
- Soundarrajan Edwin Jeyaraj
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Karunanithi Sivasangari
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Jesús García-Colunga
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76230, Mexico
| | - Koilmani Emmanuvel Rajan
- Behavioural Neuroscience Laboratory, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India.
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