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Harnett A, Mathoux J, Wilson MM, Heiland M, Mamad O, Srinivas S, Sanfeliu A, Sanz-Rodriguez A, How KLE, Delanty N, Cryan J, Brett FM, Farrell MA, O'Brien DF, Henshall DC, Brennan GP. Impact of JQ1 treatment on seizures, hippocampal gene expression, and gliosis in a mouse model of temporal lobe epilepsy. Eur J Neurosci 2024. [PMID: 39149798 DOI: 10.1111/ejn.16499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/04/2024] [Accepted: 07/24/2024] [Indexed: 08/17/2024]
Abstract
Epilepsy is a neurological disease characterised by recurrent seizures with complex aetiology. Temporal lobe epilepsy, the most common form in adults, can be acquired following brain insults including trauma, stroke, infection or sustained status epilepticus. The mechanisms that give rise to the formation and maintenance of hyperexcitable networks following acquired insults remain unknown, yet an extensive body of literature points towards persistent gene and epigenomic dysregulation as a potential mediator of this dysfunction. While much is known about the function of specific classes of epigenetic regulators (writers and erasers) in epilepsy, much less is known about the enzymes, which read the epigenome and modulate gene expression accordingly. Here, we explore the potential role for the epigenetic reader bromodomain and extra-terminal domain (BET) proteins in epilepsy. Using the intra-amygdala kainic acid model of temporal lobe epilepsy, we initially identified widespread dysregulation of important epigenetic regulators including EZH2 and REST as well as altered BRD4 expression in chronically epileptic mice. BRD4 activity was also notably affected by epilepsy-provoking insults as seen by elevated binding to and transcriptional regulation of the immediate early gene Fos. Despite influencing early aspects of epileptogenesis, blocking BET protein activity with JQ1 had no overt effects on epilepsy development in mice but did alter glial reactivity and influence gene expression patterns, promoting various neurotransmitter signalling mechanisms and inflammatory pathways in the hippocampus. Together, these results confirm that epigenetic reader activity is affected by epilepsy-provoking brain insults and that BET activity may exert cell-specific actions on inflammation in epilepsy.
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Affiliation(s)
- Aileen Harnett
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Justine Mathoux
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Mona Heiland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Omar Mamad
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Sujithra Srinivas
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Albert Sanfeliu
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Amaya Sanz-Rodriguez
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Kelvin Lau E How
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
- Beaumont Hospital, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | | | | | - David C Henshall
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
| | - Gary P Brennan
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro Research Centre, University College Dublin, Dublin, Ireland
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
- UCD Conway Institute, University College Dublin, Dublin, Ireland
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2
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Dibaj M, Haghi M, Safaralizadeh R, Saberi A. The role of EZH2 and its regulatory lncRNAs as a serum-based biomarker in Alzheimer's disease. Mol Biol Rep 2024; 51:866. [PMID: 39073683 DOI: 10.1007/s11033-024-09802-0] [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: 02/21/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have become a hot topic in the human nervous system. Moreover, circulating lncRNAs have been suggested as possible biomarkers for central nervous system processes and neurodegenerative diseases. The present research aimed to highlight the role of plasma lncRNAs TUG1, FEZF1-AS1, and EZH2 gene as diagnostic biomarkers in Alzheimer's disease (AD). METHODS Plasma samples for the study were provided by 100 AD patients and 100 matched controls. Real-time quantitative reverse transcriptase PCR was used to determine the plasma level of the aforementioned lncRNAs. Furthermore, the plasma level of EZH2 protein in the participants' blood was determined using the ELISA technique. RESULTS In contrast to controls, down-regulation of the EZH2 gene and protein was reported in the plasma of patients with AD. Additionally, plasma samples from AD patients showed up-and-down-regulation of the lncRNAs TUG1 and FEZF1-AS1, respectively. CONCLUSION Our new findings suggest that the EZH2 gene, plasma lncRNA TUG1, and FEZF1-AS1 may contribute, as valuable biomarkers, to AD diagnosis.
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Affiliation(s)
- Mohsen Dibaj
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mehdi Haghi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Alia Saberi
- Neurology Department, School of Medicine, Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
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3
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Stephens GS, Park J, Eagle A, You J, Silva-Pérez M, Fu CH, Choi S, Romain CPS, Sugimoto C, Buffington SA, Zheng Y, Costa-Mattioli M, Liu Y, Robison AJ, Chin J. Persistent ∆FosB expression limits recurrent seizure activity and provides neuroprotection in the dentate gyrus of APP mice. Prog Neurobiol 2024; 237:102612. [PMID: 38642602 DOI: 10.1016/j.pneurobio.2024.102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/14/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Recurrent seizures lead to accumulation of the activity-dependent transcription factor ∆FosB in hippocampal dentate granule cells in both mouse models of epilepsy and mouse models of Alzheimer's disease (AD), which is also associated with increased incidence of seizures. In patients with AD and related mouse models, the degree of ∆FosB accumulation corresponds with increasing severity of cognitive deficits. We previously found that ∆FosB impairs spatial memory in mice by epigenetically regulating expression of target genes such as calbindin that are involved in synaptic plasticity. However, the suppression of calbindin in conditions of neuronal hyperexcitability has been demonstrated to provide neuroprotection to dentate granule cells, indicating that ∆FosB may act over long timescales to coordinate neuroprotective pathways. To test this hypothesis, we used viral-mediated expression of ∆JunD to interfere with ∆FosB signaling over the course of several months in transgenic mice expressing mutant human amyloid precursor protein (APP), which exhibit spontaneous seizures and develop AD-related neuropathology and cognitive deficits. Our results demonstrate that persistent ∆FosB activity acts through discrete modes of hippocampal target gene regulation to modulate neuronal excitability, limit recurrent seizure activity, and provide neuroprotection to hippocampal dentate granule cells in APP mice.
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Affiliation(s)
| | - Jin Park
- Department of Neuroscience, Baylor College of Medicine, USA
| | - Andrew Eagle
- Department of Physiology, Michigan State University, USA
| | - Jason You
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Chia-Hsuan Fu
- Department of Neuroscience, Baylor College of Medicine, USA
| | - Sumin Choi
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Chiho Sugimoto
- Department of Physiology, Michigan State University, USA
| | - Shelly A Buffington
- Center for Precision Environmental Health, Department of Neuroscience, Baylor College of Medicine, USA
| | - Yi Zheng
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Yin Liu
- Department of Neurobiology and Anatomy, McGovern Medical School at UT Health, USA
| | - A J Robison
- Department of Physiology, Michigan State University, USA
| | - Jeannie Chin
- Department of Neuroscience, Baylor College of Medicine, USA.
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4
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Issa NP, Nunn KC, Wu S, Haider HA, Tao JX. Putative roles for homeostatic plasticity in epileptogenesis. Epilepsia 2023; 64:539-552. [PMID: 36617338 PMCID: PMC10015501 DOI: 10.1111/epi.17500] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Homeostatic plasticity allows neural circuits to maintain an average activity level while preserving the ability to learn new associations and efficiently transmit information. This dynamic process usually protects the brain from excessive activity, like seizures. However, in certain contexts, homeostatic plasticity might produce seizures, either in response to an acute provocation or more chronically as a driver of epileptogenesis. Here, we review three seizure conditions in which homeostatic plasticity likely plays an important role: acute drug withdrawal seizures, posttraumatic or disconnection epilepsy, and cyclic seizures. Identifying the homeostatic mechanisms active at different stages of development and in different circuits could allow better targeting of therapies, including determining when neuromodulation might be most effective, proposing ways to prevent epileptogenesis, and determining how to disrupt the cycle of recurring seizure clusters.
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Affiliation(s)
- Naoum P. Issa
- Comprehensive Epilepsy Center, Department of Neurology, 5841 S. Maryland Ave., MC 2030, University of Chicago, Chicago, IL 60637
| | | | - Shasha Wu
- Comprehensive Epilepsy Center, Department of Neurology, 5841 S. Maryland Ave., MC 2030, University of Chicago, Chicago, IL 60637
| | - Hiba A. Haider
- Comprehensive Epilepsy Center, Department of Neurology, 5841 S. Maryland Ave., MC 2030, University of Chicago, Chicago, IL 60637
| | - James X. Tao
- Comprehensive Epilepsy Center, Department of Neurology, 5841 S. Maryland Ave., MC 2030, University of Chicago, Chicago, IL 60637
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5
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Zhao CS, Liu DX, Fan YH, Wu JK. LncRNA GAS5 promotes epilepsy progression through the epigenetic repression of miR-219, in turn affecting CaMKIIγ/NMDAR pathway. J Neurogenet 2022; 36:32-42. [PMID: 35642561 DOI: 10.1080/01677063.2022.2067536] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
It has been widely reported that dysregulated long-chain noncoding RNAs (lncRNAs) are closely associated with epilepsy. This study aimed to probe the function of lncRNA growth arrest-specific 5 (GAS5), microRNA (miR)-219 and Calmodulin-dependent protein kinase II (CaMKII)γ/N-methyl-D-aspartate receptor (NMDAR) pathway in epilepsy. Epileptic cell and animal models were constructed using magnesium deficiency treatment and diazepam injection, respectively. GAS5 and miR-219 expressions in epileptic cell and animal models were determined using qRT-PCR assay. The protein levels of CaMKIIγ, NMDAR and apoptosis-related proteins levels were assessed by western blot. Cell counting kit-8 (CCK-8) assay was employed to determine cell proliferation. Besides, TNFα, IL-1β, IL-6 and IL-8 levels were analyzed using enzyme-linked immunosorbent assay (ELISA). Furthermore, cell apoptosis was evaluated using TUNEL staining and flow cytometric analysis. Finally, the binding relationship between GAS5 and EZH2 was verified using RIP and ChIP assay. Our results revealed that GAS5 was markedly upregulated in epileptic cell and animal models, while miR-219 was down-regulated. GAS5 knockdown dramatically increased cell proliferation of epileptic cells, whereas suppressed inflammation and the apoptosis. Furthermore, our results showed that GAS5 epigenetically suppressed transcriptional miR-219 expression via binding to EZH2. miR-219 mimics significantly enhanced cell proliferation of epileptic cells, while inhibited inflammation and the apoptosis, which was neutralized by CaMKIIγ overexpression. Finally, miR-219 inhibition reversed the effects of GAS5 silence on epileptic cells, which was eliminated by CaMKIIγ inhibition. In conclusion, GAS5 affected inflammatory response and cell apoptosis of epilepsy via inhibiting miR-219 and further regulating CaMKIIγ/NMDAR pathway (See graphic summary in Supplementary Material).
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Affiliation(s)
- Chen-Sheng Zhao
- Department of Neurology, Shanxi Cardiovascular Hospital, Taiyuan, P. R. China
| | - Dong-Xing Liu
- Department of Neurology, Shanxi Cardiovascular Hospital, Taiyuan, P. R. China
| | - Yan-Huai Fan
- Department of Neurology, Shanxi Cardiovascular Hospital, Taiyuan, P. R. China
| | - Jian-Kun Wu
- Department of Neurology, Shanxi Cardiovascular Hospital, Taiyuan, P. R. China
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6
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Hetzelt KLML, Winterholler M, Kerling F, Rauch C, Ekici AB, Winterpacht A, Vasileiou G, Uebe S, Thiel CT, Kraus C, Reis A, Zweier C. Manifestation of epilepsy in a patient with EED-related overgrowth (Cohen-Gibson syndrome). Am J Med Genet A 2021; 188:292-297. [PMID: 34533271 DOI: 10.1002/ajmg.a.62496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
Cohen-Gibson syndrome is a rare genetic disorder, characterized by fetal or early childhood overgrowth and mild to severe intellectual disability. It is caused by heterozygous aberrations in EED, which encodes an evolutionary conserved polycomb group (PcG) protein that forms the polycomb repressive complex-2 (PRC2) together with EZH2, SUZ12, and RBBP7/4. In total, 11 affected individuals with heterozygous pathogenic variants in EED were reported, so far. All variants affect a few key residues within the EED WD40 repeat domain. By trio exome sequencing, we identified the heterozygous missense variant c.581A > G, p.(Asn194Ser) in exon 6 of the EED-gene in an individual with moderate intellectual disability, overgrowth, and epilepsy. The same pathogenic variant was detected in 2 of the 11 previously reported cases. Epilepsy, however, was only diagnosed in one other individual with Cohen-Gibson syndrome before. Our findings further confirm that the WD40 repeat domain represents a mutational hotspot; they also expand the clinical spectrum of Cohen-Gibson syndrome and highlight the clinical variability even in individuals with the same pathogenic variant. Furthermore, they indicate a possible association between Cohen-Gibson syndrome and epilepsy.
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Affiliation(s)
- Katalin L M L Hetzelt
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Martin Winterholler
- Department of Neurology, Epilepsy and Movement Disorders Center, Sana-Krankenhaus Rummelsberg, Schwarzenbruck/Nuremberg, Germany
| | - Frank Kerling
- Department of Neurology, Epilepsy and Movement Disorders Center, Sana-Krankenhaus Rummelsberg, Schwarzenbruck/Nuremberg, Germany
| | - Christophe Rauch
- Department of Neurology, Epilepsy and Movement Disorders Center, Sana-Krankenhaus Rummelsberg, Schwarzenbruck/Nuremberg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Andreas Winterpacht
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Christian T Thiel
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg FAU, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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7
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Sasani E, Yadegari MH, Khodavaisy S, Rezaie S, Salehi M, Getso MI. Virulence Factors and Azole-Resistant Mechanism of Candida Tropicalis Isolated from Candidemia. Mycopathologia 2021; 186:847-856. [PMID: 34410566 DOI: 10.1007/s11046-021-00580-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/14/2021] [Indexed: 10/25/2022]
Abstract
BACKGROUND Limited knowledge exists on the virulence factors of Candida tropicalis and the mechanisms of azole resistance that lead to an intensified pathogenicity and treatment failure. We aimed to evaluate the virulence factors and molecular mechanisms of azole resistance among C. tropicalis isolated from patients with candidemia. MATERIALS AND METHODS Several virulence factors, including extracellular enzymatic activities, cell surface hydrophobicity (CSH), and biofilm formation, were evaluated. Antifungal susceptibility pattern and expression level of ERG11, UPC2, MDR1, and CDR1 genes of eight (4 fluconazole resistance and 4 fluconazole susceptible) clinical C. tropicalis isolates were assessed. The correlation between the virulence factors and antifungal susceptibility patterns was analyzed. RESULTS During a 4 year study, forty-five C. tropicalis isolates were recovered from candidemia patients. The isolates expressed different frequencies of virulence determinants as follows: coagulase 4 (8.9%), phospholipase 5 (11.1%), proteinase 31 (68.9%), esterase 43 (95.6%), hemolysin 44 (97.8%), biofilm formation 45 (100%) and CSH 45(100%). All the isolates were susceptible to amphotericin B and showed the highest resistance to voriconazole. There was a significant positive correlation between micafungin minimum inhibitory concentrations (MICs) and hemolysin production (rs = 0.316). However, we found a negative correlation between fluconazole MICs and esterase production (rs = -0.383). We observed the high expression of ERG11 and UPC2 genes in fluconazole-resistant C. tropicalis isolates. CONCLUSION C. tropicalis isolated from candidemia patients extensively displayed capacities for biofilm formation, hemolysis, esterase activity, and hydrophobicity. In addition, the overexpression of ERG11 and UPC2 genes was considered one of the possible mechanisms of azole resistance.
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Affiliation(s)
- Elahe Sasani
- Department of Medical Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hossein Yadegari
- Department of Medical Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Sadegh Khodavaisy
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Sassan Rezaie
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, Kano, Nigeria
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8
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Multi-omics in mesial temporal lobe epilepsy with hippocampal sclerosis: Clues into the underlying mechanisms leading to disease. Seizure 2021; 90:34-50. [DOI: 10.1016/j.seizure.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
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9
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Cavite HJM, Mactal AG, Evangelista EV, Cruz JA. Biochemical characteristics and inoculation effects of multi-trait plant growth-promoting rhizobacteria on upland rice (Oryza sativa L. cv PSB Rc23) seedling growth. Arch Microbiol 2021; 203:3533-3540. [PMID: 33938971 DOI: 10.1007/s00203-021-02337-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are known to stimulate plant growth because of their versatility in nutrient transformation. However, the success of PGPR inoculation depends not only on their ability to promote plant growth but also on their capacity to metabolize substrates that can be used as energy for the development and survival of the crops. Given the important influence of seed germination and vigor on crop yield, this study investigated the biochemical characteristics and effectiveness of multi-trait PGPR isolates in enhancing upland rice seedling growth and vigor. Biochemical identification was done using Biolog GEN III Microbial Identification System. Isolates were characterized based on their ability to metabolize all major classes of biochemicals in the carbon source utilization and chemical sensitivity assays. Identified rhizobacterial isolates were tested in vitro to evaluate their inoculation effects on the growth of PSB Rc23 upland rice seedlings. Biochemical identification results showed that rhizobacterial isolates have extensive metabolic activities in a wide range of carbon sources. Inoculation effects revealed that isolate IBBw1a was the most effective in enhancing root length and vigor index of rice seedlings in vitro, yielding a significant increase of 60% and 53%, respectively, over the uninoculated control. This study suggests that rhizobacterial isolates from upland rice may have commercial significance to improve seedling growth and vigor. These isolates will undergo a further assessment of their effectiveness in actual upland rice field conditions as they were already proven effective growth promoters in laboratory and screenhouse conditions. Such future activity can uncover their efficacy as potential biofertilizers in the actual soil environment.
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Affiliation(s)
- Harry Jay M Cavite
- Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand. .,College of Agriculture, Central Luzon State University, 3120, Science City of Muñoz, Nueva Ecija, Philippines.
| | - Ariel G Mactal
- College of Agriculture, Central Luzon State University, 3120, Science City of Muñoz, Nueva Ecija, Philippines
| | - Editha V Evangelista
- Agronomy, Soils and Plant Physiology Division, Philippine Rice Research Institute, 3119, Science City of Muñoz, Nueva Ecija, Philippines
| | - Jayvee A Cruz
- Agronomy, Soils and Plant Physiology Division, Philippine Rice Research Institute, 3119, Science City of Muñoz, Nueva Ecija, Philippines
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10
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Conboy K, Henshall DC, Brennan GP. Epigenetic principles underlying epileptogenesis and epilepsy syndromes. Neurobiol Dis 2020; 148:105179. [PMID: 33181318 DOI: 10.1016/j.nbd.2020.105179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a network disorder driven by fundamental changes in the function of the cells which compose these networks. Driving this aberrant cellular function are large scale changes in gene expression and gene expression regulation. Recent studies have revealed rapid and persistent changes in epigenetic control of gene expression as a critical regulator of the epileptic transcriptome. Epigenetic-mediated gene output regulates many aspects of cellular physiology including neuronal structure, neurotransmitter assembly and abundance, protein abundance of ion channels and other critical neuronal processes. Thus, understanding the contribution of epigenetic-mediated gene regulation could illuminate novel regulatory mechanisms which may form the basis of novel therapeutic approaches to treat epilepsy. In this review we discuss the effects of epileptogenic brain insults on epigenetic regulation of gene expression, recent efforts to target epigenetic processes to block epileptogenesis and the prospects of an epigenetic-based therapy for epilepsy, and finally we discuss technological advancements which have facilitated the interrogation of the epigenome.
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Affiliation(s)
- Karen Conboy
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Gary P Brennan
- FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland; School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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11
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Visser PJ, Reus LM, Gobom J, Jansen I, Dicks E, Tsolaki M, Verhey FRJ, Popp J, Martinez-Lage P, Vandenberghe R, Lleó A, Molinuevo JL, Engelborghs S, Freund-Levi Y, Froelich L, Sleegers K, Dobricic V, Hong S, Lovestone S, Streffer J, Vos SJB, Bos I, Smit AB, Blennow K, Scheltens P, Teunissen CE, Bertram L, Zetterberg H, Tijms BM. Cerebrospinal fluid total tau levels indicate aberrant neuronal plasticity in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 33173883 DOI: 10.1101/2020.10.29.20211920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is characterised by abnormal amyloid beta and tau processing. Previous studies reported that cerebrospinal fluid (CSF) total tau (t-tau) levels vary between patients. Here we show that CSF t-tau variability is associated with distinct impairments in neuronal plasticity mediated by gene repression factors SUZ12 and REST. AD individuals with abnormal t-tau levels have increased CSF concentrations of plasticity proteins regulated by SUZ12 and REST. AD individuals with normal t-tau, on the contrary, have decreased concentrations of these plasticity proteins and increased concentrations in proteins associated with blood-brain and blood CSF-barrier dysfunction. Genomic analyses suggested that t-tau levels in part depend on genes involved in gene expression. The distinct plasticity abnormalities in AD as signaled by t-tau urge the need for personalised treatment.
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12
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Ewald AC, Kiernan EA, Roopra AS, Radcliff AB, Timko RR, Baker TL, Watters JJ. Sex- and Region-Specific Differences in the Transcriptomes of Rat Microglia from the Brainstem and Cervical Spinal Cord. J Pharmacol Exp Ther 2020; 375:210-222. [PMID: 32661056 DOI: 10.1124/jpet.120.266171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
The neural control system underlying breathing is sexually dimorphic with males being more vulnerable to dysfunction. Microglia also display sex differences, and their role in the architecture of brainstem respiratory rhythm circuitry and modulation of cervical spinal cord respiratory plasticity is becoming better appreciated. To further understand the molecular underpinnings of these sex differences, we performed RNA sequencing of immunomagnetically isolated microglia from brainstem and cervical spinal cord of adult male and female rats. We used various bioinformatics tools (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Reactome, STRING, MAGICTRICKS) to functionally categorize identified gene sets, as well as to pinpoint common transcriptional gene drivers that may be responsible for the observed transcriptomic differences. We found few sex differences in the microglial transcriptomes derived from the brainstem, but several hundred genes were differentially expressed by sex in cervical spinal microglia. Comparing brainstem and spinal microglia within and between sexes, we found that the major factor guiding transcriptomic differences was central nervous system (CNS) location rather than sex. We further identified key transcriptional drivers that may be responsible for the transcriptomic differences observed between sexes and CNS regions; enhancer of zeste homolog 2 emerged as the predominant driver of the differentially downregulated genes. We suggest that functional gene alterations identified in metabolism, transcription, and intercellular communication underlie critical microglial heterogeneity and sex differences in CNS regions that contribute to respiratory disorders categorized by dysfunction in neural control. These data will also serve as an important resource data base to advance our understanding of innate immune cell contributions to sex differences and the field of respiratory neural control. SIGNIFICANCE STATEMENT: The contributions of central nervous system (CNS) innate immune cells to sexually dimorphic differences in the neural circuitry controlling breathing are poorly understood. We identify key transcriptomic differences, and their transcriptional drivers, in microglia derived from the brainstem and the C3-C6 cervical spinal cord of healthy adult male and female rats. Gene alterations identified in metabolism, gene transcription, and intercellular communication likely underlie critical microglial heterogeneity and sex differences in these key CNS regions that contribute to the neural control of breathing.
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Affiliation(s)
- Andrea C Ewald
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Elizabeth A Kiernan
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Avtar S Roopra
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Abigail B Radcliff
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Rebecca R Timko
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Tracy L Baker
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
| | - Jyoti J Watters
- Departments of Comparative Biosciences (A.C.E., E.A.K., A.B.R., R.R.T., T.L.B., J.J.W.) and Neuroscience (A.S.R.), University of Wisconsin-Madison, Madison, Wisconsin
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Roopra A. MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. PLoS Comput Biol 2020; 16:e1007800. [PMID: 32251445 PMCID: PMC7162552 DOI: 10.1371/journal.pcbi.1007800] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 04/16/2020] [Accepted: 03/19/2020] [Indexed: 01/26/2023] Open
Abstract
Transcriptomic profiling is an immensely powerful hypothesis generating tool. However, accurately predicting the transcription factors (TFs) and cofactors that drive transcriptomic differences between samples is challenging. A number of algorithms draw on ChIP-seq tracks to define TFs and cofactors behind gene changes. These approaches assign TFs and cofactors to genes via a binary designation of 'target', or 'non-target' followed by Fisher Exact Tests to assess enrichment of TFs and cofactors. ENCODE archives 2314 ChIP-seq tracks of 684 TFs and cofactors assayed across a 117 human cell lines under a multitude of growth and maintenance conditions. The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. When compared to other TF mining resources, MAGIC displayed favourable performance in predicting TFs and cofactors that drive gene changes in 4 settings: 1) A cell line expressing or lacking single TF, 2) Breast tumors divided along PAM50 designations 3) Whole brain samples from WT mice or mice lacking a single TF in a particular neuronal subtype 4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels. In summary, MAGIC is a standalone application that produces meaningful predictions of TFs and cofactors in transcriptomic experiments.
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Affiliation(s)
- Avtar Roopra
- Dept. of Neuroscience, 5507 WIMR, University of Wisconsin-Madison, Madison, United States of America
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