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Mehedi M, Ricklefs S, Takada A, Sturdevant D, Porcella SF, Marzi A, Feldmann H. RNA Editing as a General Trait of Ebolaviruses. J Infect Dis 2023; 228:S498-S507. [PMID: 37348869 PMCID: PMC10651210 DOI: 10.1093/infdis/jiad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
RNA editing has been discovered as an essential mechanism for the transcription of the glycoprotein (GP) gene of Ebola virus but not Marburg virus. We developed a rapid transcript quantification assay (RTQA) to analyze RNA transcripts generated through RNA editing and used immunoblotting with a pan-ebolavirus monoclonal antibody to confirm different GP gene-derived products. RTQA successfully quantified GP gene transcripts during infection with representative members of 5 ebolavirus species. Immunoblotting verified expression of the soluble GP and the transmembrane GP. Our results defined RNA editing as a general trait of ebolaviruses. The degree of editing, however, varies among ebolaviruses with Reston virus showing the lowest and Bundibugyo virus the highest degree of editing.
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Affiliation(s)
| | - Stacy Ricklefs
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dan Sturdevant
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Stephen F Porcella
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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Azad MTA, Qulsum U, Tsukahara T. Comparative Activity of Adenosine Deaminase Acting on RNA (ADARs) Isoforms for Correction of Genetic Code in Gene Therapy. Curr Gene Ther 2019; 19:31-39. [DOI: 10.2174/1566523218666181114122116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022]
Abstract
Introduction:
Members of the adenosine deaminase acting on RNA (ADAR) family of enzymes
consist of double-stranded RNA-binding domains (dsRBDs) and a deaminase domain (DD)
that converts adenosine (A) into inosine (I), which acts as guanosine (G) during translation. Using the
MS2 system, we engineered the DD of ADAR1 to direct it to a specific target. The aim of this work
was to compare the deaminase activities of ADAR1-DD and various isoforms of ADAR2-DD.
Materials and Methods:
We measured the binding affinity of the artificial enzyme system on a Biacore
™ X100. ADARs usually target dsRNA, so we designed a guide RNA complementary to the target
RNA, and then fused the guide sequence to the MS2 stem-loop. A mutated amber (TAG) stop
codon at 58 amino acid (TGG) of EGFP was targeted. After transfection of these three factors into
HEK 293 cells, we observed fluorescence signals of various intensities.
Results:
ADAR2-long without the Alu-cassette yielded a much higher fluorescence signal than
ADAR2-long with the Alu-cassette. With another isoform, ADAR2-short, which is 81 bp shorter at
the C-terminus, the fluorescence signal was undetectable. A single amino acid substitution of
ADAR2-long-DD (E488Q) rendered the enzyme more active than the wild type. The results of fluorescence
microscopy suggested that ADAR1-DD is more active than ADAR2-long-DD. Western blots
and sequencing confirmed that ADAR1-DD was more active than any other DD.
Conclusion:
This study provides information that should facilitate the rational use of ADAR variants
for genetic restoration and treatment of genetic diseases.
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Affiliation(s)
- Md. Thoufic A. Azad
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
| | - Umme Qulsum
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
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Schaefermeier P, Heinze S. Hippocampal Characteristics and Invariant Sequence Elements Distribution of GLRA2 and GLRA3 C-to-U Editing. Mol Syndromol 2016; 8:85-92. [PMID: 28611548 DOI: 10.1159/000453300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
Abstract
Glycine receptor α2 and α3 subunit (GLRA2/GLRA3) high-affinity variants, of which the subjacent amino acid substitutions issue from C-to-U RNA editing, are thought to influence tonic inhibition and pathophysiology. In light of the detection of GLRA3 NM_006529:r.1157C>U and GLRA2 NM_002063:r.1416C>U exchanges in hippocampus explants of temporal lobe epilepsy patients, we now examine the healthy situation and relate it to the epileptic situation by ascertaining controls in a legitimate reanalysis. The GLRA2 and GLRA3 editing events that would ultimately result in a glycine receptor with increased affinity occur in the postmortem nonepileptic hippocampus. Most notably, their relative amounts do not significantly differ from those in increased damaged hippocampus explants, whereas curbed relative amounts in epileptic explants without cell loss come out statistically significant. Local sequence alignment reveals invariant sequence stretches consistent in GLRA2/ GLRA3 and other edited transcripts that coincide with known APOB sequence elements. Concerning the essential mooring element, GLRA2/GLRA3 comply strictly only with the motif's 5' part. While this lack of canonical mooring elements and uncertain action of the famous deaminase APOBEC1 suggest a specific regulation of GLRA2/GLRA3 editing, its reduction in the less-damaged epileptic hippocampus could be attributed to anomalous epileptic neurogenesis.
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Affiliation(s)
- Philipp Schaefermeier
- Charité University Medicine Berlin, Germany,Helmholtz Group RNA Editing and Hyperexcitability Disorders, Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Sarah Heinze
- Institute of Forensic Sciences and Legal Medicine, Charité Berlin, Berlin, Germany,Klinikum Oldenburg gGmbH, Oldenburg, Germany,Institute of Forensic Medicine, Johannes Gutenberg University of Mainz, Mainz, Germany
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Annoni C, Endoh T, Hnedzko D, Rozners E, Sugimoto N. Triplex-forming peptide nucleic acid modified with 2-aminopyridine as a new tool for detection of A-to-I editing. Chem Commun (Camb) 2016; 52:7935-8. [PMID: 27157071 DOI: 10.1039/c6cc02164f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA editing from adenosine to inosine (A-to-I editing) is one of the mechanisms that regulate and diversify the transcriptome. Here, a triplex-forming peptide nucleic acid (PNA) modified with a 2-aminopyridine nucleobase was applied for the recognition of the A-to-I editing event in double-stranded RNAs. The triplex-forming PNA enabled sequence-specific detection of single nucleobase editing at sub-nanomolar concentration.
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Affiliation(s)
- Chiara Annoni
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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Crews LA, Jiang Q, Zipeto MA, Lazzari E, Court AC, Ali S, Barrett CL, Frazer KA, Jamieson CHM. An RNA editing fingerprint of cancer stem cell reprogramming. J Transl Med 2015; 13:52. [PMID: 25889244 PMCID: PMC4341880 DOI: 10.1186/s12967-014-0370-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deregulation of RNA editing by adenosine deaminases acting on dsRNA (ADARs) has been implicated in the progression of diverse human cancers including hematopoietic malignancies such as chronic myeloid leukemia (CML). Inflammation-associated activation of ADAR1 occurs in leukemia stem cells specifically in the advanced, often drug-resistant stage of CML known as blast crisis. However, detection of cancer stem cell-associated RNA editing by RNA sequencing in these rare cell populations can be technically challenging, costly and requires PCR validation. The objectives of this study were to validate RNA editing of a subset of cancer stem cell-associated transcripts, and to develop a quantitative RNA editing fingerprint assay for rapid detection of aberrant RNA editing in human malignancies. METHODS To facilitate quantification of cancer stem cell-associated RNA editing in exons and intronic or 3'UTR primate-specific Alu sequences using a sensitive, cost-effective method, we established an in vitro RNA editing model and developed a sensitive RNA editing fingerprint assay that employs a site-specific quantitative PCR (RESSq-PCR) strategy. This assay was validated in a stably-transduced human leukemia cell line, lentiviral-ADAR1 transduced primary hematopoietic stem and progenitor cells, and in primary human chronic myeloid leukemia stem cells. RESULTS In lentiviral ADAR1-expressing cells, increased RNA editing of MDM2, APOBEC3D, GLI1 and AZIN1 transcripts was detected by RESSq-PCR with improved sensitivity over sequencing chromatogram analysis. This method accurately detected cancer stem cell-associated RNA editing in primary chronic myeloid leukemia samples, establishing a cancer stem cell-specific RNA editing fingerprint of leukemic transformation that will support clinical development of novel diagnostic tools to predict and prevent cancer progression. CONCLUSIONS RNA editing quantification enables rapid detection of malignant progenitors signifying cancer progression and therapeutic resistance, and will aid future RNA editing inhibitor development efforts.
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Affiliation(s)
- Leslie A Crews
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
| | - Qingfei Jiang
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
| | - Maria A Zipeto
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
| | - Elisa Lazzari
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA. .,Doctoral School of Molecular and Translational Medicine, Department of Health Sciences, University of Milan, Milan, Italy.
| | - Angela C Court
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
| | - Shawn Ali
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
| | - Christian L Barrett
- Division of Genome Information Sciences, Department of Pediatrics, University of California, La Jolla, CA, 92093, USA.
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics, University of California, La Jolla, CA, 92093, USA.
| | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center at University of California, La Jolla, CA, 92093, USA. .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA.
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Brande-Eilat N, Golumbic YN, Zaidan H, Gaisler-Salomon I. Acquisition of conditioned fear is followed by region-specific changes in RNA editing of glutamate receptors. Stress 2015; 18:309-18. [PMID: 26383032 DOI: 10.3109/10253890.2015.1073254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification process that can affect synaptic function. Transcripts encoding the kainate GRIK1 and AMPA GluA2 glutamate receptor subunits undergo editing that leads to a glycine/arginine (Q/R) exchange and reduced Ca(2+) permeability. We hypothesized that editing at these sites could be experience-dependent, temporally dynamic and region-specific. We trained C57/Bl6 mice in trace and contextual fear conditioning protocols, and examined editing levels at GRIK1 and GluA2 Q/R sites in the amygdala (CeA) and hippocampus (CA1 and CA3), at two time points after training. We also examined experience-dependent changes in the expression of RNA editing enzymes and editing targets. Animals trained in the trace fear conditioning protocol exhibited a transient increase in unedited GRIK1 RNA in the amygdala, and their learning efficiency correlated with unedited RNA levels in CA1. In line with previous reports, GluA2 RNA editing levels were nearly 100%. Additionally, we observed experience-dependent changes in mRNA expression of the RNA editing enzymes ADAR2 and ADAR1 in amygdala and hippocampus, and a learning-dependent increase in the alternatively spliced inactive form of ADAR2 in the amygdala. Since unedited transcripts code for Ca(2+)-permeable receptor subunits, these findings suggest that RNA editing at Q/R sites of glutamate receptors plays an important role in experience-dependent synaptic modification processes.
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Affiliation(s)
- Noa Brande-Eilat
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Yaela N Golumbic
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Hiba Zaidan
- a Psychology Department , University of Haifa , Haifa , Israel and
| | - Inna Gaisler-Salomon
- a Psychology Department , University of Haifa , Haifa , Israel and
- b Department of Psychiatry , Columbia University , New York , NY , USA
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Van Den Bekerom RJM, Dix PJ, Diekmann K, Barth S. Variations in efficiency of plastidial RNA editing within ndh transcripts of perennial ryegrass ( Lolium perenne) are not linked to differences in drought tolerance. AOB PLANTS 2013; 5:plt035. [PMCID: PMC4455615 DOI: 10.1093/aobpla/plt035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/30/2013] [Indexed: 05/30/2023]
Abstract
Projected climate change is likely to subject key temperate grassland species, such as perennial ryegrass (Lolium perenne) to drought stress. Previous studies have shown that the NADH dehydrogenase complex (NDH) is involved with countering oxidative stress during environmental stresses like drought. We studied RNA editing within plastidial transcripts of the NDH complex in relation to the drought response of several accessions of perennial ryegrass. We found dramatic and reproducible differences in RNA editing efficiency between accessions, but efficiency was not influenced by imposition of drought stress, and a direct relationship between editing behaviour and drought response was not detected. Maintenance of healthy grasslands is essential for efficient livestock production, yet projected climate change is likely to place a heavy drought stress burden on key grassland species, such as perennial ryegrass (Lolium perenne). It is therefore important to gather an in-depth knowledge of the underlying plant response to this stress. The present study is focused on RNA editing (post-transcriptional nucleotide modifications resulting in altered transcripts) within plastidial transcripts of the NADH:ubiquinone oxidoreductase (NDH) complex (NADH dehydrogenase complex) in relation to the drought response of several accessions of perennial ryegrass. Previous studies have shown that the NDH complex is involved in countering oxidative stress during environmental stresses like drought. Owing to the nature of RNA editing within this complex, the RNA editing machinery could play a potential role in regulating the activity of the NDH complex. The investigation revealed dramatic and reproducible differences in RNA editing efficiency between accessions, but efficiency was not influenced by imposition of drought stress, and a direct relationship between editing behaviour and drought response was not detected.
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Affiliation(s)
- Rob J. M. Van Den Bekerom
- Teagasc Crops, Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
- National University of Maynooth, Maynooth, Co. Kildare, Ireland
| | - Philip J. Dix
- National University of Maynooth, Maynooth, Co. Kildare, Ireland
| | - Kerstin Diekmann
- Teagasc Crops, Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
| | - Susanne Barth
- Teagasc Crops, Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
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Eifler T, Chan D, Beal PA. A screening protocol for identification of functional mutants of RNA editing adenosine deaminases. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2012; 4:357-69. [PMID: 23788559 PMCID: PMC3690185 DOI: 10.1002/9780470559277.ch120139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic screens can be used to evaluate a spectrum of mutations and thereby infer the function of particular residues within a protein. The Adenosine Deaminase Acting on RNA (ADAR) family of RNA-editing enzymes selectively deaminate adenosines (A) in double-helical RNA, generating inosine (I). The protocol described here exploits the editing activity of ADAR2 in a yeast-based screen by inserting an editing substrate sequence with a stop codon incorporated at the editing site upstream from the sequence encoding the reporter α-galactosidase. A-to-I editing changes the stop codon to a tryptophan codon, allowing normal expression of the reporter. This technique is particularly well-suited for screening ADAR and ADAR substrate mutant libraries for editing activity. Curr. Protoc. Chem. Biol. 4:357-369 © 2012 by John Wiley & Sons, Inc.
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Affiliation(s)
- Tristan Eifler
- Department of Chemistry, University of California, Davis
| | - Dalen Chan
- Department of Chemistry, University of California, Davis
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis
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Schirle NT, Goodman RA, Krishnamurthy M, Beal PA. Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide. Org Biomol Chem 2010; 8:4898-904. [DOI: 10.1039/c0ob00309c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Legendre P, Förstera B, Jüttner R, Meier JC. Glycine Receptors Caught between Genome and Proteome - Functional Implications of RNA Editing and Splicing. Front Mol Neurosci 2009; 2:23. [PMID: 19936314 PMCID: PMC2779093 DOI: 10.3389/neuro.02.023.2009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 10/13/2009] [Indexed: 11/13/2022] Open
Abstract
Information processing in the brain requires a delicate balance between excitation and inhibition. Glycine receptors (GlyR) are involved in inhibitory mechanisms mainly at a synaptic level, but potential novel roles for these receptors recently emerged due to the discovery of posttranscriptional processing. GLR transcripts are edited through enzymatic modification of a single nucleotide leading to amino acid substitution within the neurotransmitter binding domain. RNA editing produces gain-of-function receptors well suited for generation and maintenance of tonic inhibition of neuronal excitability. As neuronal activity deprivation in early stages of development or in epileptic tissue is detrimental to neurons and because RNA editing of GlyR is up-regulated in temporal lobe epilepsy patients with a severe course of disease a pathophysiological role of these receptors emerges. This review contains a state-of-the-art discussion of (patho)physiological implications of GlyR RNA editing.
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TaqMan-based, real-time quantitative polymerase chain reaction method for RNA editing analysis. Anal Biochem 2009; 390:173-80. [DOI: 10.1016/j.ab.2009.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/06/2009] [Accepted: 04/07/2009] [Indexed: 11/18/2022]
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Jiang P, Kong Y, Zhang XB, Wang W, Liu CF, Xu TL. Glycine receptor in rat hippocampal and spinal cord neurons as a molecular target for rapid actions of 17-beta-estradiol. Mol Pain 2009; 5:2. [PMID: 19138413 PMCID: PMC2651124 DOI: 10.1186/1744-8069-5-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 01/12/2009] [Indexed: 12/20/2022] Open
Abstract
Glycine receptors (GlyRs) play important roles in regulating hippocampal neural network activity and spinal nociception. Here we show that, in cultured rat hippocampal (HIP) and spinal dorsal horn (SDH) neurons, 17-β-estradiol (E2) rapidly and reversibly reduced the peak amplitude of whole-cell glycine-activated currents (IGly). In outside-out membrane patches from HIP neurons devoid of nuclei, E2 similarly inhibited IGly, suggesting a non-genomic characteristic. Moreover, the E2 effect on IGly persisted in the presence of the calcium chelator BAPTA, the protein kinase inhibitor staurosporine, the classical ER (i.e. ERα and ERβ) antagonist tamoxifen, or the G-protein modulators, favoring a direct action of E2 on GlyRs. In HEK293 cells expressing various combinations of GlyR subunits, E2 only affected the IGly in cells expressing α2, α2β or α3β subunits, suggesting that either α2-containing or α3β-GlyRs mediate the E2 effect observed in neurons. Furthermore, E2 inhibited the GlyR-mediated tonic current in pyramidal neurons of HIP CA1 region, where abundant GlyR α2 subunit is expressed. We suggest that the neuronal GlyR is a novel molecular target of E2 which directly inhibits the function of GlyRs in the HIP and SDH regions. This finding may shed new light on premenstrual dysphoric disorder and the gender differences in pain sensation at the CNS level.
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Affiliation(s)
- Peng Jiang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, PR China
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