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Zhawar VK, Kandpal RP, Athwal RS. Alternative Promoters of GRIK2 (GluR6) Gene in Human Carcinoma Cell Lines Are Regulated by Differential Methylation of CpG Dinucleotides. Genes (Basel) 2022; 13:genes13030490. [PMID: 35328043 PMCID: PMC8954616 DOI: 10.3390/genes13030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 02/04/2023] Open
Abstract
The ionotropic glutamate receptor 6 (GluR6 or GRIK2) gene is transcribed by two cell-type-specific promoters in neuronal and non-neuronal cells, which results in five different transcript variants. The purpose of this study was to explore cell-type-specific silencing of these promoters by epigenetic mechanisms. The neuronal and non-neuronal promoter sequences were cloned upstream of the luciferase gene in the pGL3 luciferase reporter vector. Promoter susceptibility to methylation was confirmed by 5-azacytidine and trichostatin treatment, and the status of CpG dinucleotides was determined by bisulfite sequencing of the promoter was determined by bisulfite sequences. GluR6A transcript variant was expressed in the brain, and GluR6B was most abundant in tumor cell lines. The neuronal promoter was methylated in non-neuronal cell lines. The treatment with 5-azacytidine and trichostatin upregulated transcription of the GluR6 gene, and methylation of the GluR6 promoter sequence in the luciferase reporter system led to downregulation of the luciferase gene transcription. Bisulfite sequencing revealed methylation of 3 and 41 CpG sites in non-neuronal and neuronal promoters, respectively. The differential activation/silencing of GluR6 promoters suggests that the transcript variants of GluR6 are involved in tissue-specific biological processes and their aberrant regulation in tumor cells may contribute to distinct properties of tumor cells.
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Affiliation(s)
- Vikramjit K. Zhawar
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19067, USA;
| | - Raj P. Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
- Correspondence: (R.P.K.); (R.S.A.)
| | - Raghbir S. Athwal
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19067, USA;
- Correspondence: (R.P.K.); (R.S.A.)
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Herbrechter R, Hube N, Buchholz R, Reiner A. Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data. Cell Mol Life Sci 2021; 78:5605-5630. [PMID: 34100982 PMCID: PMC8257547 DOI: 10.1007/s00018-021-03865-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/12/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.
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Affiliation(s)
- Robin Herbrechter
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Nadine Hube
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Raoul Buchholz
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Andreas Reiner
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
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Zhawar VK, Kandpal RP, Athwal RS. Senescence of Normal Human Fibroblasts Relates to the Expression of Ionotropic Glutamate Receptor GluR6/Grik2. Cancer Genomics Proteomics 2020; 17:707-714. [PMID: 33099472 PMCID: PMC7675648 DOI: 10.21873/cgp.20225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Glutamate receptor GRIK2, previously designated as GluR6, is best described in neuronal cells. However, its biological relevance in non-neuronal cells is not well understood. We have investigated the expression of this important protein in normal human fibroblasts as a function of cell proliferation. MATERIALS AND METHODS We introduced expression constructs of all five isoforms (A-E) of GRIK2 in normal human fibroblasts and investigated the cells for the presence and localization of GRIK2, as well as for cell proliferation and senescence over a period of 24 days. RESULTS The expression of GRIK2-A isoform led to immediate cessation of cell proliferation. However, the cell numbers increased by 1.5- to 9.0-fold in 24 days upon transfection with B, C, D and E isoforms, after which they entered a state of senescence. The decreased proliferation was reflected by incorporation of BrdU in only 2-8% of transfected cells even after culturing them for 16 days. CONCLUSION Our results are indicative of an association between GRIK2 and aging of fibroblasts.
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Affiliation(s)
- Vikramjit K Zhawar
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A
| | - Raj P Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A.
| | - Raghbir S Athwal
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A.
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Mesdom P, Colle R, Lebigot E, Trabado S, Deflesselle E, Fève B, Becquemont L, Corruble E, Verstuyft C. Human Dermal Fibroblast: A Promising Cellular Model to Study Biological Mechanisms of Major Depression and Antidepressant Drug Response. Curr Neuropharmacol 2020; 18:301-318. [PMID: 31631822 PMCID: PMC7327943 DOI: 10.2174/1570159x17666191021141057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human dermal fibroblasts (HDF) can be used as a cellular model relatively easily and without genetic engineering. Therefore, HDF represent an interesting tool to study several human diseases including psychiatric disorders. Despite major depressive disorder (MDD) being the second cause of disability in the world, the efficacy of antidepressant drug (AD) treatment is not sufficient and the underlying mechanisms of MDD and the mechanisms of action of AD are poorly understood. OBJECTIVE The aim of this review is to highlight the potential of HDF in the study of cellular mechanisms involved in MDD pathophysiology and in the action of AD response. METHODS The first part is a systematic review following PRISMA guidelines on the use of HDF in MDD research. The second part reports the mechanisms and molecules both present in HDF and relevant regarding MDD pathophysiology and AD mechanisms of action. RESULTS HDFs from MDD patients have been investigated in a relatively small number of works and most of them focused on the adrenergic pathway and metabolism-related gene expression as compared to HDF from healthy controls. The second part listed an important number of papers demonstrating the presence of many molecular processes in HDF, involved in MDD and AD mechanisms of action. CONCLUSION The imbalance in the number of papers between the two parts highlights the great and still underused potential of HDF, which stands out as a very promising tool in our understanding of MDD and AD mechanisms of action.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Céline Verstuyft
- Address correspondence to this author at the Laboratoire de Pharmacologie, Salle 416, Bâtiment Université, Hôpital du Kremlin Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France; Tel: +33145213588; E-mail:
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Zhawar VK, Kandpal RP, Athwal RS. Isoforms of Ionotropic Glutamate Receptor GRIK2 Induce Senescence of Carcinoma Cells. Cancer Genomics Proteomics 2019; 16:59-64. [PMID: 30587499 PMCID: PMC6348395 DOI: 10.21873/cgp.20111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The aberrant regulation of growth and proliferation is a key feature of carcinoma cells. In order to use molecular strategies to correct these defects toward therapeutic purposes, it is important to characterize the entire spectrum of causative molecules. MATERIALS AND METHODS By using gene transfer technique, SKOV3 ovarian carcinoma cells were transduced with an expression construct of glutamate receptor 6 (glutamate ionotropic receptor kainate type subunit 2, GRIK2) in retroviral vector PQCXIP. The senescence of transduced cells was subsequently characterized. RESULTS Our results demonstrated that retroviral transduction occurs with high frequency and transduced cells continue to proliferate, albeit at a significantly reduced rate, up to 39 days. Some transduced colonies stopped proliferating after 12 days, and none of the clones proliferated beyond 37 days. The doubling time for these transduced cells increased progressively until they reached a complete cell-cycle arrest. The proliferating cells were distinguished by bromodeoxyuridine incorporation and 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide assay. The growth and cell cycle arrest in transduced cells accompanied activation of senescence-associated β-galactosidase. Furthermore, we have demonstrated a decrease in the levels of active protein kinase B and increase in the abundance of inactive cyclin-dependent kinase 1. CONCLUSION These results indicate involvement of GRIK2 in senescence and suggests GRIK2 as a potential target for therapeutic intervention of cancer cells.
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Affiliation(s)
- Vikramjit K Zhawar
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A
| | - Raj P Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A.
| | - Raghbir S Athwal
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A.
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Kandpal RP, Sandhu AK, Kaur G, Kaur GP, Athwal RS. Monochromosomal Hybrids and Chromosome Transfer: A Functional Approach for Gene Identification. Cancer Genomics Proteomics 2017; 14:93-101. [PMID: 28387649 PMCID: PMC5369314 DOI: 10.21873/cgp.20022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 11/10/2022] Open
Abstract
Functional complementation of cellular defects has been a valuable approach for localizing causative genes to specific chromosomes. The complementation strategy was followed by positional cloning and characterization of genes for their biological relevance. We herein describe strategies used for the construction of monochromosomal hybrids and their applications for cloning and characterization of genes related to cell growth, cell senescence and DNA repair. We have cloned RNaseT2, GluR6 (glutamate ionotropic receptor kainate type subunit 2-GRIK2) and protein tyrosine phosphatase, receptor type K (PTPRK) genes using these strategies.
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Affiliation(s)
- Raj P Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA, U.S.A.
| | - Arbans K Sandhu
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A
| | - Gurpreet Kaur
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A
| | - Gursurinder P Kaur
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A
| | - Raghbir S Athwal
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, U.S.A.
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Strunk D, Weber P, Röthlisberger B, Filges I. Autism and intellectual disability in a patient with two microdeletions in 6q16: a contiguous gene deletion syndrome? Mol Cytogenet 2016; 9:88. [PMID: 27980676 PMCID: PMC5135825 DOI: 10.1186/s13039-016-0299-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 01/19/2023] Open
Abstract
Background Copy number variations play a significant role in the aetiology of developmental disabilities including non-syndromic intellectual disability and autism. Case presentation We describe a 19-year old patient with intellectual disability and autism for whom chromosomal microarray (CMA) analysis showed the unusual finding of two de novo microdeletions in cis position on chromosome 6q16.1q16.2 and 6q16.3. The two deletions span 10 genes, including FBXL4, POU3F2, PRDM13, CCNC, COQ3 and GRIK2. We compared phenotypes of patients with similar deletions and looked at the involvement of the genes in neuronal networks in order to determine the pathogenicity of our patient’s deletions. Conclusions We suggest that both deletions on 6q are causing his disease phenotype since they harbour several genes which are implicated in pathways of neuronal development and function. Further studies regarding the interaction between PRDM13 and GRIK2 specifically may be interesting.
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Affiliation(s)
- Daniela Strunk
- Medical Genetics, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
| | - Peter Weber
- Division of Neuropediatrics and Developmental Pediatrics, University Children's Hospital, Spitalstrasse 33, CH-4056 Basel, Switzerland
| | - Benno Röthlisberger
- Medical Genetics, Department of Laboratory Medicine, Cantonal Hospital Aarau, Tellstrasse, CH-5001 Aarau, Switzerland
| | - Isabel Filges
- Medical Genetics, University Hospital Basel and University of Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
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