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Torso NDG, Quintanilha JCF, Cursino MA, Pincinato EDC, Lima CSP, Moriel P. Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin. Int J Mol Sci 2023; 24:10884. [PMID: 37446060 DOI: 10.3390/ijms241310884] [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: 06/07/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
The microRNA (miRNA) expression profile by qRT-PCR depends directly on the most appropriate normalization strategy adopted; however, currently there is no universally adequate reference gene. Therefore, this study aimed to determine, considering RNA-Seq results, the most adequate endogenous normalizer for use in the relative quantification of urine miRNAs from head and neck cancer patients, treated with cisplatin chemoradiotherapy. The massive sequencing was performed to identify the miRNAs differentially expressed between the group with cisplatin nephrotoxicity (n = 6) and the one without (n = 6). The candidate endogen normalizer was chosen according to four criteria: (1) the miRNA must be expressed in most samples; (2) the miRNA must have a fold change value between 0.99 and 1.01; (3) the miRNA must have a p-value ≥ 0.98; and (4) the miRNA must not be commented on by the final GeneGlobe (Qiagen, Hilden, Germany) analysis. Four miRNAs met all the criteria (hsa-miR-363-5p, hsa-miR-875-5p, hsa-miR-4302, and hsa-miR-6749-5p) and were selected for validation by qRT-PCR in a cohort of 49 patients (including the 12 sequencing participants). Only hsa-miR-875-5p was shown to be an adequate normalizer for the experimental condition under investigation, as it exhibited invariant expression between the two groups.
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Affiliation(s)
| | | | | | | | | | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083970, Brazil
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2
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Cheng TY, Zimmerman JJ, Giménez-Lirola LG. Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens. Anim Health Res Rev 2022; 23:147-156. [PMID: 36330795 DOI: 10.1017/s1466252322000044] [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] [Indexed: 11/06/2022]
Abstract
In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
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Affiliation(s)
- Ting-Yu Cheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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3
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Dachet F, Brown JB, Valyi-Nagy T, Narayan KD, Serafini A, Boley N, Gingeras TR, Celniker SE, Mohapatra G, Loeb JA. Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Sci Rep 2021; 11:6078. [PMID: 33758256 PMCID: PMC7988150 DOI: 10.1038/s41598-021-85801-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
As a means to understand human neuropsychiatric disorders from human brain samples, we compared the transcription patterns and histological features of postmortem brain to fresh human neocortex isolated immediately following surgical removal. Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern. To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval. Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization. Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection. Predicted transcriptional changes were confirmed histologically on the same tissue demonstrating that while neurons were degenerating, glial cells underwent an outgrowth of their processes. The rapid loss of neuronal genes and reciprocal expression of glial genes highlights highly dynamic transcriptional and cellular changes that occur during the postmortem interval. Understanding these time-dependent changes in gene expression in post mortem brain samples is critical for the interpretation of research studies on human brain disorders.
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Affiliation(s)
- Fabien Dachet
- University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - James B Brown
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | | | - Anna Serafini
- University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Nathan Boley
- University of California, Berkeley, CA, 94720, USA
| | | | | | | | - Jeffrey A Loeb
- University of Illinois at Chicago, Chicago, IL, 60612, USA.
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4
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Schank JR, Lee S, Gonzalez-Islas CE, Nennig SE, Fulenwider HD, Chang J, Li JM, Kim Y, Jeffers LA, Chung J, Lee JK, Jin Z, Aalkjaer C, Boedtkjer E, Choi I. Increased Alcohol Consumption in Mice Lacking Sodium Bicarbonate Transporter NBCn1. Sci Rep 2020; 10:11017. [PMID: 32620847 PMCID: PMC7335059 DOI: 10.1038/s41598-020-67291-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022] Open
Abstract
The previous reports on an addiction vulnerability marker in the human SLC4A7 gene encoding the Na/HCO3 transporter NBCn1 suggest that this pH-regulating protein may affect alcohol-related behavior and response. Here, we examined alcohol consumption and sensitivity to the sedative effects of alcohol in male NBCn1 knockout mice. These mice displayed lower pH in neurons than wildtype controls, determined by intracellular pH in hippocampal neuronal cultures. Neurons from knockout mice had a higher action potential threshold and a more depolarized membrane potential, thus reducing membrane excitability. In a two-bottle free choice procedure, knockout mice consumed more alcohol than controls and consistently increased alcohol consumption after repeated alcohol deprivation periods. Quinine and sucrose preference was similar between genotypes. Knockout mice showed increased propensity for alcohol-induced conditioned place preference. In loss of righting reflex assessment, knockout mice revealed increased sensitivity to alcohol-induced sedation and developed tolerance to the sedation after repeated alcohol administrations. Furthermore, chronic alcohol consumption caused NBCn1 downregulation in the hippocampus and striatum of mice and humans. These results demonstrate an important role of NBCn1 in regulation of alcohol consumption and sensitivity to alcohol-induced sedation.
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Affiliation(s)
- Jesse R Schank
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, 30602, USA
| | - Soojung Lee
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Sadie E Nennig
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, 30602, USA
| | - Hannah D Fulenwider
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, 30602, USA
| | - Jianjun Chang
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jun Ming Li
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yejin Kim
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lauren A Jeffers
- Department of Medicine, Pulmonary Division, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jaegwon Chung
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, 30602, USA
| | - Jae-Kyung Lee
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA, 30602, USA
| | - Zhe Jin
- Department of Neuroscience, Uppsala University, Uppsala, 75124, Sweden
| | | | - Ebbe Boedtkjer
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Inyeong Choi
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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5
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Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Taqi MM, Stålhandske L, Verbeek DS, Mulder J, Rajkowska G, Sheedy D, Kril J, Sun X, Syvänen AC, Yakovleva T, Bakalkin G. Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain. Cereb Cortex 2019; 28:3129-3142. [PMID: 28968778 DOI: 10.1093/cercor/bhx181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Indexed: 12/13/2022] Open
Abstract
Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF). USF2 activates PDYN transcription in model systems, and binds to nonmethylated CGI in dlPFC. USF2 and PDYN expression is correlated, and USF2 and PDYN proteins are co-localized in dlPFC. Segregation of activatory TF and repressive CGI methylation may ensure contrasting PDYN expression in neurons and glia in human brain.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mumtaz Malik Taqi
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Faculty of Medicine, NORMENT, University of Oslo, Oslo, Norway
| | - Lada Stålhandske
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Jan Mulder
- Department of Neuroscience, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Donna Sheedy
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Jillian Kril
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Xueguang Sun
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, CA, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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6
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Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Karpyak VM, Yakovleva T, Bakalkin G. Downregulation of the neuronal opioid gene expression concomitantly with neuronal decline in dorsolateral prefrontal cortex of human alcoholics. Transl Psychiatry 2018; 8:122. [PMID: 29925858 PMCID: PMC6010434 DOI: 10.1038/s41398-017-0075-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/02/2017] [Accepted: 11/01/2017] [Indexed: 01/03/2023] Open
Abstract
Molecular changes in cortical areas of addicted brain may underlie cognitive impairment and loss of control over intake of addictive substances and alcohol. Prodynorphin (PDYN) gives rise to dynorphin (DYNs) opioid peptides which target kappa-opioid receptor (KOR). DYNs mediate alcohol-induced impairment of learning and memory, while KOR antagonists block excessive, compulsive-like drug and alcohol self-administration in animal models. In human brain, the DYN/KOR system may undergo adaptive changes, which along with neuronal loss, may contribute to alcohol-associated cognitive deficit. We addressed this hypothesis by comparing the expression levels and co-expression (transcriptionally coordinated) patterns of PDYN and KOR (OPRK1) genes in dorsolateral prefrontal cortex (dlPFC) between human alcoholics and controls. Postmortem brain specimens of 53 alcoholics and 55 controls were analyzed. PDYN was found to be downregulated in dlPFC of alcoholics, while OPRK1 transcription was not altered. PDYN downregulation was confined to subgroup of subjects carrying C, a high-risk allele of PDYN promoter SNP rs1997794 associated with alcoholism. Changes in PDYN expression did not depend on the decline in neuronal proportion in alcoholics, and thereby may be attributed to transcriptional adaptations in alcoholic brain. Absolute expression levels of PDYN were lower compared to those of OPRK1, suggesting that PDYN expression is a limiting factor in the DYN/KOR signaling, and that the PDYN downregulation diminishes efficacy of DYN/KOR signaling in dlPFC of human alcoholics. The overall outcome of the DYN/KOR downregulation may be disinhibition of neurotransmission, which when overactivated could contribute to formation of alcohol-related behavior.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Daniil Sarkisyan
- 0000 0004 1936 9457grid.8993.bDivision of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Olga Kononenko
- 0000 0004 1936 9457grid.8993.bDivision of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Hiroyuki Watanabe
- 0000 0004 1936 9457grid.8993.bDivision of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Victor M. Karpyak
- 0000 0004 0459 167Xgrid.66875.3aDepartment of Psychiatry and Psychology, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Tatiana Yakovleva
- 0000 0004 1936 9457grid.8993.bDivision of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24, Uppsala, Sweden.
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7
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Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Yakovleva T, Hansson AC, Sommer WH, Spanagel R, Bakalkin G. Dynorphin and κ-Opioid Receptor Dysregulation in the Dopaminergic Reward System of Human Alcoholics. Mol Neurobiol 2018; 55:7049-7061. [PMID: 29383684 PMCID: PMC6061161 DOI: 10.1007/s12035-017-0844-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022]
Abstract
Molecular changes induced by excessive alcohol consumption may underlie formation of dysphoric state during acute and protracted alcohol withdrawal which leads to craving and relapse. A main molecular addiction hypothesis is that the upregulation of the dynorphin (DYN)/κ-opioid receptor (KOR) system in the nucleus accumbens (NAc) of alcohol-dependent individuals causes the imbalance in activity of D1- and D2 dopamine receptor (DR) expressing neural circuits that results in dysphoria. We here analyzed post-mortem NAc samples of human alcoholics to assess changes in prodynorphin (PDYN) and KOR (OPRK1) gene expression and co-expression (transcriptionally coordinated) patterns. To address alterations in D1- and D2-receptor circuits, we studied the regulatory interactions between these pathways and the DYN/KOR system. No significant differences in PDYN and OPRK1 gene expression levels between alcoholics and controls were evident. However, PDYN and OPRK1 showed transcriptionally coordinated pattern that was significantly different between alcoholics and controls. A downregulation of DRD1 but not DRD2 expression was seen in alcoholics. Expression of DRD1 and DRD2 strongly correlated with that of PDYN and OPRK1 suggesting high levels of transcriptional coordination between these gene clusters. The differences in expression and co-expression patterns were not due to the decline in neuronal proportion in alcoholic brain and thereby represent transcriptional phenomena. Dysregulation of DYN/KOR system and dopamine signaling through both alterations in co-expression patterns of opioid genes and decreased DRD1 gene expression may contribute to imbalance in the activity of D1- and D2-containing pathways which may lead to the negative affective state in human alcoholics.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden.
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
| | - Anita C Hansson
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Wolfgang H Sommer
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Rainer Spanagel
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, BMC Husargatan 3, SE-75124, Uppsala, Sweden
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8
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Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation. Acta Neuropathol 2017; 133:485-487. [PMID: 28097436 DOI: 10.1007/s00401-017-1675-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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9
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Stassen QEM, Riemers FM, Reijmerink H, Leegwater PAJ, Penning LC. Reference genes for reverse transcription quantitative PCR in canine brain tissue. BMC Res Notes 2015; 8:761. [PMID: 26654363 PMCID: PMC4673830 DOI: 10.1186/s13104-015-1628-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Background In the last decade canine models have been used extensively to study genetic causes of neurological disorders such as epilepsy and Alzheimer’s disease and unravel their pathophysiological pathways. Reverse transcription quantitative polymerase chain reaction is a sensitive and inexpensive method to study expression levels of genes involved in disease processes. Accurate normalisation with stably expressed so-called reference genes is crucial for reliable expression analysis. Results Following the minimum information for publication of quantitative real-time PCR experiments precise guidelines, the expression of ten frequently used reference genes, namely YWHAZ, HMBS, B2M, SDHA, GAPDH, HPRT, RPL13A, RPS5, RPS19 and GUSB was evaluated in seven brain regions (frontal lobe, parietal lobe, occipital lobe, temporal lobe, thalamus, hippocampus and cerebellum) and whole brain of healthy dogs. The stability of expression varied between different brain areas. Using the GeNorm and Normfinder software HMBS, GAPDH and HPRT were the most reliable reference genes for whole brain. Furthermore based on GeNorm calculations it was concluded that as little as two to three reference genes are sufficient to obtain reliable normalisation, irrespective the brain area. Conclusions Our results amend/extend the limited previously published data on canine brain reference genes. Despite the excellent expression stability of HMBS, GAPDH and HRPT, the evaluation of expression stability of reference genes must be a standard and integral part of experimental design and subsequent data analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1628-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quirine E M Stassen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Frank M Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Hannah Reijmerink
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Peter A J Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
| | - Louis C Penning
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, 3508 TD, Utrecht, The Netherlands.
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10
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Sarkisyan D, Hussain MZ, Watanabe H, Kononenko O, Bazov I, Zhou X, Yamskova O, Krishtal O, Karpyak VM, Yakovleva T, Bakalkin G. Downregulation of the endogenous opioid peptides in the dorsal striatum of human alcoholics. Front Cell Neurosci 2015; 9:187. [PMID: 26029055 PMCID: PMC4428131 DOI: 10.3389/fncel.2015.00187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 04/28/2015] [Indexed: 01/18/2023] Open
Abstract
The endogenous opioid peptides dynorphins and enkephalins may be involved in brain-area specific synaptic adaptations relevant for different stages of an addiction cycle. We compared the levels of prodynorphin (PDYN) and proenkephalin (PENK) mRNAs (by qRT-PCR), and dynorphins and enkephalins (by radioimmunoassay) in the caudate nucleus and putamen between alcoholics and control subjects. We also evaluated whether PDYN promoter variant rs1997794 associated with alcoholism affects PDYN expression. Postmortem specimens obtained from 24 alcoholics and 26 controls were included in final statistical analysis. PDYN mRNA and Met-enkephalin-Arg-Phe, a marker of PENK were downregulated in the caudate of alcoholics, while PDYN mRNA and Leu-enkephalin-Arg, a marker of PDYN were decreased in the putamen of alcoholics carrying high risk rs1997794 C allele. Downregulation of opioid peptides in the dorsal striatum may contribute to development of alcoholism including changes in goal directed behavior and formation of a compulsive habit in alcoholics.
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Affiliation(s)
- Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | | | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden ; Department for Cellular Membranology, Bogomoletz Institute of Physiology Kyiv, Ukraine
| | - Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Xingwu Zhou
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Olga Yamskova
- Department of Functional Pharmacology, Institute for Neuroscience, Uppsala University Uppsala, Sweden
| | - Oleg Krishtal
- Department for Cellular Membranology, Bogomoletz Institute of Physiology Kyiv, Ukraine
| | - Victor M Karpyak
- Department of Psychiatry and Psychology, Mayo Clinic Rochester, MN, USA
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
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11
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Bhandage AK, Jin Z, Bazov I, Kononenko O, Bakalkin G, Korpi ER, Birnir B. GABA-A and NMDA receptor subunit mRNA expression is altered in the caudate but not the putamen of the postmortem brains of alcoholics. Front Cell Neurosci 2014; 8:415. [PMID: 25538565 PMCID: PMC4257153 DOI: 10.3389/fncel.2014.00415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/15/2014] [Indexed: 01/16/2023] Open
Abstract
Chronic consumption of alcohol by humans has been shown to lead to impairment of executive and cognitive functions. Here, we have studied the mRNA expression of ion channel receptors for glutamate and GABA in the dorsal striatum of post-mortem brains from alcoholics (n = 29) and normal controls (n = 29), with the focus on the caudate nucleus that is associated with the frontal cortex executive functions and automatic thinking and on the putamen area that is linked to motor cortices and automatic movements. The results obtained by qPCR assay revealed significant changes in the expression of specific excitatory ionotropic glutamate and inhibitory GABA-A receptor subunit genes in the caudate but not the putamen. Thus, in the caudate we found reduced levels of mRNAs encoding the GluN2A glutamate receptor and the δ, ε, and ρ2 GABA-A receptor subunits, and increased levels of the mRNAs encoding GluD1, GluD2, and GABA-A γ1 subunits in the alcoholics as compared to controls. Interestingly in the controls, 11 glutamate and 5 GABA-A receptor genes were more prominently expressed in the caudate than the putamen (fold-increase varied from 1.24 to 2.91). Differences in gene expression patterns between the striatal regions may underlie differences in associated behavioral outputs. Our results suggest an altered balance between caudate-mediated voluntarily controlled and automatic behaviors in alcoholics, including diminished executive control on goal-directed alcohol-seeking behavior.
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Affiliation(s)
- Amol K Bhandage
- Molecular Physiology and Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
| | - Zhe Jin
- Molecular Physiology and Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
| | - Igor Bazov
- Pharmacology, Institute of Biomedicine, University of Helsinki Helsinki, Finland
| | - Olga Kononenko
- Pharmacology, Institute of Biomedicine, University of Helsinki Helsinki, Finland
| | - Georgy Bakalkin
- Pharmacology, Institute of Biomedicine, University of Helsinki Helsinki, Finland
| | - Esa R Korpi
- Department of Pharmaceutical Bioscience (Biological Research on Drug Dependence), Biomedical Center, Uppsala University Uppsala, Sweden
| | - Bryndis Birnir
- Molecular Physiology and Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
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12
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Ranjan AK, Joglekar MV, Atre AN, Patole M, Bhonde RR, Hardikar A. Simultaneous imaging of microRNA or mRNA territories with protein territory in mammalian cells at single cell resolution. RNA Biol 2014; 9:949-53. [DOI: 10.4161/rna.20484] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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13
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Jin Z, Bhandage AK, Bazov I, Kononenko O, Bakalkin G, Korpi ER, Birnir B. Expression of specific ionotropic glutamate and GABA-A receptor subunits is decreased in central amygdala of alcoholics. Front Cell Neurosci 2014; 8:288. [PMID: 25278838 PMCID: PMC4165314 DOI: 10.3389/fncel.2014.00288] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/29/2014] [Indexed: 01/20/2023] Open
Abstract
The central amygdala (CeA) has a role for mediating fear and anxiety responses. It is also involved in emotional imbalance caused by alcohol abuse and dependence and in regulating relapse to alcohol abuse. Growing evidences suggest that excitatory glutamatergic and inhibitory γ-aminobutyric acid-ergic (GABAergic) transmissions in the CeA are affected by chronic alcohol exposure. Human post-mortem CeA samples from male alcoholics (n = 9) and matched controls (n = 9) were assayed for the expression level of ionotropic glutamate and GABA-A receptors subunit mRNAs using quantitative real-time reverse transcription-PCR (RT-qPCR). Our data revealed that out of the 16 ionotropic glutamate receptor subunits, mRNAs encoding two AMPA [2-amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propanoic acid] receptor subunits GluA1 and GluA4; one kainate receptor subunit GluK2; one NMDA (N-methyl-D-aspartate) receptor subunit GluN2D and one delta receptor subunit GluD2 were significantly decreased in the CeA of alcoholics. In contrast, of the 19 GABA-A receptor subunits, only the mRNA encoding the α2 subunit was significantly down-regulated in the CeA of the alcoholics as compared with control subjects. Our findings imply that the down-regulation of specific ionotropic glutamate and GABA-A receptor subunits in the CeA of alcoholics may represent one of the molecular substrates underlying the new balance between excitatory and inhibitory neurotransmission in alcohol dependence.
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Affiliation(s)
- Zhe Jin
- Molecular Physiology and Neuroscience Unit, Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
| | - Amol K Bhandage
- Molecular Physiology and Neuroscience Unit, Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
| | - Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Esa R Korpi
- Pharmacology, Institute of Biomedicine, University of Helsinki Helsinki, Finland
| | - Bryndis Birnir
- Molecular Physiology and Neuroscience Unit, Neuroscience, Biomedical Center, Uppsala University Uppsala, Sweden
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14
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Henriksson R, Bäckman CM, Harvey BK, Kadyrova H, Bazov I, Shippenberg TS, Bakalkin G. PDYN, a gene implicated in brain/mental disorders, is targeted by REST in the adult human brain. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1226-32. [PMID: 25220237 DOI: 10.1016/j.bbagrm.2014.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/21/2014] [Accepted: 09/02/2014] [Indexed: 11/29/2022]
Abstract
The dynorphin κ-opioid receptor system is implicated in mental health and brain/mental disorders. However, despite accumulating evidence that PDYN and/or dynorphin peptide expression is altered in the brain of individuals with brain/mental disorders, little is known about transcriptional control of PDYN in humans. In the present study, we show that PDYN is targeted by the transcription factor REST in human neuroblastoma SH-SY5Y cells and that that interfering with REST activity increases PDYN expression in these cells. We also show that REST binding to PDYN is reduced in the adult human brain compared to SH-SY5Y cells, which coincides with higher PDYN expression. This may be related to MIR-9 mediated down-regulation of REST as suggested by a strong inverse correlation between REST and MIR-9 expression. Our results suggest that REST represses PDYN expression in SH-SY5Y cells and the adult human brain and may have implications for mental health and brain/mental disorders.
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Affiliation(s)
- Richard Henriksson
- Integrative Neuroscience Section, Integrative Neuroscience Research Branch, NIDA-IRP, NIH, 333 Cassell Dr, Baltimore, MD 21224, USA; Department of Clinical Neuroscience, Karolinska Institutet, Cell and Molecular Medicine, L8:01, 17176 Stockholm, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Uppsala Biomedical Centre, Box 591, Husargatan 3, 751 24 Uppsala, Sweden.
| | - Cristina M Bäckman
- Cellular Neurophysiology Section, Cellular Neurobiology Research Branch, NIDA-IRP, NIH, 333 Cassell Dr, Baltimore, MD 21224, USA
| | - Brandon K Harvey
- Neural Protection and Regeneration Section, Molecular Neuropsychiatry Research Branch, NIDA-IRP, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Helena Kadyrova
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala Biomedical Centre, Box 591, Husargatan 3, 751 24 Uppsala, Sweden
| | - Igor Bazov
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala Biomedical Centre, Box 591, Husargatan 3, 751 24 Uppsala, Sweden
| | - Toni S Shippenberg
- Integrative Neuroscience Section, Integrative Neuroscience Research Branch, NIDA-IRP, NIH, 333 Cassell Dr, Baltimore, MD 21224, USA
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala Biomedical Centre, Box 591, Husargatan 3, 751 24 Uppsala, Sweden
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15
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Han TU, Park J, Domingues CF, Moretti-Ferreira D, Paris E, Sainz E, Gutierrez J, Drayna D. A study of the role of the FOXP2 and CNTNAP2 genes in persistent developmental stuttering. Neurobiol Dis 2014; 69:23-31. [PMID: 24807205 DOI: 10.1016/j.nbd.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/09/2014] [Accepted: 04/27/2014] [Indexed: 11/24/2022] Open
Abstract
A number of speech disorders including stuttering have been shown to have important genetic contributions, as indicated by high heritability estimates from twin and other studies. We studied the potential contribution to stuttering from variants in the FOXP2 gene, which have previously been associated with developmental verbal dyspraxia, and from variants in the CNTNAP2 gene, which have been associated with specific language impairment (SLI). DNA sequence analysis of these two genes in a group of 602 unrelated cases, all with familial persistent developmental stuttering, revealed no excess of potentially deleterious coding sequence variants in the cases compared to a matched group of 487 well characterized neurologically normal controls. This was compared to the distribution of variants in the GNPTAB, GNPTG, and NAGPA genes which have previously been associated with persistent stuttering. Using an expanded subject data set, we again found that NAGPA showed significantly different mutation frequencies in North Americans of European descent (p=0.0091) and a significant difference existed in the mutation frequency of GNPTAB in Brazilians (p=0.00050). No significant differences in mutation frequency in the FOXP2 and CNTNAP2 genes were observed between cases and controls. To examine the pattern of expression of these five genes in the human brain, real time quantitative reverse transcription PCR was performed on RNA purified from 27 different human brain regions. The expression patterns of FOXP2 and CNTNAP2 were generally different from those of GNPTAB, GNPTG and NAPGA in terms of relatively lower expression in the cerebellum. This study provides an improved estimate of the contribution of mutations in GNPTAB, GNPTG and NAGPA to persistent stuttering, and suggests that variants in FOXP2 and CNTNAP2 are not involved in the genesis of familial persistent stuttering. This, together with the different brain expression patterns of GNPTAB, GNPTG, and NAGPA compared to that of FOXP2 and CNTNAP2, suggests that the genetic neuropathological origins of stuttering differ from those of verbal dyspraxia and SLI.
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Affiliation(s)
- Tae-Un Han
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - John Park
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Carlos F Domingues
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA; Department of Genetics, Institute of Bioscience, São Paulo State University (UNESP), Botucatu, São Paulo 18618-000, Brazil
| | - Danilo Moretti-Ferreira
- Department of Genetics, Institute of Bioscience, São Paulo State University (UNESP), Botucatu, São Paulo 18618-000, Brazil
| | - Emily Paris
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Eduardo Sainz
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Joanne Gutierrez
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
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16
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Jin Z, Bhandage AK, Bazov I, Kononenko O, Bakalkin G, Korpi ER, Birnir B. Selective increases of AMPA, NMDA, and kainate receptor subunit mRNAs in the hippocampus and orbitofrontal cortex but not in prefrontal cortex of human alcoholics. Front Cell Neurosci 2014; 8:11. [PMID: 24523671 PMCID: PMC3905203 DOI: 10.3389/fncel.2014.00011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/08/2014] [Indexed: 12/31/2022] Open
Abstract
Glutamate is the main excitatory transmitter in the human brain. Drugs that affect the glutamatergic signaling will alter neuronal excitability. Ethanol inhibits glutamate receptors. We examined the expression level of glutamate receptor subunit mRNAs in human post-mortem samples from alcoholics and compared the results to brain samples from control subjects. RNA from hippocampal dentate gyrus (HP-DG), orbitofrontal cortex (OFC), and dorso-lateral prefrontal cortex (DL-PFC) samples from 21 controls and 19 individuals with chronic alcohol dependence were included in the study. Total RNA was assayed using quantitative RT-PCR. Out of the 16 glutamate receptor subunits, mRNAs encoding two AMPA [2-amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propanoic acid] receptor subunits GluA2 and GluA3; three kainate receptor subunits GluK2, GluK3 and GluK5 and five NMDA (N-methyl-D-aspartate) receptor subunits GluN1, GluN2A, GluN2C, GluN2D, and GluN3A were significantly increased in the HP-DG region in alcoholics. In the OFC, mRNA encoding the NMDA receptor subunit GluN3A was increased, whereas in the DL-PFC, no differences in mRNA levels were observed. Our laboratory has previously shown that the expression of genes encoding inhibitory GABA-A receptors is altered in the HP-DG and OFC of alcoholics (Jin et al., 2011). Whether the changes in one neurotransmitter system drives changes in the other or if they change independently is currently not known. The results demonstrate that excessive long-term alcohol consumption is associated with altered expression of genes encoding glutamate receptors in a brain region-specific manner. It is an intriguing possibility that genetic predisposition to alcoholism may contribute to these gene expression changes.
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Affiliation(s)
- Zhe Jin
- Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Amol K Bhandage
- Department of Neuroscience, Uppsala University Uppsala, Sweden
| | - Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University Uppsala, Sweden
| | - Esa R Korpi
- Institute of Biomedicine, Pharmacology, University of Helsinki Helsinki, Finland
| | - Bryndis Birnir
- Department of Neuroscience, Uppsala University Uppsala, Sweden
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17
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Wang R, Halper-Stromberg E, Szymanski-Pierce M, Bassett SS, Avramopoulos D. Genetic determinants of neuroglobin transcription. Neurogenetics 2013; 15:65-75. [PMID: 24362753 DOI: 10.1007/s10048-013-0388-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/06/2013] [Indexed: 11/29/2022]
Abstract
Neuroglobin (NGB) is a neuron-specific vertebrate globin shown to protect against hypoxia, ischemia, oxidative stress and the toxic effects of Amyloid-beta. Following on our and others' results highlighting the importance of NGB expression in disease, we searched for genetic determinants of its expression. We found that a microRNA expressed with the NGB transcript shows significant target enrichments in the angiogenesis pathway and the Alzheimer disease/presenilin pathway. Using reporter constructs we identified potential promoter/enhancer elements between the transcription start site and 1,142 bp upstream. Using 184 post-mortem temporal lobe samples we replicated the reported negative effect of age, and after genotyping tagging SNPs we found one (rs981471) showing a significant correlation with the gene's expression and another (rs8014408) showing an interaction with age, the rare C allele being correlated with higher expression and faster decline. The two SNPs are towards the 3' end of NGB within the same LD block, 52 Kb apart and modestly correlated (r (2) = 0.5). Next generation sequencing of the same 184 temporal lobe samples and 79 confirmed AD patients across the entire gene region (including >12 Kb on the 3' and 5' flank) revealed limited coding variation, suggesting purifying selection of NGB, but did not identify regulatory or disease associated rare variants. A dinucleotide repeat in intron 1 with extensive evidence of functionality showed interesting but inconclusive results, as it was not amenable to further molecular analysis.
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Affiliation(s)
- R Wang
- Department of Psychiatry, Johns Hopkins University, School of Medicine, 733 North Broadway, MRB-507, Baltimore, MD, 21205, USA
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18
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Shimamoto Y, Kitamura H, Niimi K, Yoshikawa Y, Hoshi F, Ishizuka M, Takahashi E. Selection of suitable reference genes for mRNA quantification studies using common marmoset tissues. Mol Biol Rep 2013; 40:6747-55. [DOI: 10.1007/s11033-013-2791-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/14/2013] [Indexed: 01/25/2023]
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19
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Identification of cell-specific patterns of reference gene stability in quantitative reverse-transcriptase polymerase chain reaction studies of embryonic, placental and neural stem models of prenatal ethanol exposure. Alcohol 2013; 47:109-20. [PMID: 23317542 DOI: 10.1016/j.alcohol.2012.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 12/01/2012] [Accepted: 12/01/2012] [Indexed: 01/22/2023]
Abstract
Identification of the transcriptional networks disrupted by prenatal ethanol exposure remains a core requirement to better understanding the molecular mechanisms of alcohol-induced teratogenesis. In this regard, quantitative reverse-transcriptase polymerase chain reaction (qPCR) has emerged as an essential technique in our efforts to characterize alterations in gene expression brought on by exposure to alcohol. However, many publications continue to report the utilization of inappropriate methods of qPCR normalization, and for many in vitro models, no consistent set of empirically tested normalization controls have been identified. In the present study, we sought to identify a group of candidate reference genes for use within studies of alcohol exposed embryonic, placental, and neurosphere stem cells under both conditions maintaining stemness as well as throughout in vitro differentiation. To this end, we surveyed the recent literature and compiled a short list of fourteen candidate genes commonly used as normalization controls in qPCR studies of gene expression. This list included: Actb, B2m, Gapdh, Gusb, H2afz, Hk2, Hmbs, Hprt, Mrpl1, Pgk1, Ppia, Sdha, Tbp, and Ywhaz. From these studies, we find no single candidate gene was consistently refractory to the influence of alcohol nor completely stable throughout in vitro differentiation. Accordingly, we propose normalizing qPCR measurements to the geometric mean C(T) values obtained for three independent reference mRNAs as a reliable method to accurately interpret qPCR data and assess alterations in gene expression within alcohol treated cultures. Highlighting the importance of careful and empirical reference gene selection, the commonly used reference gene Actb was often amongst the least stable candidate genes tested. In fact, it would not serve as a valid normalization control in many cases. Data presented here will aid in the design of future experiments using stem cells to study the transcriptional processes driving differentiation, and model the developmental impact of teratogens.
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20
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Bazov I, Kononenko O, Watanabe H, Kuntić V, Sarkisyan D, Taqi MM, Hussain MZ, Nyberg F, Yakovleva T, Bakalkin G. The endogenous opioid system in human alcoholics: molecular adaptations in brain areas involved in cognitive control of addiction. Addict Biol 2013; 18:161-9. [PMID: 21955155 DOI: 10.1111/j.1369-1600.2011.00366.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The endogenous opioid system (EOS) plays a critical role in addictive processes. Molecular dysregulations in this system may be specific for different stages of addiction cycle and neurocircuitries involved and therefore may differentially contribute to the initiation and maintenance of addiction. Here we evaluated whether the EOS is altered in brain areas involved in cognitive control of addiction including the dorsolateral prefrontal cortex (dl-PFC), orbitofrontal cortex (OFC) and hippocampus in human alcohol-dependent subjects. Levels of EOS mRNAs were measured by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and levels of dynorphins by radioimmunoassay (RIA) in post-mortem specimens obtained from 14 alcoholics and 14 controls. Prodynorphin mRNA and dynorphins in dl-PFC, κ-opioid receptor mRNA in OFC and dynorphins in hippocampus were up-regulated in alcoholics. No significant changes in expression of proenkephalin, and µ- and δ-opioid receptors were evident; pro-opiomelanocortin mRNA levels were below the detection limit. Activation of the κ-opioid receptor by up-regulated dynorphins in alcoholics may underlie in part neurocognitive dysfunctions relevant for addiction and disrupted inhibitory control.
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Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Sweden.
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21
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Durrenberger PF, Fernando FS, Magliozzi R, Kashefi SN, Bonnert TP, Ferrer I, Seilhean D, Nait-Oumesmar B, Schmitt A, Gebicke-Haerter PJ, Falkai P, Grünblatt E, Palkovits M, Parchi P, Capellari S, Arzberger T, Kretzschmar H, Roncaroli F, Dexter DT, Reynolds R. Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study. Acta Neuropathol 2012; 124:893-903. [PMID: 22864814 DOI: 10.1007/s00401-012-1027-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/15/2012] [Accepted: 07/24/2012] [Indexed: 01/17/2023]
Abstract
The use of an appropriate reference gene to ensure accurate normalisation is crucial for the correct quantification of gene expression using qPCR assays and RNA arrays. The main criterion for a gene to qualify as a reference gene is a stable expression across various cell types and experimental settings. Several reference genes are commonly in use but more and more evidence reveals variations in their expression due to the presence of on-going neuropathological disease processes, raising doubts concerning their use. We conducted an analysis of genome-wide changes of gene expression in the human central nervous system (CNS) covering several neurological disorders and regions, including the spinal cord, and were able to identify a number of novel stable reference genes. We tested the stability of expression of eight novel (ATP5E, AARS, GAPVD1, CSNK2B, XPNPEP1, OSBP, NAT5 and DCTN2) and four more commonly used (BECN1, GAPDH, QARS and TUBB) reference genes in a smaller cohort using RT-qPCR. The most stable genes out of the 12 reference genes were tested as normaliser to validate increased levels of a target gene in CNS disease. We found that in human post-mortem tissue the novel reference genes, XPNPEP1 and AARS, were efficient in replicating microarray target gene expression levels and that XPNPEP1 was more efficient as a normaliser than BECN1, which has been shown to change in expression as a consequence of neuronal cell loss. We provide herein one more suitable novel reference gene, XPNPEP1, with no current neuroinflammatory or neurodegenerative associations that can be used for gene quantitative gene expression studies with human CNS post-mortem tissue and also suggest a list of potential other candidates. These data also emphasise the importance of organ/tissue-specific stably expressed genes as reference genes for RNA studies.
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Affiliation(s)
- Pascal F Durrenberger
- Wolfson Neuroscience Laboratories, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
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22
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Impact of Thawing on Reference Gene Expression Stability in Renal Cell Carcinoma Samples. ACTA ACUST UNITED AC 2012; 21:157-63. [DOI: 10.1097/pdm.0b013e31824d3435] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Alexander GM, Graef JD, Hammarback JA, Nordskog BK, Burnett EJ, Daunais JB, Bennett AJ, Friedman DP, Suomi SJ, Godwin DW. Disruptions in serotonergic regulation of cortical glutamate release in primate insular cortex in response to chronic ethanol and nursery rearing. Neuroscience 2012; 207:167-81. [PMID: 22305886 DOI: 10.1016/j.neuroscience.2012.01.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 01/12/2012] [Accepted: 01/13/2012] [Indexed: 11/29/2022]
Abstract
Early-life stress has been shown to increase susceptibility to anxiety and substance abuse. Disrupted activity within the anterior insular cortex (AIC) has been shown to play a role in both of these disorders. Altered serotonergic processing is implicated in controlling the activity levels of the associated cognitive networks. We therefore investigated changes in both serotonin receptor expression and glutamatergic synaptic activity in the AIC of alcohol-drinking rhesus monkeys. We studied tissues from male rhesus monkeys raised under two conditions: Male rhesus monkeys (1) "mother reared" (MR) by adult females (n=9) or (2) "Nursery reared" (NR), that is, separated from their mothers and reared as a separate group under surrogate/peer-reared conditions (n=9). The NR condition represents a long-standing and well-validated nonhuman primate model of early life stress. All monkeys were trained to self-administer ethanol (4% w/v) or an isocaloric maltose-dextrin control solution. Subsets from each rearing condition were then given daily access to ethanol, water, or maltose-dextrin for 12 months. Tissues were collected at necropsy and were further analyzed. Using real time RT-PCR we found that ethanol-naive, NR monkeys had lower AIC levels of 5-HT(1A) and 5-HT(2A) receptor mRNA compared with ethanol-naive, MR animals. Although NR monkeys consumed more ethanol over the 12-month period compared with MR animals, both MR and NR animals expressed greater 5-HT(1A) and 5-HT(2A) receptor mRNA levels following chronic alcohol self-administration. The interaction between nursery-rearing conditions and alcohol consumption resulted in a significant enhancement of both 5-HT(1A) and 5-HT(2A) receptor mRNA levels such that lower expression levels observed in nursery-rearing conditions were not found in the alcohol self-administration group. Using voltage clamp recordings in the whole cell configuration we recorded excitatory postsynaptic currents in both ethanol-naive and chronic self-administration groups of NR and MR monkeys. Both groups that self-administered ethanol showed greater glutamatergic activity within the AIC. This AIC hyperactivity in MR alcohol-consuming monkeys was accompanied by an increased sensitivity to regulation by presynaptic 5-HT(1A) receptors that was not apparent in the ethanol-naive, MR group. Our data indicate that chronic alcohol consumption leads to greater AIC activity and may indicate a compensatory upregulation of presynaptic 5-HT(1A) receptors. Our results also indicate that AIC activity may be less effectively regulated by 5-HT in ethanol-naive NR animals than in NR monkeys in response to chronic ethanol self-administration. These data suggest possible mechanisms for increased alcohol seeking and possible addiction potential among young adults who had previously experienced early-life stress that include disruptions in both AIC activity and serotonin system dynamics.
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Affiliation(s)
- G M Alexander
- Department of Neurobiology, Duke University Medical Center, Bryan Research Building, Durham, NC 27710, USA
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24
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Jin Z, Bazov I, Kononenko O, Korpi ER, Bakalkin G, Birnir B. Selective Changes of GABA(A) Channel Subunit mRNAs in the Hippocampus and Orbitofrontal Cortex but not in Prefrontal Cortex of Human Alcoholics. Front Cell Neurosci 2012; 5:30. [PMID: 22319468 PMCID: PMC3249692 DOI: 10.3389/fncel.2011.00030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 12/14/2011] [Indexed: 11/13/2022] Open
Abstract
Alcohol dependence is a common chronic relapsing disorder. The development of alcohol dependence has been associated with changes in brain GABA(A) channel-mediated neurotransmission and plasticity. We have examined mRNA expression of the GABA(A) channel subunit genes in three brain regions in individuals with or without alcohol dependence using quantitative real-time PCR assay. The levels of selective GABA(A) channel subunit mRNAs were altered in specific brain regions in alcoholic subjects. Significant increase in the α1, α4, α5, β1, and γ1 subunit mRNAs in the hippocampal dentate gyrus region, and decrease in the β2 and δ subunit mRNAs in the orbitofrontal cortex were identified whereas no changes in the dorsolateral prefrontal cortex were detected. The data increase our understanding of the role of GABA(A) channels in the development of alcohol dependence.
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Affiliation(s)
- Zhe Jin
- The Division of Molecular Physiology and Neuroscience, Department of Neuroscience, Uppsala University Uppsala, Sweden
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25
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Abstract
Genetic variation in CLU encoding clusterin has been associated with Alzheimer's disease (AD) through replicated genome-wide studies, but the underlying mechanisms remain unknown. Following earlier reports that tightly regulated CLU alternative transcripts have different functions, we tested CLU single nucleotide polymorphisms (SNPs) including those associated with AD for quantitative effects on individual alternative transcripts. In 190 temporal lobe samples without pathology we found that the risk allele of the AD associated SNP rs9331888 increases the relative abundance of transcript NM_203339 (P=4.3×10(-12)). Using an independent set of 115 AD and control samples, we replicated this result (p=0.0014) and further observed that multiple CLU transcripts are at higher levels in AD compared to controls. The AD SNP rs9331888 is located in the first exon of NM_203339 and therefore, it is a functional candidate for the observed effects. We tested this hypothesis by in vitro dual luciferase assays using SK-N-SH cells and mouse primary cortical neurons and found allelic effects on enhancer function, consistent with our results on post-mortem human brain. These results suggest a biological mechanism for the genetic association of CLU with AD risk and indicate that rs9331888 is one of the functional DNA variants underlying this association.
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26
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Li L, Yan Y, Xu H, Qu T, Wang B. Selection of reference genes for gene expression studies in ultraviolet B-irradiated human skin fibroblasts using quantitative real-time PCR. BMC Mol Biol 2011; 12:8. [PMID: 21324211 PMCID: PMC3050716 DOI: 10.1186/1471-2199-12-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 02/17/2011] [Indexed: 11/19/2022] Open
Abstract
Background Reference genes are frequently used to normalise mRNA levels between different samples. The expression level of these genes, however, may vary between tissues or cells and may change under certain circumstances. Cytoskeleton genes have served as multifunctional tools for experimental studies as reference genes. Our previous studies have demonstrated that the expression of vimentin, one cytoskeletal protein, was increased in ultraviolet B (UVB)-irradiated fibroblasts. Thus, we examined the expression of other cytoskeleton protein genes, ACTB (actin, beta), TUBA1A (tubulin, alpha 1a), and TUBB1 (tubulin, beta 1), in human dermal fibroblasts irradiated by UVB to determine which of these candidates were the most appropriate reference genes. Results Quantitative real-time PCR followed by analysis with the NormFinder and geNorm software programmes was performed. The initial screening of the expression patterns demonstrated that the expression of VIM was suppressed after UVB irradiation at doses ≥25 mJ/cm2 and that the expression of TUBA1A was significantly reduced by UVB doses ≥75 mJ/cm2 in cultured human dermal fibroblasts. The analysis of the experimental data revealed ACTB to be the most stably expressed gene, followed by GAPDH (aglyceraldehyde-3-phosphate dehydrogenase), under these experimental conditions. By contrast, VIM was found to be the least stable gene. The combination of ACTB and TUBB1 was revealed to be the gene pair that introduced the least systematic error into the data normalisation. Conclusion The data herein provide evidence that ACTB and TUBB1 are suitable reference genes in human skin fibroblasts irradiated by UVB, whereas VIM and TUBA1A are not and should therefore be excluded as reference genes in any gene expression studies involving UVB-irradiated human skin fibroblasts.
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Affiliation(s)
- Li Li
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
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Tunbridge EM, Eastwood SL, Harrison PJ. Changed relative to what? Housekeeping genes and normalization strategies in human brain gene expression studies. Biol Psychiatry 2011; 69:173-9. [PMID: 20673871 DOI: 10.1016/j.biopsych.2010.05.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/25/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
Abstract
Many studies in biological psychiatry compare the abundance of individual messenger RNAs between cases and control subjects or, more recently, between genotype groups. Most utilize some form of normalization procedure, usually expressing the transcript(s) of interest relative to that of a housekeeping gene or genes (also called reference genes), to overcome various sources of experimental error. Indeed, normalization is such a standard procedure that its purpose, principles, and limitations are sometimes overlooked, and some papers lack sufficient information as to its implementation. Here, we review the rationales for normalization and argue that in well-conducted psychiatric gene expression studies using human brain tissue, it is reducing intersubject variability rather than experimental error that is the major benefit of normalization. We also review the conceptual and empirical basis for the category of housekeeping genes-i.e., genes with a ubiquitous and invariant expression. We conclude that the evidence is against any such simple categorization and that a more pragmatic, less dogmatic, approach to the selection and implementation of reference genes is required, which takes into account the particular issues that pertain to human brain tissue studies. This pragmatism extends to the issue of whether normalization should be to one or multiple reference genes. We end by making several recommendations toward a more flexible, transparent, and comprehensive approach to data presentation and analysis. We illustrate the review with examples from studies of schizophrenia and mood disorder.
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Affiliation(s)
- Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
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Harrison PJ, Laatikainen LM, Tunbridge EM, Eastwood SL. Human brain weight is correlated with expression of the 'housekeeping genes' beta-2-microglobulin (β2M) and TATA-binding protein (TBP). Neuropathol Appl Neurobiol 2011; 36:498-504. [PMID: 20831744 DOI: 10.1111/j.1365-2990.2010.01098.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AIMS Many variables affect mRNA measurements in post mortem human brain tissue. Brain weight has not hitherto been considered to be such a factor. This study examined whether there is any relationship between brain weight and mRNA abundance. METHODS We investigated quantitative real-time RT-PCR data for five 'housekeeping genes' using the 104 adult brains of the Stanley Microarray Consortium series. Eleven data sets were analysed, from cerebellum, hippocampus, and anterior cingulate cortex. We used a specified sequence of correlations, partial correlations and multiple regression analyses. RESULTS Brain weight correlated with the 'raw' (i.e. non-normalized) data for two mRNAs, β2-microglobulin and TATA-binding protein, measured in cerebellum and hippocampus, respectively. In hippocampus, the geometric mean of three housekeeping gene transcripts also correlated with brain weight. The correlations were significant after adjusting for age, sex and other confounders, and the effect of brain weight was confirmed using multiple regression. No correlations with brain weight were seen in the anterior cingulate cortex, nor for the other mRNAs examined. CONCLUSIONS The findings were not anticipated; they need replication in another brain series, and a more systematic survey is indicated. In the interim, we suggest that quantitative gene expression studies in human brain should inspect for a potential influence of brain weight, especially as the affected transcripts are commonly used as reference genes for normalization purposes in studies of neurological and psychiatric disorders. The relationship of brain weight with β2-microglobulin mRNA may reflect the roles of major histocompatibility complex class I genes in synapse formation and plasticity.
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Affiliation(s)
- P J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK.
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Sørby LA, Andersen SN, Bukholm IRK, Jacobsen MB. Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:144. [PMID: 21059236 PMCID: PMC2988724 DOI: 10.1186/1756-9966-29-144] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Background Real-time reverse transcription PCR (qRT-PCR) is frequently used for gene expression quantification due to its methodological reproducibility and sensitivity. The gene expression is quantified by normalization to one or more reference genes which are presumed stably expressed throughout a given experiment. The aim of this study was to validate a standardized experimental setup to identifying reference genes for normalization of qRT-PCR in the metastatic and non-metastatic colon cancer. Methods In this study, expression of 16 commonly used reference genes was quantified in tumour tissue and individual-matched normal mucosa in 18 non-metastatic colon cancer patients and 20 colon cancer patients with distant metastases using TaqMan Low Density Array (TLDA). The expression stability was determined and compared by means of geNorm and NormFinder. Results Two pairs of genes, HPRT1/PPIA and IPO8/PPIA, were identified to be suitable to normalize gene expression data in metastatic and non-metastatic colon cancer patients, according to geNorm and NormFinder respectively. Conclusion We propose a standardized approach of finding the most suitable reference gene(s) in every qRT-PCR experiment using TLDA.
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Affiliation(s)
- Lise Aa Sørby
- Quality and Research Department, Ostfold Hospital Trust, 1603 Fredrikstad, Norway.
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Wang Y, Han Z, Yan S, Mao A, Wang B, Ren H, Chi Y, Han Z. Evaluation of suitable reference gene for real-time PCR in human umbilical cord mesenchymal stem cells with long-term in vitro expansion. In Vitro Cell Dev Biol Anim 2010; 46:595-9. [DOI: 10.1007/s11626-010-9318-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 04/06/2010] [Indexed: 02/08/2023]
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Hurtado del Pozo C, Calvo RM, Vesperinas-García G, Gómez-Ambrosi J, Frühbeck G, Corripio-Sánchez R, Rubio MA, Obregon MJ. IPO8 and FBXL10: new reference genes for gene expression studies in human adipose tissue. Obesity (Silver Spring) 2010; 18:897-903. [PMID: 19876011 DOI: 10.1038/oby.2009.374] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Housekeeping genes frequently used in gene expression studies are highly regulated in human adipose tissue. To ensure a correct interpretation of results, it is critical to select appropriate reference genes. Subcutaneous (SC) and omental (OM) adipose tissue expression was analyzed from lean and obese subjects using whole genome complementary DNA (cDNA) microarrays to identify stably expressed genes and commercial TaqMan low density arrays (LDAs), with 16 common control genes. The best candidate gene from microarrays analysis was F-box and leucine-rich repeat protein-10 (FBXL10) (fold-change 10(-3) P < 0.01), an ubiquitous nucleolar protein evolutionarily conserved. Hypoxanthine phosphoribosyltransferase 1 (HPRT1) and importin 8 (IPO8), were the best reference genes among the 16 genes in the LDAs with coefficient of variation (CV) of 4.51 and 4.55%, respectively. However, when the LDAs data were further analyzed by the geNorm and NormFinder softwares, IPO8, a nuclear protein mediating import of proteins, was the first and the third better reference gene, respectively. IPO8 and FBXL10 were further validated by real-time PCR in additional OM and SC fat samples and primary cultured preadipocytes. According to their CV, IPO8 resulted more suitable than FBXL10 in both adipose tissue depots and SC preadipocytes, whereas FBXL10 performed better than IPO8 in OM cultured preadipocytes. Both genes expression levels did not change throughout adipogenesis. Thus, we provide clear evidence that IPO8 and FBXL10 are good candidates to use as reference genes in gene expression studies in human OM and SC adipose tissues as well as differentiated primary preadipocytes.
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Affiliation(s)
- Carmen Hurtado del Pozo
- Instituto de Investigaciones Biomedicas, Consejo Superior de Investigaciones Cientificas-UAM, Madrid, Spain
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Housekeeping gene stability influences the quantification of osteogenic markers during stem cell differentiation to the osteogenic lineage. Cytotechnology 2010; 62:109-20. [PMID: 20396946 DOI: 10.1007/s10616-010-9265-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/18/2010] [Indexed: 10/19/2022] Open
Abstract
Real-time reverse transcription PCR (RT-qPCR) relies on a housekeeping or normalizer gene whose expression remains constant throughout the experiment. RT-qPCR is commonly used for characterization of human bone marrow mesenchymal stem cells (hBMSCs). However, to the best of our knowledge, there are no studies validating the expression stability of the genes used as normalizers during hBMSCs differentiation. This work aimed to study the stability of the housekeeping genes beta-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ribosomal protein L13A (RPL13A) during the osteogenic differentiation of hBMSCs. Their stability was evaluated via RT-qPCR in 14 and 20 day differentiation assays to the osteogenic lineage. Different normalization strategies were evaluated to quantify the osteogenic markers collagen type I, bone sialoprotein and osteonectin. Cell differentiation was confirmed via alizarin red staining. The results demonstrated up-regulation of beta-actin with maximum fold changes (MFC) of 4.38. GAPDH and RPL13A were not regulated by osteogenic media after 14 days and presented average fold changes lower than 2 in 20 day cultures. RPL13A (MFC < 2) had a greater stability when normalizing as a function of culture time compared with GAPDH (MFC </= 2.2), which resulted in expression patterns of the osteogenic markers more consistent with the observed differentiation process. The results suggest that beta-actin regulation could be associated with the morphological changes characteristic of hBMSCs osteogenic differentiation, and provide evidence for the superior performance of RPL13A as a normalizer gene in osteogenic differentiation studies of hBMSCs. This work highlights the importance of validating the normalizer genes used for stem cells characterization via RT-qPCR.
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Brkljacić J, Tanić N, Milutinović DV, Elaković I, Jovanović SM, Perisić T, Dundjerski J, Matić G. Validation of endogenous controls for gene expression studies in peripheral lymphocytes from war veterans with and without PTSD. BMC Mol Biol 2010; 11:26. [PMID: 20380724 PMCID: PMC2858027 DOI: 10.1186/1471-2199-11-26] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 04/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selection of appropriate endogenous control is a critical step in gene expression analysis. The aim of this study was to evaluate expression stability of four frequently used endogenous controls: beta-actin, glyceraldehyde-3-phosphate dehydrogenase, beta2-microglobulin and RNA polymerase II polypeptide A in peripheral blood mononuclear cells from war veterans with and without posttraumatic stress disorder (PTSD). The study was designed as to identify suitable reference gene(s) for normalization of gene expression in peripheral blood mononuclear cells in response to war trauma and/or PTSD. RESULTS The variability in expression of the four endogenous controls was assessed by TaqMan Real-time RT-PCR in peripheral blood mononuclear cells from: war veterans with current PTSD, those with lifetime PTSD, trauma controls and healthy subjects. Expression stability was analyzed by GeNorm and NormFinder software packages, and by direct comparison of Ct values. Both, GeNorm and NormFinder identified beta-actin and glyceraldehyde-3-phosphate dehydrogenase as a pair of genes with the lowest stability value. CONCLUSIONS The combination of beta-actin and glyceraldehyde-3-phosphate dehydrogenase appeared to be the most suitable reference for studying alterations in gene expression in peripheral blood mononuclear cells related to vulnerability and resilience to PTSD, as well as to trauma-provoked developing of this disorder and recovery from it. Using glyceraldehyde-3-phosphate dehydrogenase, beta-actin and beta2-microglobulin as individual endogenous controls would provide satisfactory data, while RNA polymerase II polypeptide A could not be recommended.
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Affiliation(s)
- Jelena Brkljacić
- Department of Biochemistry, Institute for Biological Research Sinisa Stanković, University of Belgrade, 142 Despot Stefan Blvd., Belgrade, 11000, Serbia
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Harris JL, Reeves TM, Phillips LL. Injury modality, survival interval, and sample region are critical determinants of qRT-PCR reference gene selection during long-term recovery from brain trauma. J Neurotrauma 2010; 26:1669-81. [PMID: 19505177 DOI: 10.1089/neu.2009.0875] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the present study we examined expression of four real-time quantitative RT-PCR reference genes commonly applied to rodent models of brain injury. Transcripts for beta-actin, cyclophilin A, GAPDH, and 18S rRNA were assessed at 2-15 days post-injury, focusing on the period of synaptic recovery. Diffuse moderate central fluid percussion injury (FPI) was contrasted with unilateral entorhinal cortex lesion (UEC), a model of targeted deafferentation. Expression in UEC hippocampus, as well as in FPI hippocampus and parietotemporal cortex was analyzed by qRT-PCR. Within-group variability of gene expression was assessed and change in expression relative to paired controls was determined. None of the four common reference genes tested was invariant across brain region, survival time, and type of injury. Cyclophilin A appeared appropriate as a reference gene in UEC hippocampus, while beta-actin was most stable for the hippocampus subjected to FPI. However, each gene may fail as a suitable reference with certain test genes whose RNA expression is targeted for measurement. In FPI cortex, all reference genes were significantly altered over time, compromising their utility for time-course studies. Despite such temporal variability, certain genes may be appropriate references if limited to single survival times. These data provide an extended baseline for identification of appropriate reference genes in rodent studies of recovery from brain injury. In this context, we outline additional considerations for selecting a qRT-PCR normalization strategy in such studies. As previously concluded for acute post-injury intervals, we stress the importance of reference gene validation for each brain injury paradigm and each set of experimental conditions.
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Affiliation(s)
- Janna L Harris
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University Medical Center, Richmond, Virginia 23298, USA
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Weickert CS, Sheedy D, Rothmond DA, Dedova I, Fung S, Garrick T, Wong J, Harding AJ, Sivagnanansundaram S, Hunt C, Duncan C, Sundqvist N, Tsai SY, Anand J, Draganic D, Harper C. Selection of Reference Gene Expression in a Schizophrenia Brain Cohort. Aust N Z J Psychiatry 2010; 44:59-70. [PMID: 20073568 PMCID: PMC2950262 DOI: 10.3109/00048670903393662] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE In order to conduct postmortem human brain research into the neuropatho-logical basis of schizophrenia, it is critical to establish cohorts that are well-characterized and well-matched. The aim of the present study was therefore to determine if specimen characteristics including: diagnosis, age, postmortem interval (PMI), brain acidity (pH), and/or the agonal state of the subject at death related to RNA quality, and to determine the most appropriate reference gene mRNAs. METHODS A matched cohort was selected of 74 subjects (schizophrenia/schizoaffective disorder, n = 37; controls, n = 37). Middle frontal gyrus tissue was pulverized, tissue pH was measured, RNA isolated for cDNA from each case, and RNA integrity number (RIN) measurements were assessed. Using quantitative reverse transcription-polymerase chain reaction, nine housekeeper genes were measured and a geomean calculated per case in each diagnostic group. RESULTS The RINs were very good (mean = 7.3) and all nine housekeeper control genes were significantly correlated with RIN. Seven of nine housekeeper genes were also correlated with pH; two clinical variables, agonal state and duration of illness, did have an effect on some control mRNAs. No major impact of PMI or freezer time on housekeeper mRNAs was detected. The results show that people with schizophrenia had significantly less PPIA and SDHA mRNA and tended to have less GUSB and B2M mRNA, suggesting that these control genes may not be good candidates for normalization. CONCLUSIONS In the present cohort <10% variability in RINs was detected and the diagnostic groups were well matched overall. The cohort was adequately powered (0.80-0.90) to detect mRNA differences (25%) due to disease. The study suggests that multiple factors should be considered in mRNA expression studies of human brain tissues. When schizophrenia cases are adequately matched to control cases subtle differences in gene expression can be reliably detected.
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Affiliation(s)
- Cynthia Shannon Weickert
- Schizophrenia Research Institute, Sydney, AU,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Donna Sheedy
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Debora A. Rothmond
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Irina Dedova
- Schizophrenia Research Institute, Sydney, AU,New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Samantha Fung
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, AU
| | - Therese Garrick
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Jenny Wong
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, AU
| | - Antony J. Harding
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Sinthuja Sivagnanansundaram
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Clare Hunt
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Carlotta Duncan
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Nina Sundqvist
- Schizophrenia Research Institute, Sydney, AU,New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Shan-Yuan Tsai
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Jasna Anand
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | | | - Clive Harper
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
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Lallemant B, Evrard A, Combescure C, Chapuis H, Chambon G, Raynal C, Reynaud C, Sabra O, Joubert D, Hollande F, Lallemant JG, Lumbroso S, Brouillet JP. Reference gene selection for head and neck squamous cell carcinoma gene expression studies. BMC Mol Biol 2009; 10:78. [PMID: 19650912 PMCID: PMC2729078 DOI: 10.1186/1471-2199-10-78] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 08/03/2009] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND It is no longer adequate to choose reference genes blindly. We present the first study that defines the suitability of 12 reference genes commonly used in cancer studies (ACT, ALAS, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPL27, RPS29, SHAD and TBP) for the normalization of quantitative expression data in the field of head and neck squamous cell carcinoma (HNSCC). RESULTS Raw expression levels were measured by RT-qPCR in HNSCC and normal matched mucosa of 46 patients. We analyzed the expression stability using geNorm and NormFinder and compared the expression levels between subgroups. In HNSCC and/or normal mucosa, the four best normalization genes were ALAS, GAPDH, RPS18 and SHAD and the most stable combination of two genes was GAPDH-SHAD. We recommend using KALPHA-TBP for the study of T1T2 tumors, RPL27-SHAD for T3T4 tumors, KALPHA-SHAD for N0 tumors, and ALAS-TBP for N+ tumors. ACT, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPS29, SHAD and TBP were slightly misregulated (<1.7-fold) between tumor and normal mucosa but can be used for normalization, depending on the resolution required for the assay. CONCLUSION In the field of HNSCC, this study will guide researchers in selecting the most appropriate reference genes from among 12 potentially suitable reference genes, depending on the specific setting of their experiments.
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Affiliation(s)
- Benjamin Lallemant
- Service d'ORL et Chirurgie Maxillo-faciale, Centre Hospitalier Universitaire de Nîmes, Place du Pr, Robert Debré, 30029 Nîmes Cedex 9, France.
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Silberberg G, Baruch K, Navon R. Detection of stable reference genes for real-time PCR analysis in schizophrenia and bipolar disorder. Anal Biochem 2009; 391:91-7. [DOI: 10.1016/j.ab.2009.05.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/14/2009] [Accepted: 05/14/2009] [Indexed: 10/20/2022]
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Chen J, Yamahachi H, Gilbert CD. Experience-dependent gene expression in adult visual cortex. Cereb Cortex 2009; 20:650-60. [PMID: 19571270 DOI: 10.1093/cercor/bhp131] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Experience-dependent plasticity of the adult visual cortex underlies perceptual learning and recovery of function following central nervous system lesions. To reveal the signal transduction cascades involved in adult cortical plasticity, we utilized a model of remapping of cortical topography following binocular retinal lesions. In this model, the lesion projection zone (LPZ) of primary visual cortex (V1) recovers visually driven activity by the sprouting of horizontal axonal connections originating from the cells in the surrounding region. To explore the molecular mechanism underlying this process, we used gene microarrays from an expression library prepared from Macaque V1. By microarray analysis of gene expression levels in the LPZ and the surrounding region, and subsequent confirmation with Quantitative Real-Time polymerase chain reaction and in situ hybridization, the participation of a number of genes was observed, including the Rho GTPase family. Its role in regulation of cytoskeleton assembly provides a possible link between the alteration of neural activity and cortical functional reorganization.
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Affiliation(s)
- Jiabin Chen
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Kuzmin A, Bazov I, Sheedy D, Garrick T, Harper C, Bakalkin G. Expression of pronociceptin and its receptor is downregulated in the brain of human alcoholics. Brain Res 2009; 1305 Suppl:S80-5. [PMID: 19501074 DOI: 10.1016/j.brainres.2009.05.067] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/18/2009] [Accepted: 05/28/2009] [Indexed: 11/28/2022]
Abstract
Animal studies demonstrated a role of neuropeptide nociceptin (NC) and its receptor (opiate receptor like-1, OPRL1) in ethanol-induced reward; activation of the OPRL1 by natural or synthetic ligands reduced ethanol self-administration and prevented relapse to ethanol drinking. The endogenous NC may function in neuronal circuits involved in reinforcing or conditioning effects of ethanol as a "brake" to limit ethanol intake (Roberto, M., Siggins, G.R. 2006. Nociceptin/orphanin FQ presynaptically decreases GABAergic transmission and blocks the ethanol-induced increase of GABA release in central amygdala. Proc. Natl. Acad. Sci. USA 103. 9715-9720), whereas repeated ethanol intake may downregulate the endogenous NC/OPRL1 system resulting in activation of ethanol consumption. To address this hypothesis, we evaluated whether expression of the pronociceptin (PNOC) and OPRL1 genes is altered in human alcoholics. mRNAs transcribed from these genes were analyzed by quantitative RT-PCR in the prefrontal and orbitofrontal cortices, central amygdala and hippocampal dentate gyrus, structures controlling alcohol consumption. Reduction in PNOC mRNA (1.7-fold) was found in the hippocampus of alcoholics, whereas OPRL1 mRNA levels were decreased (1.4-fold) in the central amygdala. No changes in expression of these genes in other brain areas analyzed were evident. We hypothesise that chronic ethanol intake downregulates PNOC and OPRL1 gene expression in the hippocampus and amygdala, respectively. The findings may be also interpreted as inherited molecular differences between alcoholics and controls. The PNOC/OPRL1 downregulation may underlie impairment of cognitive control over alcohol seeking in alcoholics. Stimulation of the OPRL1 receptors with synthetic agonists may increase threshold for activation of ethanol-related behaviour by environmental cues, and thus may reduce cue- or stress-primed relapse to ethanol consumption.
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Affiliation(s)
- Alexander Kuzmin
- The Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
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Barbeito AG, Garringer HJ, Baraibar MA, Gao X, Arredondo M, Núñez MT, Smith MA, Ghetti B, Vidal R. Abnormal iron metabolism and oxidative stress in mice expressing a mutant form of the ferritin light polypeptide gene. J Neurochem 2009; 109:1067-78. [PMID: 19519778 DOI: 10.1111/j.1471-4159.2009.06028.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Insertional mutations in exon 4 of the ferritin light chain (FTL) gene are associated with hereditary ferritinopathy (HF) or neuroferritinopathy, an autosomal dominant neurodegenerative disease characterized by progressive impairment of motor and cognitive functions. To determine the pathogenic mechanisms by which mutations in FTL lead to neurodegeneration, we investigated iron metabolism and markers of oxidative stress in the brain of transgenic (Tg) mice that express the mutant human FTL498-499InsTC cDNA. Compared with wild-type mice, brain extracts from Tg (FTL-Tg) mice showed an increase in the cytoplasmic levels of both FTL and ferritin heavy chain polypeptides, a decrease in the protein and mRNA levels of transferrin receptor-1, and a significant increase in iron levels. Transgenic mice also showed the presence of markers for lipid peroxidation, protein carbonyls, and nitrone-protein adducts in the brain. However, gene expression analysis of iron management proteins in the liver of Tg mice indicates that the FTL-Tg mouse liver is iron deficient. Our data suggest that disruption of iron metabolism in the brain has a primary role in the process of neurodegeneration in HF and that the pathogenesis of HF is likely to result from a combination of reduction in iron storage function and enhanced toxicity associated with iron-induced ferritin aggregates in the brain.
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Affiliation(s)
- Ana G Barbeito
- Department of Pathology and Laboratory Medicine, Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Johansson S, Ekström TJ, Marinova Z, Okvist A, Sheedy D, Garrick T, Harper C, Kuzmin A, Yakovleva T, Bakalkin G. Dysregulation of cell death machinery in the prefrontal cortex of human alcoholics. Int J Neuropsychopharmacol 2009; 12:109-15. [PMID: 18937880 PMCID: PMC3391550 DOI: 10.1017/s1461145708009589] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In human alcoholics, the cell density is decreased in the prefrontal cortex (PFC) and other brain areas. This may be due to persistent activation of cell death pathways. To address this hypothesis, we examined the status of cell death machinery in the dorsolateral PFC in alcoholics. Protein and mRNA expression levels of several key pro- and anti-apoptotic genes were compared in post-mortem samples of 14 male human alcoholics and 14 male controls. The findings do not support the hypothesis. On the contrary, they show that several components of intrinsic apoptotic pathway are decreased in alcoholics. No differences were evident in the motor cortex, which is less damaged in alcoholics and was analysed for comparison. Thus, cell death mechanisms may be dysregulated by inhibition of intrinsic apoptotic pathway in the PFC in human alcoholics. This inhibition may reflect molecular adaptations that counteract alcohol neurotoxicity in cells that survive after many years of alcohol exposure and withdrawal.
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Affiliation(s)
- Sofia Johansson
- Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
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Dedova I, Harding A, Sheedy D, Garrick T, Sundqvist N, Hunt C, Gillies J, Harper CG. The importance of brain banks for molecular neuropathological research: The New South Wales Tissue Resource Centre experience. Int J Mol Sci 2009; 10:366-384. [PMID: 19333451 PMCID: PMC2662458 DOI: 10.3390/ijms10010366] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 01/14/2009] [Accepted: 01/22/2009] [Indexed: 12/28/2022] Open
Abstract
New developments in molecular neuropathology have evoked increased demands for postmortem human brain tissue. The New South Wales Tissue Resource Centre (TRC) at The University of Sydney has grown from a small tissue collection into one of the leading international brain banking facilities, which operates with best practice and quality control protocols. The focus of this tissue collection is on schizophrenia and allied disorders, alcohol use disorders and controls. This review highlights changes in TRC operational procedures dictated by modern neuroscience, and provides examples of applications of modern molecular techniques to study the neuropathogenesis of many different brain disorders.
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Affiliation(s)
- Irina Dedova
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Antony Harding
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Donna Sheedy
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Therese Garrick
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Nina Sundqvist
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Clare Hunt
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Juliette Gillies
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Clive G Harper
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
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Boda E, Pini A, Hoxha E, Parolisi R, Tempia F. Selection of reference genes for quantitative real-time RT-PCR studies in mouse brain. J Mol Neurosci 2008; 37:238-53. [PMID: 18607772 DOI: 10.1007/s12031-008-9128-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
Abstract
Since a growing number of studies based on the real-time reverse transcriptase polymerase chain reaction (RT-PCR) continue to be published in order to highlight genes specifically involved in brain development, maturation, and function, the identification of reference genes suitable for this kind of experiments is now an urgent need in the neuroscience field. The aim of this work was to verify the suitability of some very common housekeeping genes (such as Gapdh, 18s, and B2m) and of some relatively new control genes (such as Pgk1, Tfrc, and Gusb) during mouse brain maturation. We tested the candidate reference genes in mouse whole brain, cerebellum, brain stem, hippocampus, medial septum, frontal neocortex, and olfactory bulb. Moreover, we reported the first complete study of Pgk1 expression throughout the development and the aging of mouse brain. Although no tested gene showed to be the optimal reference for all mouse brain regions, in general, the new housekeeping genes were highly stable in most of the analyzed regions. Above all, with few exceptions, Pgk1 showed to be a reliable control for the analyzed mouse brain regions during development, maturation, and aging.
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Affiliation(s)
- Enrica Boda
- Department of Neuroscience, University of Torino, Torino, Italy.
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Coulson DTR, Brockbank S, Quinn JG, Murphy S, Ravid R, Irvine GB, Johnston JA. Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue. BMC Mol Biol 2008; 9:46. [PMID: 18460208 PMCID: PMC2396658 DOI: 10.1186/1471-2199-9-46] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Accepted: 05/06/2008] [Indexed: 11/10/2022] Open
Abstract
Background Studies of gene expression in post mortem human brain can contribute to understanding of the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Quantitative real-time PCR (RT qPCR) is often used to analyse gene expression. The validity of results obtained using RT qPCR is reliant on accurate data normalization. Reference genes are generally used to normalize RT qPCR data. Given that expression of some commonly used reference genes is altered in certain conditions, this study aimed to establish which reference genes were stably expressed in post mortem brain tissue from individuals with AD, PD or DLB. Results The present study investigated the expression stability of 8 candidate reference genes, (ubiquitin C [UBC], tyrosine-3-monooxygenase [YWHAZ], RNA polymerase II polypeptide [RP II], hydroxymethylbilane synthase [HMBS], TATA box binding protein [TBP], β-2-microglobulin [B2M], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], and succinate dehydrogenase complex-subunit A, [SDHA]) in cerebellum and medial temporal gyrus of 6 AD, 6 PD, 6 DLB subjects, along with 5 matched controls using RT qPCR (TaqMan® Gene Expression Assays). Gene expression stability was analysed using geNorm to rank the candidate genes in order of decreasing stability in each disease group. The optimal number of genes recommended for accurate data normalization in each disease state was determined by pairwise variation analysis. Conclusion This study identified validated sets of mRNAs which would be appropriate for the normalization of RT qPCR data when studying gene expression in brain tissue of AD, PD, DLB and control subjects.
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Affiliation(s)
- David T R Coulson
- Division of Psychiatry and Neuroscience, School of Medicine and Dentistry, Queen's University Belfast, Whitla Medical Building, Belfast, BT9 7BL, Northern Ireland, UK.
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Hashimoto JG, Wiren KM. Neurotoxic consequences of chronic alcohol withdrawal: expression profiling reveals importance of gender over withdrawal severity. Neuropsychopharmacology 2008; 33:1084-96. [PMID: 17593928 PMCID: PMC3019135 DOI: 10.1038/sj.npp.1301494] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
While women are more vulnerable than men to many of the medical consequences of alcohol abuse, the role of sex in the response to ethanol is controversial. Neuroadaptive responses that result in the hyperexcitability associated with withdrawal from chronic ethanol likely reflect gene expression changes. We have examined both genders for the effects of withdrawal on brain gene expression using mice with divergent withdrawal severity that have been selectively bred from a genetically heterogeneous population. A total of 295 genes were identified as ethanol regulated from each gender of each selected line by microarray analyses. Hierarchical cluster analysis of the arrays revealed that the transcriptional response correlated with sex rather than with the selected withdrawal phenotype. Consistent with this, gene ontology category over-representation analysis identified cell death and DNA/RNA binding as targeted classes of genes in females, while in males, protein degradation, and calcium ion binding pathways were more altered by alcohol. Examination of ethanol-regulated genes and these distinct signaling pathways suggested enhanced neurotoxicity in females. Histopathological analysis of brain damage following ethanol withdrawal confirmed elevated cell death in female but not male mice. The sexually dimorphic response was observed irrespective of withdrawal phenotype. Combined, these results indicate a fundamentally distinct neuroadaptive response in females compared to males during chronic ethanol withdrawal and are consistent with observations that female alcoholics may be more vulnerable than males to ethanol-induced brain damage associated with alcohol abuse.
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Affiliation(s)
- Joel G Hashimoto
- Research Service, Veterans Affairs Medical Center, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Kristine M Wiren
- Research Service, Veterans Affairs Medical Center, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- Department of Medicine, Oregon Health and Science University, Portland, OR, USA
- Correspondence: Dr KM Wiren, OHSU, Portland VA Medical Center, Research Service, P3 R&D39, Portland, OR 97239, USA, Tel: 503 220 8262, ext. 56595, Fax: 503 273 5351,
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Lyng MB, Laenkholm AV, Pallisgaard N, Ditzel HJ. Identification of genes for normalization of real-time RT-PCR data in breast carcinomas. BMC Cancer 2008; 8:20. [PMID: 18211679 PMCID: PMC2248196 DOI: 10.1186/1471-2407-8-20] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 01/22/2008] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Quantitative real-time RT-PCR (RT-qPCR) has become a valuable molecular technique in basic and translational biomedical research, and is emerging as an equally valuable clinical tool. Correlation of inter-sample values requires data normalization, which can be accomplished by various means, the most common of which is normalization to internal, stably expressed, reference genes. Recently, such traditionally utilized reference genes as GAPDH and B2M have been found to be regulated in various circumstances in different tissues, emphasizing the need to identify genes independent of factors influencing the tissue, and that are stably expressed within the experimental milieu. In this study, we identified genes for normalization of RT-qPCR data for invasive breast cancer (IBC), with special emphasis on estrogen receptor positive (ER+) IBC, but also examined their applicability to ER- IBC, normal breast tissue and breast cancer cell lines. METHODS The reference genes investigated by qRT-PCR were RPLP0, TBP, PUM1, ACTB, GUS-B, ABL1, GAPDH and B2M. Biopsies of 18 surgically-excised tissue specimens (11 ER+ IBCs, 4 ER- IBCs, 3 normal breast tissues) and 3 ER+ cell lines were examined and the data analyzed by descriptive statistics, geNorm and NormFinder. In addition, the expression of selected reference genes in laser capture microdissected ER+ IBC cells were compared with that of whole-tissue. RESULTS A group of 3 genes, TBP, RPLP0 and PUM1, were identified for both the combined group of human tissue samples (ER+ and ER- IBC and normal breast tissue) and for the invasive cancer samples (ER+ and ER- IBC) by GeNorm, where NormFinder consistently identified PUM1 at the single best gene for all sample combinations. CONCLUSION The reference genes of choice when performing RT-qPCR on normal and malignant breast specimens should be either the collected group of 3 genes (TBP, RPLP0 and PUM1) employed as an average, or PUM1 as a single gene.
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Affiliation(s)
- Maria B Lyng
- Department of Pathology, Odense University Hospital, Odense, Denmark.
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Ökvist A, Johansson S, Kuzmin A, Bazov I, Merino-Martinez R, Ponomarev I, Mayfield RD, Harris RA, Sheedy D, Garrick T, Harper C, Hurd YL, Terenius L, Ekström TJ, Bakalkin G, Yakovleva T. Neuroadaptations in human chronic alcoholics: dysregulation of the NF-kappaB system. PLoS One 2007; 2:e930. [PMID: 17895971 PMCID: PMC1976556 DOI: 10.1371/journal.pone.0000930] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 09/03/2007] [Indexed: 12/27/2022] Open
Abstract
Background Alcohol dependence and associated cognitive impairments apparently result from neuroadaptations to chronic alcohol consumption involving changes in expression of multiple genes. Here we investigated whether transcription factors of Nuclear Factor-kappaB (NF-κB) family, controlling neuronal plasticity and neurodegeneration, are involved in these adaptations in human chronic alcoholics. Methods and Findings Analysis of DNA-binding of NF-κB (p65/p50 heterodimer) and the p50 homodimer as well as NF-κB proteins and mRNAs was performed in postmortem human brain samples from 15 chronic alcoholics and 15 control subjects. The prefrontal cortex involved in alcohol dependence and cognition was analyzed and the motor cortex was studied for comparison. The p50 homodimer was identified as dominant κB binding factor in analyzed tissues. NF-κB and p50 homodimer DNA-binding was downregulated, levels of p65 (RELA) mRNA were attenuated, and the stoichiometry of p65/p50 proteins and respective mRNAs was altered in the prefrontal cortex of alcoholics. Comparison of a number of p50 homodimer/NF-κB target DNA sites, κB elements in 479 genes, down- or upregulated in alcoholics demonstrated that genes with κB elements were generally upregulated in alcoholics. No significant differences between alcoholics and controls were observed in the motor cortex. Conclusions We suggest that cycles of alcohol intoxication/withdrawal, which may initially activate NF-κB, when repeated over years downregulate RELA expression and NF-κB and p50 homodimer DNA-binding. Downregulation of the dominant p50 homodimer, a potent inhibitor of gene transcription apparently resulted in derepression of κB regulated genes. Alterations in expression of p50 homodimer/NF-κB regulated genes may contribute to neuroplastic adaptation underlying alcoholism.
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Affiliation(s)
- Anna Ökvist
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Sofia Johansson
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Alexander Kuzmin
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Igor Bazov
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | | | - Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
| | - R. Adron Harris
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
| | - Donna Sheedy
- Discipline of Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Therese Garrick
- Discipline of Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Clive Harper
- Discipline of Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Yasmin L. Hurd
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, United States of America
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Lars Terenius
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Tomas J. Ekström
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Georgy Bakalkin
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
- Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence, Uppsala University, Uppsala, Sweden
- * To whom correspondence should be addressed. E-mail:
| | - Tatjana Yakovleva
- The Section of Alcohol and Drug Dependence Research, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
- Department of Pharmaceutical Biosciences, Division of Biological Research on Drug Dependence, Uppsala University, Uppsala, Sweden
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