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Lerner R, Post JM, Ellis SR, Vos DRN, Heeren RMA, Lutz B, Bindila L. Simultaneous lipidomic and transcriptomic profiling in mouse brain punches of acute epileptic seizure model compared to controls. J Lipid Res 2017; 59:283-297. [PMID: 29208697 DOI: 10.1194/jlr.m080093] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/28/2017] [Indexed: 01/07/2023] Open
Abstract
In this study, we report the development of a dual extraction protocol for RNA and lipids, including phospholipids, endocannabinoids, and arachidonic acid, at high spatial resolution, e.g., brain punches obtained from whole frozen brains corresponding to four brain subregions: dorsal hippocampus, ventral hippocampus, basolateral amygdala, and hypothalamus. This extraction method combined with LC/multiple reaction monitoring for lipid quantifi-cation and quantitative PCR for RNA investigation allows lipidomic and transcriptomic profiling from submilligram amounts of tissue, thus benefiting the time and animal costs for analysis and the data reliability due to prevention of biological variability between animal batches and/or tissue heterogeneity, as compared with profiling in distinct animal batches. Moreover, the method allows a higher extraction efficiency and integrity preservation for RNA, while allowing concurrently quantitative analysis of low and high abundant lipids. The method was applied for brain punches obtained 1 h after kainic acid-induced epileptic seizures in mice (n = 10) compared with controls (n = 10), and enabled the provision of valuable new insights into the subregional lipid and RNA changes with epilepsy, highlighting its potential as a new viable tool in quantitative neurobiology.
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Affiliation(s)
- Raissa Lerner
- University Medical Center of Johannes Gutenberg University Mainz, Institute of Physiological Chemistry, 55128 Mainz, Germany; and
| | - Julia M Post
- University Medical Center of Johannes Gutenberg University Mainz, Institute of Physiological Chemistry, 55128 Mainz, Germany; and
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - D R Naomi Vos
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Beat Lutz
- University Medical Center of Johannes Gutenberg University Mainz, Institute of Physiological Chemistry, 55128 Mainz, Germany; and
| | - Laura Bindila
- University Medical Center of Johannes Gutenberg University Mainz, Institute of Physiological Chemistry, 55128 Mainz, Germany; and
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2
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Partridge LMM, Carter DA. Novel Rbfox2 isoforms associated with alternative exon usage in rat cortex and suprachiasmatic nucleus. Sci Rep 2017; 7:9929. [PMID: 28855650 PMCID: PMC5577181 DOI: 10.1038/s41598-017-10535-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/09/2017] [Indexed: 12/20/2022] Open
Abstract
Transcriptome diversity in adult neurons is partly mediated by RNA binding proteins (RBPs), including the RBFOX factors. RBFOX3/NeuN, a neuronal maturity marker, is strangely depleted in suprachiasmatic nucleus (SCN) neurons, and may be compensated by a change in Rbfox2 expression. In this study, we found no superficial changes in Rbfox2 expression in the SCN, but mRNA population analysis revealed a distinct SCN transcript profile that includes multiple novel Rbfox2 isoforms. Of eleven isoforms in SCN and cerebral cortex that exhibit exon variation across two protein domains, we found a 3-fold higher abundance of a novel (‘−12–40’) C-terminal domain (CTD)-variant in the SCN. This isoform embraces an alternative reading frame that imparts a 50% change in CTD protein sequence, and functional impairment of exon 7 exclusion activity in a RBFOX2-target, the L-type calcium channel gene, Cacna1c. We have also demonstrated functional correlates in SCN gene transcripts; inclusion of Cacna1c exon 7, and also exclusion of both NMDA receptor gene Grin1 exon 4, and Enah exon 12, all consistent with a change in SCN RBFOX activity. The demonstrated regional diversity of Rbfox2 in adult brain highlights the functional adaptability of this RBP, enabling neuronal specialization, and potentially responding to disease-related neuronal dysfunction.
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Affiliation(s)
| | - D A Carter
- School of Biosciences, Cardiff University, Cardiff, UK.
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3
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Modelling the Effect of Genes on the Dynamics of Probabilistic Spiking Neural Networks for Computational Neurogenetic Modelling. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/978-3-642-35686-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Benuskova L, Jain V, Wysoski SG, Kasabov NK. COMPUTATIONAL NEUROGENETIC MODELLING: A PATHWAY TO NEW DISCOVERIES IN GENETIC NEUROSCIENCE. Int J Neural Syst 2011; 16:215-26. [PMID: 17044242 DOI: 10.1142/s0129065706000627] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The paper presents a methodology for using computational neurogenetic modelling (CNGM) to bring new original insights into how genes influence the dynamics of brain neural networks. CNGM is a novel computational approach to brain neural network modelling that integrates dynamic gene networks with artificial neural network model (ANN). Interaction of genes in neurons affects the dynamics of the whole ANN model through neuronal parameters, which are no longer constant but change as a function of gene expression. Through optimization of interactions within the internal gene regulatory network (GRN), initial gene/protein expression values and ANN parameters, particular target states of the neural network behaviour can be achieved, and statistics about gene interactions can be extracted. In such a way, we have obtained an abstract GRN that contains predictions about particular gene interactions in neurons for subunit genes of AMPA, GABAA and NMDA neuro-receptors. The extent of sequence conservation for 20 subunit proteins of all these receptors was analysed using standard bioinformatics multiple alignment procedures. We have observed abundance of conserved residues but the most interesting observation has been the consistent conservation of phenylalanine (F at position 269) and leucine (L at position 353) in all 20 proteins with no mutations. We hypothesise that these regions can be the basis for mutual interactions. Existing knowledge on evolutionary linkage of their protein families and analysis at molecular level indicate that the expression of these individual subunits should be coordinated, which provides the biological justification for our optimized GRN.
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Affiliation(s)
- Lubica Benuskova
- Knowledge Engineering & Discovery Research Institute, Auckland University of Technology, Ronald Trotter Building, 581-585 Great South Road, Penrose, Auckland, New Zealand.
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Liu L, Li Q, Sapolsky R, Liao M, Mehta K, Bhargava A, Pasricha PJ. Transient gastric irritation in the neonatal rats leads to changes in hypothalamic CRF expression, depression- and anxiety-like behavior as adults. PLoS One 2011; 6:e19498. [PMID: 21589865 PMCID: PMC3093391 DOI: 10.1371/journal.pone.0019498] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/05/2011] [Indexed: 12/27/2022] Open
Abstract
AIMS A disturbance of the brain-gut axis is a prominent feature in functional bowel disorders (such as irritable bowel syndrome and functional dyspepsia) and psychological abnormalities are often implicated in their pathogenesis. We hypothesized that psychological morbidity in these conditions may result from gastrointestinal problems, rather than causing them. METHODS Functional dyspepsia was induced by neonatal gastric irritation in male rats. 10-day old male Sprague-Dawley rats received 0.1% iodoacetamide (IA) or vehicle by oral gavage for 6 days. At 8-10 weeks of age, rats were tested with sucrose preference and forced-swimming tests to examine depression-like behavior. Elevated plus maze, open field and light-dark box tests were used to test anxiety-like behaviors. ACTH and corticosterone responses to a minor stressor, saline injection, and hypothalamic CRF expression were also measured. RESULTS Behavioral tests revealed changes of anxiety- and depression-like behaviors in IA-treated, but not control rats. As compared with controls, hypothalamic and amygdaloid CRF immunoreactivity, basal levels of plasma corticosterone and stress-induced ACTH were significantly higher in IA-treated rats. Gastric sensory ablation with resiniferatoxin had no effect on behaviors but treatment with CRF type 1 receptor antagonist, antalarmin, reversed the depression-like behavior in IA-treated rats CONCLUSIONS The present results suggest that transient gastric irritation in the neonatal period can induce a long lasting increase in depression- and anxiety-like behaviors, increased expression of CRF in the hypothalamus, and an increased sensitivity of HPA axis to stress. The depression-like behavior may be mediated by the CRF1 receptor. These findings have significant implications for the pathogenesis of psychological co-morbidity in patients with functional bowel disorders.
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Affiliation(s)
- Liansheng Liu
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Stanford, California, United States of America
| | - Qian Li
- Department of Pharmacology and Toxicology, University of Kansas, Kansas City, Kansas, United States of America
| | - Robert Sapolsky
- Department of Biology, School of Humanities and Sciences, Stanford University, Stanford, California, United States of America
| | - Min Liao
- Department of Surgery, University of California San Francisco, San Francisco, United States of America
| | - Kshama Mehta
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Stanford, California, United States of America
| | - Aditi Bhargava
- Department of Surgery, University of California San Francisco, San Francisco, United States of America
| | - Pankaj J. Pasricha
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Stanford, California, United States of America
- * E-mail:
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Poirier G, Shires K, Sugden D, Amin E, Thomas K, Carter D, Aggleton J. Anterior thalamic lesions produce chronic and profuse transcriptional de-regulation in retrosplenial cortex: A model of retrosplenial hypoactivity and covert pathology. THALAMUS & RELATED SYSTEMS 2008; 4:59-77. [PMID: 21289865 PMCID: PMC3031093 DOI: 10.1017/s1472928808000368] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Anterior thalamic lesions are thought to produce 'covert pathology' in retrosplenial cortex, but the causes are unknown. Microarray analyses tested the hypothesis that thalamic damage causes a chronic, hypo-function of metabolic and plasticity-related pathways (Experiment 1). Rats with unilateral, anterior thalamic lesions were exposed to a novel environment for 20 minutes, and granular retrosplenial tissue sampled from both hemispheres 30 minutes, 2h, or 8h later. Complementary statistical approaches (analyses of variance, predictive patterning and gene set enrichment analysis) revealed pervasive gene expression differences between retrosplenial cortex ipsilateral to the thalamic lesion and contralateral to the lesion. Selected gene differences were validated by QPCR, immunohistochemistry (Experiment 1), and in situ hybridisation (Experiment 2). Following thalamic lesions, the retrosplenial cortex undergoes profuse cellular transcriptome changes including lower relative levels of specific mRNAs involved in energy metabolism and neuronal plasticity. These changes in functional gene expression may be largely driven by decreases in the expression of multiple transcription factors, including brd8, c-fos, fra-2, klf5, nfix, nr4a1, smad3, smarcc2, and zfp9, with a much smaller number (nfat5, neuroD1, RXRγ) showing increases. These findings have implications for conditions such as diencephalic amnesia and Alzheimer's disease, where both anterior thalamic pathology and retrosplenial cortex hypometabolism are prominent.
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Affiliation(s)
- G.L. Poirier
- School of Psychology, Cardiff University, Wales, UK
| | - K.L. Shires
- School of Psychology, Cardiff University, Wales, UK
- School of Biosciences, Cardiff University, Wales, UK
| | - D. Sugden
- Division of Reproduction and Endocrinology, School of Biomedical and Health Sciences, King’s College, London, UK
| | - E. Amin
- School of Psychology, Cardiff University, Wales, UK
| | - K.L. Thomas
- School of Biosciences, Cardiff University, Wales, UK
| | - D.A. Carter
- School of Biosciences, Cardiff University, Wales, UK
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Carter D. Cellular transcriptomics -- the next phase of endocrine expression profiling. Trends Endocrinol Metab 2006; 17:192-8. [PMID: 16730453 DOI: 10.1016/j.tem.2006.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2006] [Revised: 04/24/2006] [Accepted: 05/12/2006] [Indexed: 12/15/2022]
Abstract
Transcriptome analysis, or global gene expression profiling, has become a commonly used and valuable tool in both basic and clinical endocrine research. Novel endocrine regulators have 'surfaced' and greater consideration is now given to understanding function at the level of gene networks. Recent developments have shown that the transcriptome is considerably larger and more divergently expressed than was previously thought. Endocrine cells express a great variety of coding and noncoding RNAs in a highly cell-specific manner. If further value is to be taken from this research area, then steps towards defined cellular transcriptomics must be taken. New sampling techniques that utilize novel genetic models are a key first step.
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Affiliation(s)
- David Carter
- School of Biosciences, Cardiff University, Cardiff, CF10 3US, UK.
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Aleström P, Holter JL, Nourizadeh-Lillabadi R. Zebrafish in functional genomics and aquatic biomedicine. Trends Biotechnol 2006; 24:15-21. [PMID: 16309768 DOI: 10.1016/j.tibtech.2005.11.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/01/2005] [Accepted: 11/10/2005] [Indexed: 12/29/2022]
Abstract
The zebrafish (Danio rerio) has many features that make it an ideal model for the study of developmental biology. It is small and easy to contain, it has transparent embryos, it is easy to breed and its early development is well characterized; these same characteristics have also made it an ideal vertebrate model in the areas of biomedicine and biotechnology. In aquaculture, the need for a well-characterized fish model has been satisfied by the zebrafish owing to the availability of functional genomics and molecular biology data to facilitate studies of growth, reproduction, meat quality and disease biology, with the corresponding development of vaccines and therapies. Zebrafish are also increasingly used in toxicogenomics to analyze the effects of toxins and pollutants in the environment, and for creating biomonitors that emit alarm signals when a toxic compound is detected. As detailed in this review, the zebrafish is a versatile and well-characterized model with applications in many fields of study.
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Affiliation(s)
- Peter Aleström
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, PO Box 8146 Dep, N-0033 Oslo, Norway.
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Holter J, Carter D, Leresche N, Crunelli V, Vincent P. A TASK3 channel (KCNK9) mutation in a genetic model of absence epilepsy. J Mol Neurosci 2005; 25:37-51. [PMID: 15781965 DOI: 10.1385/jmn:25:1:037] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 04/24/2004] [Indexed: 12/28/2022]
Abstract
Childhood absence epilepsy is an idiopathic, generalized, nonconvulsive epilepsy with a multifactorial genetic etiology. The KCNK9 gene coding for the TASK3 (Twik-like acid-sensitive K</U)+) channel is present on chromosome 8 at position 8q24, a locus that has shown positive linkage to the human absence epilepsy phenotype. Sequencing of the KCNK9 gene in the genetic absence epilepsy rats from Strasbourg (GAERS), a well established genetic model of this disease, reveals an additional alanine residue in a polyalanine tract within the C-terminal intracellular domain. This additional alanine is absent in the inbred nonepileptic control (NEC) strain, Wistar, and Wistar albino Glaxo strain bred in Rijswijk, another inbred rat model of absence epilepsy. Expression of the mutant channel in CHO cells produces a K+ current that is blocked by acidic pH and millimolar concentrations of barium or ruthenium red and is not different from the wild-type channel. In brain slices, thalamic neurons display a prominent pH-sensitive tonic K+ current, but no difference was observed between GAERS and NEC or Wistar rats. Ruthenium red had no effect in cortical, reticular thalamic, or sensory thalamic neurons in either GAERS or NEC, indicating that the TASK3 homodimer is not present in these structures. Twik-like acid-sensitive K+(TASK3) channels, therefore, are probably associated with TASK1 to form ruthenium red-insensitive heterodimers in these neurons. Finally, no difference was found between GAERS and NEC rats in the modulation of the leak K+ current following activation of muscarinic receptors. These studies describe the first mutation found in a genetic model of absence epilepsy. Although our experiments showed no difference in the leak K+ current between GAERS and NEC rats, further work is needed to ascertain whether this mutation contributes to the generation of absence seizures, possibly by mechanisms related to the expansion of the polyalanine run.
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Affiliation(s)
- Jethro Holter
- School of Bioscience, Cardiff University, Cardiff, CF10 3US, UK
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Holter J, Davies J, Leresche N, Crunelli V, Carter DA. Identification of two further splice variants of GABABR1 characterizes the conserved micro-exon 4 as a hot spot for regulated splicing in the rat brain. J Mol Neurosci 2005; 26:99-108. [PMID: 15968089 DOI: 10.1385/jmn:26:1:099] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 11/23/2004] [Indexed: 11/11/2022]
Abstract
Inhibitory neurotransmission in the mammalian brain is principally mediated by gamma-aminobutyric acid (GABA) acting through different subtypes of cell membrane GABA receptor (GABAR). The expression of one GABAR gene, GABABR1, is distinguished by the expression of multiple splice variants that encode different isoforms of the receptor. In the present study, we have identified two novel GABABR1 variants, GABABR1h (R1h) and GABABR1i (R1i), which appear to arise from alternative splicing of the GABABR1 gene. The expression of R1h and R1i is differentially regulated in brain and peripheral tissues, but expression is not altered in the brain of a genetic model of absence epilepsy (GAERS rat [genetic absence epilepsy rat from Strasbourg]). Both the R1h and R1i variants exhibit a novel 80-bp insert downstream of exon 4 that is flanked by consensus splice sites, and both encode C-terminal-truncated proteins. The new insight into the family of GABABR1 variants gained from this study identifies exon 4 as a preferred locus, or hot spot for regulated splicing in the GABABR1 gene. This finding correlates with the micro-exonic nature of exon 4 (21 bp). Bioinformatic analysis of micro-exon 4 and its flanking pre-mRNA sequences has revealed multiple, potentially competitive, exonic splicing enhancers that provide a mechanistic basis for the preponderance of alternative splicing events at this locus. Conservation of GABABR1 micro-exon 4 across species suggests a conserved functional role, facilitating either N-terminal protein production or post-transcriptional gene regulation through regulated splicing coupled to transcript decay.
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Affiliation(s)
- Jethro Holter
- School of Biosciences, Cardiff University, Cardiff, UK
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Hofmann HA. Functional genomics of neural and behavioral plasticity. JOURNAL OF NEUROBIOLOGY 2003; 54:272-82. [PMID: 12486709 DOI: 10.1002/neu.10172] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
How does the environment, particularly the social environment, influence brain and behavior and what are the underlying physiologic, molecular, and genetic mechanisms? Adaptations of brain and behavior to changes in the social or physical environment are common in the animal world, either as short-term (i.e., modulatory) or as long-term modifications (e.g., via gene expression changes) in behavioral or physiologic properties. The study of the mechanisms and constraints underlying these dynamic changes requires model systems that offer plastic phenotypes as well as a sufficient level of quantifiable behavioral complexity while being accessible at the physiological and molecular level. In this article, I explore how the new field of functional genomics can contribute to an understanding of the complex relationship between genome and environment that results in highly plastic phenotypes. This approach will lead to the discovery of genes under environmental control and provide the basis for the study of the interrelationship between an individual's gene expression profile and its social phenotype in a given environmental context.
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Affiliation(s)
- Hans A Hofmann
- Harvard University, Bauer Center for Genomics Research, 7 Divinity Ave, Cambridge, Massachusetts 02138, USA.
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Crunelli V, Leresche N. Childhood absence epilepsy: genes, channels, neurons and networks. Nat Rev Neurosci 2002; 3:371-82. [PMID: 11988776 DOI: 10.1038/nrn811] [Citation(s) in RCA: 430] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Childhood absence epilepsy is an idiopathic, generalized non-convulsive epilepsy with a multifactorial genetic aetiology. Molecular-genetic analyses of affected human families and experimental models, together with neurobiological investigations, have led to important breakthroughs in the identification of candidate genes and loci, and potential pathophysiological mechanisms for this type of epilepsy. Here, we review these results, and compare the human and experimental phenotypes that have been investigated. Continuing efforts and comparisons of this type will help us to elucidate the multigenetic traits and pathophysiology of this form of generalized epilepsy.
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Affiliation(s)
- Vincenzo Crunelli
- School of Bioscience, Cardiff University, Museum Avenue, Cardiff CF10 3US, Wales, UK.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448432 DOI: 10.1002/cfg.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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