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Smith ML, Sergi Z, Mignogna KM, Rodriguez NE, Tatom Z, MacLeod L, Choi KB, Philip V, Miles MF. Identification of Genetic and Genomic Influences on Progressive Ethanol Consumption in Diversity Outbred Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.554349. [PMID: 37745421 PMCID: PMC10515943 DOI: 10.1101/2023.09.15.554349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Genetic factors play a significant role in the risk for development of alcohol use disorder (AUD). Using 3-bottle choice intermittent access ethanol (IEA), we have employed the Diversity Outbred (DO) mouse panel as a model of alcohol use disorder in a genetically diverse population. Through use of gene expression network analysis techniques, in combination with expression quantitative trait loci (eQTL) mapping, we have completed an extensive analysis of the influence of genetic background on gene expression changes in the prefrontal cortex (PFC). This approach revealed that, in DO mice, genes whose expression was significantly disrupted by intermittent ethanol in the PFC also tended to be those whose expression correlated to intake. This finding is in contrast to previous studies of both mice and nonhuman primates. Importantly, these analyses identified genes involved in myelination in the PFC as significantly disrupted by IEA, correlated to ethanol intake, and having significant eQTLs. Genes that code for canonical components of the myelin sheath, such as Mbp, also emerged as key drivers of the gene expression response to intermittent ethanol drinking. Several regulators of myelination were also key drivers of gene expression, and had significant QTLs, indicating that genetic background may play an important role in regulation of brain myelination. These findings underscore the importance of disruption of normal myelination in the PFC in response to prolonged ethanol exposure, that genetic variation plays an important role in this response, and that this interaction between genetics and myelin disruption in the presence of ethanol may underlie previously observed behavioral changes under intermittent access ethanol drinking such as escalation of consumption.
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Affiliation(s)
- M L Smith
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Z Sergi
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - K M Mignogna
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - N E Rodriguez
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Z Tatom
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - L MacLeod
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - K B Choi
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - V Philip
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - M F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
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2
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Bogenpohl JW, Weston RM, Foreman TN, Kitchen KE, Miles MF. Chloride intracellular channel 4 (CLIC4) expression profile in the mouse medial prefrontal cortex and its regulation by ethanol. Alcohol Clin Exp Res 2022; 46:29-39. [PMID: 34839533 PMCID: PMC8799520 DOI: 10.1111/acer.14754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Chloride intracellular channel 4 (CLIC4) is a multifunctional metamorphic protein for which a growing body of evidence supports a major role in the brain's molecular and behavioral responses to ethanol (EtOH). Although key to understanding the functional biology underlying this role, little is known about the cellular and subcellular expression patterns of CLIC4 in brain and how they are affected by EtOH. METHODS We used qRT-PCR to assess Clic4 mRNA expression in the medial prefrontal cortex (mPFC) of C57BL/6J mice in the absence and presence of acute EtOH exposure. Two complementary immunohistochemical techniques were employed to assess the subcellular localization of the CLIC4 protein and its pattern of expression across brain cell types in the mPFC in the absence and presence of acute EtOH. RESULTS Through immunohistochemical and stereological techniques, we show that CLIC4 protein is robustly expressed by oligodendrocytes (most abundant), microglia, and astrocytes, with minimal expression in neurons. Following acute EtOH exposure, we observed a rapid increase in Clic4 mRNA expression in female but not male mice and an overall increase in the number of oligodendrocytes and astrocytes expressing the CLIC4 protein. CONCLUSIONS These findings suggest that Clic4 functions as an early response gene for acute EtOH in brain, which likely underlies its ability to modulate EtOH behavior. Our results also suggest that the role of CLIC4 in the brain's response to EtOH is mediated through oligodendrocytes.
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Affiliation(s)
- James W. Bogenpohl
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA,Corresponding author: Correspondence:
James Bogenpohl PhD; Christopher Newport University; Department of Molecular
Biology and Chemistry; 1 Avenue of the Arts, Newport News, VA 23606;
757-594-8289;
| | - Rory M. Weston
- Department of Pharmacology and Toxicology, Virginia
Commonwealth University, Richmond, VA, USA
| | - Taylor N. Foreman
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA
| | - Kaitlyn E. Kitchen
- Department of Molecular Biology and Chemistry, Christopher
Newport University, Newport News, VA, USA
| | - Michael F. Miles
- Department of Pharmacology and Toxicology, Virginia
Commonwealth University, Richmond, VA, USA,VCU Alcohol Research Center, Virginia Commonwealth
University, Richmond, VA, USA
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3
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Weston RM, Schmitt RE, Grotewiel M, Miles MF. Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation. PLoS One 2021; 16:e0246224. [PMID: 34228751 PMCID: PMC8259981 DOI: 10.1371/journal.pone.0246224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/18/2021] [Indexed: 01/22/2023] Open
Abstract
Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 7% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under normoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.
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Affiliation(s)
- Rory M. Weston
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rebecca E. Schmitt
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Mike Grotewiel
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F. Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
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4
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Harris GM, Abbas S, Miles MF. GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays. BMC Genomics 2021; 22:96. [PMID: 33522903 PMCID: PMC7848880 DOI: 10.1186/s12864-021-07370-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Background Despite the increasing use of RNAseq for transcriptome analysis, microarrays remain a widely-used methodology for genomic studies. The latest generation of Affymetrix/Thermo-Fisher microarrays, the ClariomD/XTA and ClariomS array, provide a sensitive and facile method for complex transcriptome expression analysis. However, existing methods of analysis for these high-density arrays do not leverage the statistical power contained in having multiple oligonucleotides representing each gene/exon, but rather summarize probes into a single expression value. We previously developed a methodology, the Sscore algorithm, for probe-level identification of differentially expressed genes (DEGs) between treatment and control samples with oligonucleotide microarrays. The Sscore algorithm was validated for sensitive detection of DEGs by comparison with existing methods. However, the prior version of the Sscore algorithm and a R-based implementation software, sscore, do not function with the latest generations of Affymetrix/Fisher microarrays due to changes in microarray design that eliminated probes previously used for estimation of non-specific binding. Results Here we describe the GCSscore algorithm, which utilizes the GC-content of a given oligonucleotide probe to estimate non-specific binding using antigenomic background probes found on new generations of arrays. We implemented this algorithm in an improved GCSscore R package for analysis of modern oligonucleotide microarrays. GCSscore has multiple methods for grouping individual probes on the ClariomD/XTA chips, providing the user with differential expression analysis at the gene-level and the exon-level. By utilizing the direct probe-level intensities, the GCSscore algorithm was able to detect DEGs under stringent statistical criteria for all Clariom-based arrays. We demonstrate that for older 3′-IVT arrays, GCSscore produced very similar differential gene expression analysis results compared to the original Sscore method. However, GCSscore functioned well for both the ClariomS and ClariomD/XTA newer microarrays and outperformed existing analysis approaches insofar as the number of DEGs and cognate biological functions identified. This was particularly striking for analysis of the highly complex ClariomD/XTA based arrays. Conclusions The GCSscore package represents a powerful new application for analysis of the newest generation of oligonucleotide microarrays such as the ClariomS and ClariomD/XTA arrays produced by Affymetrix/Fisher. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07370-2.
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Affiliation(s)
- Guy M Harris
- VCU Pharmacology and Toxicology, Richmond, Virginia, 23298, USA
| | - Shahroze Abbas
- VCU Center for the Study of Biological Complexity, Richmond, Virginia, 23298, USA
| | - Michael F Miles
- VCU Pharmacology and Toxicology, Richmond, Virginia, 23298, USA. .,VCU Center for the Study of Biological Complexity, Richmond, Virginia, 23298, USA. .,Department of Pharmacology & Toxicology and Neurology, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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5
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Smith ML, Lopez MF, Wolen AR, Becker HC, Miles MF. Brain regional gene expression network analysis identifies unique interactions between chronic ethanol exposure and consumption. PLoS One 2020; 15:e0233319. [PMID: 32469986 PMCID: PMC7259766 DOI: 10.1371/journal.pone.0233319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/01/2020] [Indexed: 11/28/2022] Open
Abstract
Progressive increases in ethanol consumption is a hallmark of alcohol use disorder (AUD). Persistent changes in brain gene expression are hypothesized to underlie the altered neural signaling producing abusive consumption in AUD. To identify brain regional gene expression networks contributing to progressive ethanol consumption, we performed microarray and scale-free network analysis of expression responses in a C57BL/6J mouse model utilizing chronic intermittent ethanol by vapor chamber (CIE) in combination with limited access oral ethanol consumption. This model has previously been shown to produce long-lasting increased ethanol consumption, particularly when combining oral ethanol access with repeated cycles of intermittent vapor exposure. The interaction of CIE and oral consumption was studied by expression profiling and network analysis in medial prefrontal cortex, nucleus accumbens, hippocampus, bed nucleus of the stria terminalis, and central nucleus of the amygdala. Brain region expression networks were analyzed for ethanol-responsive gene expression, correlation with ethanol consumption and functional content using extensive bioinformatics studies. In all brain-regions studied the largest number of changes in gene expression were seen when comparing ethanol naïve mice to those exposed to CIE and drinking. In the prefrontal cortex, however, unique patterns of gene expression were seen compared to other brain-regions. Network analysis identified modules of co-expressed genes in all brain regions. The prefrontal cortex and nucleus accumbens showed the greatest number of modules with significant correlation to drinking behavior. Across brain-regions, however, many modules with strong correlations to drinking, both baseline intake and amount consumed after CIE, showed functional enrichment for synaptic transmission and synaptic plasticity.
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Affiliation(s)
- Maren L. Smith
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Marcelo F. Lopez
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Aaron R. Wolen
- Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Howard C. Becker
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Department of Neuroscience, Medical University of South Carolina, Charleston, South Carolina, United States of America
- RHJ Department of Veterans Affairs Medical Center, Charleston, South Carolina, United States of America
| | - Michael F. Miles
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
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6
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Nam HW, Grant CA, Jorgensen AN, Holtz-Heppelmann CJ, Trutschl M, Cvek U. Neurogranin Regulates Alcohol Sensitivity through AKT Pathway in the Nucleus Accumbens. Proteomics 2019; 20:e1900266. [PMID: 31814311 DOI: 10.1002/pmic.201900266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/19/2019] [Indexed: 01/03/2023]
Abstract
Dysfunction of glutamate neurotransmission in the nucleus accumbens (NAc) has been implicated in the pathophysiology of alcohol use disorders (AUD). Neurogranin (Ng) is exclusively expressed in the brain and mediates N-methyl-d-aspartate receptor (NMDAR) hypo-function by regulating the intracellular calcium-calmodulin (Ca2+ -CaM) pathway. Ng null mice (Ng-/- mice) demonstrate increased alcohol drinking compared to wild-type mice, while also showing less tolerance to the effect of alcohol. To identify the molecular mechanism related to alcohol seeking, both in vivo microdialysis and label-free quantification proteomics comparing Ng genotype and effects of alcohol treatment on the NAc are utilized. There is significant difference in glutamate and gamma-aminobutyric acid (GABA) neurotransmission between genotypes; however, alcohol administration normalizes both glutamate and GABA levels in the NAc. Using label-free proteomics, 427 protein expression changes are identified against alcohol treatment in the NAc among 4347 total proteins detected. Bioinformatics analyses reveal significant molecular differences in Ng null mice in response to acute alcohol treatment. Ingenuity pathway analysis found that the AKT network is altered significantly between genotypes, which may increase the sensitivity of alcohol in Ng null mice. The pharmacoproteomics results presented here illustrate a possible molecular basis of the alcohol sensitivity through Ng signaling in the NAc.
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Affiliation(s)
- Hyung W Nam
- Department of Pharmacology, Toxicology, and Neuroscience, Health Science Center, Louisiana State University, Shreveport, LA, 71130, USA
| | - Caleb A Grant
- Department of Pharmacology, Toxicology, and Neuroscience, Health Science Center, Louisiana State University, Shreveport, LA, 71130, USA
| | - Ashton N Jorgensen
- Department of Pharmacology, Toxicology, and Neuroscience, Health Science Center, Louisiana State University, Shreveport, LA, 71130, USA
| | | | - Marjan Trutschl
- Department of Computer Science, Louisiana State University-Shreveport, Shreveport, LA, 71115, USA
| | - Urska Cvek
- Department of Computer Science, Louisiana State University-Shreveport, Shreveport, LA, 71115, USA
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7
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Bogenpohl JW, Smith ML, Farris SP, Dumur CI, Lopez MF, Becker HC, Grant KA, Miles MF. Cross-Species Co-analysis of Prefrontal Cortex Chronic Ethanol Transcriptome Responses in Mice and Monkeys. Front Mol Neurosci 2019; 12:197. [PMID: 31456662 PMCID: PMC6701453 DOI: 10.3389/fnmol.2019.00197] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Despite recent extensive genomic and genetic studies on behavioral responses to ethanol, relatively few new therapeutic targets for the treatment of alcohol use disorder have been validated. Here, we describe a cross-species genomic approach focused on identifying gene networks associated with chronic ethanol consumption. To identify brain mechanisms underlying a chronic ethanol consumption phenotype highly relevant to human alcohol use disorder, and to elucidate potential future therapeutic targets, we conducted a genomic study in a non-human primate model of chronic open-access ethanol consumption. Microarray analysis of RNA expression in anterior cingulate and subgenual cortices from rhesus macaques was performed across multiple cohorts of animals. Gene networks correlating with ethanol consumption or showing enrichment for ethanol-regulated genes were identified, as were major ethanol-related hub genes within these networks. A subsequent consensus module analysis was used to co-analyze monkey data with expression data from a chronic intermittent ethanol vapor-exposure and consumption model in C57BL/6J mice. Ethanol-related gene networks conserved between primates and rodents were enriched for genes involved in discrete biological functions, including; myelination, synaptic transmission, chromatin modification, Golgi apparatus function, translation, cellular respiration, and RNA processing. The myelin-related network, in particular, showed strong correlations with ethanol consumption behavior and displayed marked network reorganization between control and ethanol-drinking animals. Further bioinformatics analysis revealed that these networks also showed highly significant overlap with other ethanol-regulated gene sets. Altogether, these studies provide robust primate and rodent cross-species validation of gene networks associated with chronic ethanol consumption. Our results also suggest potential novel focal points for future therapeutic interventions in alcohol use disorder.
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Affiliation(s)
- James W Bogenpohl
- Department of Molecular Biology and Chemistry, Christopher Newport University, Newport News, VA, United States
| | - Maren L Smith
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States
| | - Catherine I Dumur
- Aurora Diagnostics-Sonic Healthcare, Bernhardt Laboratories, Jacksonville, FL, United States
| | - Marcelo F Lopez
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Howard C Becker
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Kathleen A Grant
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States.,Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Michael F Miles
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States.,Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States.,Department of Neurology, Virginia Commonwealth University, Richmond, VA, United States.,VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
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8
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Mignogna KM, Bacanu SA, Riley BP, Wolen AR, Miles MF. Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data. PLoS One 2019; 14:e0202063. [PMID: 31017905 PMCID: PMC6481773 DOI: 10.1371/journal.pone.0202063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 04/07/2019] [Indexed: 01/06/2023] Open
Abstract
Genome-wide association studies on alcohol dependence, by themselves, have yet to account for the estimated heritability of the disorder and provide incomplete mechanistic understanding of this complex trait. Integrating brain ethanol-responsive gene expression networks from model organisms with human genetic data on alcohol dependence could aid in identifying dependence-associated genes and functional networks in which they are involved. This study used a modification of the Edge-Weighted Dense Module Searching for genome-wide association studies (EW-dmGWAS) approach to co-analyze whole-genome gene expression data from ethanol-exposed mouse brain tissue, human protein-protein interaction databases and alcohol dependence-related genome-wide association studies. Results revealed novel ethanol-responsive and alcohol dependence-associated gene networks in prefrontal cortex, nucleus accumbens, and ventral tegmental area. Three of these networks were overrepresented with genome-wide association signals from an independent dataset. These networks were significantly overrepresented for gene ontology categories involving several mechanisms, including actin filament-based activity, transcript regulation, Wnt and Syndecan-mediated signaling, and ubiquitination. Together, these studies provide novel insight for brain mechanisms contributing to alcohol dependence.
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Affiliation(s)
- Kristin M. Mignogna
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Center for Clinical & Translational Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Silviu A. Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Aaron R. Wolen
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael F. Miles
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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9
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Salvatore JE, Han S, Farris SP, Mignogna KM, Miles MF, Agrawal A. Beyond genome-wide significance: integrative approaches to the interpretation and extension of GWAS findings for alcohol use disorder. Addict Biol 2019; 24:275-289. [PMID: 29316088 PMCID: PMC6037617 DOI: 10.1111/adb.12591] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a heritable complex behavior. Due to the highly polygenic nature of AUD, identifying genetic variants that comprise this heritable variation has proved to be challenging. With the exception of functional variants in alcohol metabolizing genes (e.g. ADH1B and ALDH2), few other candidate loci have been confidently linked to AUD. Genome-wide association studies (GWAS) of AUD and other alcohol-related phenotypes have either produced few hits with genome-wide significance or have failed to replicate on further study. These issues reinforce the complex nature of the genetic underpinnings for AUD and suggest that both GWAS studies with larger samples and additional analysis approaches that better harness the nominally significant loci in existing GWAS are needed. Here, we review approaches of interest in the post-GWAS era, including in silico functional analyses; functional partitioning of single nucleotide polymorphism heritability; aggregation of signal into genes and gene networks; and validation of identified loci, genes and gene networks in postmortem brain tissue and across species. These integrative approaches hold promise to illuminate our understanding of the biological basis of AUD; however, we recognize that the main challenge continues to be the extremely polygenic nature of AUD, which necessitates large samples to identify multiple loci associated with AUD liability.
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Affiliation(s)
- Jessica E. Salvatore
- Department of Psychology; Virginia Commonwealth University; Richmond VA USA
- Virginia Institute for Psychiatric and Behavioral Genetics; Virginia Commonwealth University; Richmond VA USA
| | - Shizhong Han
- Department of Psychiatry; University of Iowa; Iowa City IA USA
- Department of Psychiatry and Behavioral Sciences; Johns Hopkins School of Medicine; Baltimore MD USA
| | - Sean P. Farris
- Waggoner Center for Alcohol and Addiction Research; The University of Texas at Austin; Austin TX USA
| | - Kristin M. Mignogna
- Virginia Institute for Psychiatric and Behavioral Genetics; Virginia Commonwealth University; Richmond VA USA
| | - Michael F. Miles
- Department of Pharmacology and Toxicology; Virginia Commonwealth University; Richmond VA USA
| | - Arpana Agrawal
- Department of Psychiatry; Washington University School of Medicine; Saint Louis MO USA
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10
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Wolstenholme JT, Mahmood T, Harris GM, Abbas S, Miles MF. Intermittent Ethanol during Adolescence Leads to Lasting Behavioral Changes in Adulthood and Alters Gene Expression and Histone Methylation in the PFC. Front Mol Neurosci 2017; 10:307. [PMID: 29018328 PMCID: PMC5622951 DOI: 10.3389/fnmol.2017.00307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/12/2017] [Indexed: 01/23/2023] Open
Abstract
Adolescents primarily consume alcohol in binges, which can be particularly harmful to the developing frontal cortex and increase risk for an adult alcohol use disorder. We conducted a study investigating immediate and long lasting changes to the prefrontal cortex (PFC) transcriptome to determine the molecular mechanisms underlying adult ethanol behavioral sensitivity following binge ethanol in adolescence. DBA/2J mice were orally dosed with 4 g/kg ethanol intermittently from day 29 to 42. Adolescent mice were tested for anxiety-like behavior and ethanol sensitivity using the loss of righting reflex task. As adults, mice were tested for cognitive changes using the novel object recognition task, ethanol-induced anxiolysis and ethanol sensitivity. Adolescent binge ethanol altered ethanol sensitivity in young mice and led to lasting memory deficits in the object recognition test and greater ethanol sensitivity in adulthood. Using genomic profiling of transcripts in the PFC, we found that binge ethanol reduced myelin-related gene expression and altered chromatin modifying genes involved in histone demethylation at H3K9 and H3K36. We hypothesize that ethanol's actions on histone methylation may be a switch for future transcriptional changes that underlie the behavioral changes lasting into adulthood.
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Affiliation(s)
- Jennifer T Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States.,VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Tariq Mahmood
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Guy M Harris
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Shahroze Abbas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States.,VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States.,Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States
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11
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Colville AM, Iancu OD, Oberbeck DL, Darakjian P, Zheng CL, Walter NAR, Harrington CA, Searles RP, McWeeney S, Hitzemann RJ. Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice. GENES BRAIN AND BEHAVIOR 2017; 16:462-471. [PMID: 28058793 DOI: 10.1111/gbb.12367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/16/2016] [Accepted: 01/03/2017] [Indexed: 12/15/2022]
Abstract
Previous studies on changes in murine brain gene expression associated with the selection for ethanol preference have used F2 intercross or heterogeneous stock (HS) founders, derived from standard laboratory strains. However, these populations represent only a small proportion of the genetic variance available in Mus musculus. To investigate a wider range of genetic diversity, we selected mice for ethanol preference using an HS derived from the eight strains of the collaborative cross. These HS mice were selectively bred (four generations) for high and low ethanol preference. The nucleus accumbens shell of naive S4 mice was interrogated using RNA sequencing (RNA-Seq). Gene networks were constructed using the weighted gene coexpression network analysis assessing both coexpression and cosplicing. Selection targeted one of the network coexpression modules (greenyellow) that was significantly enriched in genes associated with receptor signaling activity including Chrna7, Grin2a, Htr2a and Oprd1. Connectivity in the module as measured by changes in the hub nodes was significantly reduced in the low preference line. Of particular interest was the observation that selection had marked effects on a large number of cell adhesion molecules, including cadherins and protocadherins. In addition, the coexpression data showed that selection had marked effects on long non-coding RNA hub nodes. Analysis of the cosplicing network data showed a significant effect of selection on a large cluster of Ras GTPase-binding genes including Cdkl5, Cyfip1, Ndrg1, Sod1 and Stxbp5. These data in part support the earlier observation that preference is linked to Ras/Mapk pathways.
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Affiliation(s)
- A M Colville
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - O D Iancu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - D L Oberbeck
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - P Darakjian
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - C L Zheng
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - N A R Walter
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - C A Harrington
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - R P Searles
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - S McWeeney
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - R J Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA.,Research Service, Portland Veterans Affairs Medical Center, Portland, OR, USA
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12
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Brief isoflurane anaesthesia affects differential gene expression, gene ontology and gene networks in rat brain. Behav Brain Res 2017; 317:453-460. [DOI: 10.1016/j.bbr.2016.09.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/14/2016] [Accepted: 09/18/2016] [Indexed: 11/19/2022]
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13
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Carter JM, Landin JD, Gigante ED, Rieger SP, Diaz MR, Werner DF. Inhibitors of Calcium-Activated Anion Channels Modulate Hypnotic Ethanol Responses in Adult Sprague Dawley Rats. Alcohol Clin Exp Res 2016; 40:301-8. [PMID: 26842249 DOI: 10.1111/acer.12957] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND Ethanol is widely known for its depressant effects; however, the underlying neurobiological mechanisms are not clear. Calcium-activated anion channels (CAACs) contribute to extracellular chloride levels and thus may be involved in regulating inhibitory mechanisms within the central nervous system. Therefore, we hypothesized that CAACs influence ethanol behavioral sensitivity by altering CAAC expression. METHODS We assessed the role of CAACs in ethanol-induced loss of righting reflex (LORR) and locomotor activity using intracerebroventricular infusions of several nonselective CAAC blockers. CAAC expression was determined after ethanol exposure. RESULTS Ethanol-induced LORR (4.0 g/kg, intraperitoneally [i.p.]) was significantly attenuated by all 4 CAAC blockers. Blocking CAACs did not impact ethanol's low-dose (1.5 g/kg, i.p.) locomotor-impairing effects. Biochemical analysis of CAAC protein expression revealed that cortical Bestrophin1 (Best1) and Tweety1 levels were reduced as early as 30 minutes following a single ethanol injection (3.5 g/kg, intraperitoneally [i.p.]) and remained decreased 24 hours later in P2 fractions. Cortical Best1 levels were also reduced following 1.5 g/kg. However, CAAC expression was unaltered in the striatum following a single ethanol exposure. Ethanol did not affect Tweety2 levels in either brain region. CONCLUSIONS These results suggest that CAACs are a major target of ethanol in vivo, and the regulation of these channels contributes to select behavioral actions of ethanol.
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Affiliation(s)
- Jenna M Carter
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York
| | - Justine D Landin
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York
| | - Eduardo D Gigante
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York.,Department of Health and Human Services, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland
| | - Samuel P Rieger
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York
| | - Marvin R Diaz
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York
| | - David F Werner
- Department of Psychology, Center for Development and Behavioral Neuroscience, Binghamton University - State University of New York, Binghamton, New York
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14
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Bennett B, Larson C, Richmond PA, Odell AT, Saba LM, Tabakoff B, Dowell R, Radcliffe RA. Quantitative trait locus mapping of acute functional tolerance in the LXS recombinant inbred strains. Alcohol Clin Exp Res 2016; 39:611-20. [PMID: 25833023 DOI: 10.1111/acer.12678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/09/2015] [Indexed: 01/23/2023]
Abstract
BACKGROUND We previously reported that acute functional tolerance (AFT) to the hypnotic effects of alcohol was significantly correlated with drinking in the dark (DID) in the LXS recombinant inbred panel, but only in mice that had been pretreated with alcohol. Here, we have conducted quantitative trait locus (QTL) mapping for AFT. DNA sequencing of the progenitor ILS and ISS strains and microarray analyses were also conducted to identify candidate genes and functional correlates. METHODS LXS mice were given either saline or alcohol (5 g/kg) on day 1 and then tested for loss of righting reflex AFT on day 2. QTLs were mapped using standard procedures. Two microarray analyses from brain were conducted: (i) naïve LXS mice and (ii) an alcohol treatment time course in the ILS and ISS. The full genomes of the ILS and ISS were sequenced to a depth of approximately 30×. RESULTS A significant QTL for AFT in the alcohol pretreatment group was mapped to distal chromosome 4; numerous suggestive QTLs were also mapped. Preference drinking and DID have previously been mapped to the chromosome 4 locus. The credible interval of the significant chromosome 4 QTL spanned 23 Mb and included 716 annotated genes of which 150 had at least 1 nonsynonymous single nucleotide polymorphism or small indel that differed between the ILS and ISS; expression of 48 of the genes was cis-regulated. Enrichment analysis indicated broad functional categories underlying AFT, including proteolysis, transcription regulation, chromatin modification, protein kinase activity, and apoptosis. CONCLUSIONS The chromosome 4 QTL is a key region containing possibly pleiotropic genes for AFT and drinking behavior. Given that the region contains many viable candidates and a large number of the genes in the interval fall into 1 or more of the enriched functional categories, we postulate that many genes of varying effect size contribute to the observed QTL effect.
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Affiliation(s)
- Beth Bennett
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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15
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Time-Course Analysis of Brain Regional Expression Network Responses to Chronic Intermittent Ethanol and Withdrawal: Implications for Mechanisms Underlying Excessive Ethanol Consumption. PLoS One 2016; 11:e0146257. [PMID: 26730594 PMCID: PMC4701666 DOI: 10.1371/journal.pone.0146257] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/15/2015] [Indexed: 01/17/2023] Open
Abstract
Long lasting abusive consumption, dependence, and withdrawal are characteristic features of alcohol use disorders (AUD). Mechanistically, persistent changes in gene expression are hypothesized to contribute to brain adaptations leading to ethanol toxicity and AUD. We employed repeated chronic intermittent ethanol (CIE) exposure by vapor chamber as a mouse model to simulate the cycles of ethanol exposure and withdrawal commonly seen with AUD. This model has been shown to induce progressive ethanol consumption in rodents. Brain CIE-responsive expression networks were identified by microarray analysis across five regions of the mesolimbic dopamine system and extended amygdala with tissue harvested from 0-hours to 7-days following CIE. Weighted Gene Correlated Network Analysis (WGCNA) was used to identify gene networks over-represented for CIE-induced temporal expression changes across brain regions. Differential gene expression analysis showed that long-lasting gene regulation occurred 7-days after the final cycle of ethanol exposure only in prefrontal cortex (PFC) and hippocampus. Across all brain regions, however, ethanol-responsive expression changes occurred mainly within the first 8-hours after removal from ethanol. Bioinformatics analysis showed that neuroinflammatory responses were seen across multiple brain regions at early time-points, whereas co-expression modules related to neuroplasticity, chromatin remodeling, and neurodevelopment were seen at later time-points and in specific brain regions (PFC or HPC). In PFC a module containing Bdnf was identified as highly CIE responsive in a biphasic manner, with peak changes at 0 hours and 5 days following CIE, suggesting a possible role in mechanisms underlying long-term molecular and behavioral response to CIE. Bioinformatics analysis of this network and several other modules identified Let-7 family microRNAs as potential regulators of gene expression changes induced by CIE. Our results suggest a complex temporal and regional pattern of widespread gene network responses involving neuroinflammatory and neuroplasticity related genes as contributing to physiological and behavioral responses to chronic ethanol.
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16
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Transcriptome organization for chronic alcohol abuse in human brain. Mol Psychiatry 2015; 20:1438-47. [PMID: 25450227 PMCID: PMC4452464 DOI: 10.1038/mp.2014.159] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 10/07/2014] [Accepted: 10/09/2014] [Indexed: 12/18/2022]
Abstract
Alcohol dependence is a heterogeneous psychiatric disorder characterized by high genetic heritability and neuroadaptations occurring from repeated drug exposure. Through an integrated systems approach we observed consistent differences in transcriptome organization within postmortem human brain tissue associated with the lifetime consumption of alcohol. Molecular networks, determined using high-throughput RNA sequencing, for drinking behavior were dominated by neurophysiological targets and signaling mechanisms of alcohol. The systematic structure of gene sets demonstrates a novel alliance of multiple ion channels, and related processes, underlying lifetime alcohol consumption. Coordinate expression of these transcripts was enriched for genome-wide association signals in alcohol dependence and a meta-analysis of alcohol self-administration in mice. Further dissection of genes within alcohol consumption networks revealed the potential interaction of alternatively spliced transcripts. For example, expression of a human-specific isoform of the voltage-gated sodium channel subunit SCN4B was significantly correlated to lifetime alcohol consumption. Overall, our work demonstrates novel convergent evidence for biological networks related to excessive alcohol consumption, which may prove fundamentally important in the development of pharmacotherapies for alcohol dependence.
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17
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Batman AM. Translating Alcohol Research: Opportunities and Challenges. Alcohol Res 2015; 37:7-14. [PMID: 26259085 PMCID: PMC4476605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of stream-lining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD.
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18
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Vicente-Rodríguez M, Pérez-García C, Ferrer-Alcón M, Uribarri M, Sánchez-Alonso MG, Ramos MP, Herradón G. Pleiotrophin differentially regulates the rewarding and sedative effects of ethanol. J Neurochem 2014; 131:688-95. [PMID: 25073406 DOI: 10.1111/jnc.12841] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/24/2014] [Accepted: 07/28/2014] [Indexed: 01/07/2023]
Abstract
Pleiotrophin (PTN) is a cytokine with important roles in dopaminergic neurons. We found that an acute ethanol (2.0 g/kg, i.p.) administration causes a significant up-regulation of PTN mRNA and protein levels in the mouse prefrontal cortex, suggesting that endogenous PTN could modulate behavioural responses to ethanol. To test this hypothesis, we studied the behavioural effects of ethanol in PTN knockout (PTN(-/-) ) mice and in mice with cortex- and hippocampus-specific transgenic PTN over-expression (PTN-Tg). Ethanol (1.0 and 2.0 g/kg) induced an enhanced conditioned place preference in PTN(-/-) compared to wild type mice, suggesting that PTN prevents ethanol rewarding effects. Accordingly, the conditioning effects of ethanol were completely abolished in PTN-Tg mice. The ataxic effects induced by ethanol (2.0 g/kg) were not affected by the genotype. However, the sedative effects of ethanol (3.6 g/kg) tested in a loss of righting reflex paradigm were significantly reduced in PTN-Tg mice, suggesting that up-regulation of PTN levels prevents the sedative effects of ethanol. These results indicate that PTN may be a novel genetic factor of importance in alcohol use disorders, and that potentiation of the PTN signalling pathway may be a promising therapeutic strategy in the treatment of these disorders.
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Affiliation(s)
- Marta Vicente-Rodríguez
- Pharmacology lab, Department of Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain
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19
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Farris SP, Mayfield RD. RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:275-300. [PMID: 25172479 DOI: 10.1016/b978-0-12-801105-8.00011-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA microarrays have been used for over a decade to profile gene expression on a genomic scale. While this technology has advanced our understanding of complex cellular function, the reliance of microarrays on hybridization kinetics results in several technical limitations. For example, knowledge of the sequences being probed is required, distinguishing similar sequences is difficult because of cross-hybridization, and the relatively narrow dynamic range of the signal limits sensitivity. Recently, new technologies have been introduced that are based on novel sequencing methodologies. These next-generation sequencing methods do not have the limitations inherent to microarrays. Next-generation sequencing is unique since it allows the detection of all known and novel RNAs present in biological samples without bias toward known transcripts. In addition, the expression of coding and noncoding RNAs, alternative splicing events, and expressed single nucleotide polymorphisms (SNPs) can be identified in a single experiment. Furthermore, this technology allows for remarkably higher throughput while lowering sequencing costs. This significant shift in throughput and pricing makes low-cost access to whole genomes possible and more importantly expands sequencing applications far beyond traditional uses (Morozova & Marra, 2008) to include sequencing the transcriptome (RNA-Seq), providing detail on gene structure, alternative splicing events, expressed SNPs, and transcript size (Mane et al., 2009; Tang et al., 2009; Walter et al., 2009), in a single experiment, while also quantifying the absolute abundance of genes, all with greater sensitivity and dynamic range than the competing cDNA microarray technology (Mortazavi, Williams, McCue, Schaeffer, & Wold, 2008).
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Affiliation(s)
- Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712.
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20
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Abstract
This chapter provides an overview of current knowledge on the molecular and clinical aspects of chronic alcohol effects on the central nervous system. This drug is almost ubiquitous, widely enjoyed socially, but produces a diverse spectrum of neurologic disease when abused. Acutely, alcohol interacts predominantly with γ-aminobutyric acid-A (GABA-A) and N-methyl-d-aspartate (NMDA) receptors, but triggers diverse signaling events within well-defined neural pathways. These events result in adaptive changes in gene expression that ultimately produce two major states: addiction and toxicity. Epigenetic modifications of chromatin could lead to long-lived or even transgenerational changes in gene expression, thus producing aspects of the heritability of alcohol use disorders (AUD) and long-term behaviors such as recidivism. The diverse clinical syndromes produced by chronic alcohol actions in the central nervous system reflect the molecular pathology and predominantly involve aspects of tolerance/withdrawal, selective vulnerability (manifest as central pontine myelinolysis, Marchiafava-Bignami disease), and additional environmental factors (e.g., thiamine deficiency in Wernicke-Korsakoff's syndrome). Additionally, deleterious aspects of chronic alcohol on signaling, synaptic transmission, and cell toxicity lead to primary alcoholic dementia. Genetically determined aspects of myelin structure and alcohol actions on myelin gene expression may be a prominent molecular mechanism resulting in a predisposition to, or causation of, AUD and multiple other neurologic complications of chronic alcohol. The dramatic progress made in understanding molecular actions of alcohol holds great promise for our eventual treatment or prevention of AUD and neurologic complications resulting from chronic alcohol abuse.
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Affiliation(s)
- B N Costin
- Virginia Commonwealth University Alcohol Research Center and Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - M F Miles
- Virginia Commonwealth University Alcohol Research Center, Department of Pharmacology and Toxicology, Center for Study of Biological Complexity and Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA.
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