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Baker JA, Mulligan MK, Hamre KM. Effects of genetics and sex on adolescent behaviors following neonatal ethanol exposure in BXD recombinant inbred strains. Front Neurosci 2023; 17:1197292. [PMID: 37564365 PMCID: PMC10410115 DOI: 10.3389/fnins.2023.1197292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Fetal alcohol spectrum disorders (FASD) are the leading preventable neurodevelopmental disorders and two hallmark symptoms of FASD are abnormal behavior, and cognitive and learning deficits. The severity of alcohol's teratogenic effects on the developing brain is influenced by genetics and sex. We previously identified recombinant inbred BXD mouse strains that show differential vulnerability to ethanol-induced cell death in the developing hippocampus, a brain region important in learning and memory. The present study aimed to test the hypothesis that strains with increased vulnerability to ethanol-induced cell death in the hippocampus have concomitant deficits in multiple hippocampal-related behaviors during adolescence. Methods The current study evaluated the effects of developmental ethanol exposure on adolescent behavior in two BXD strains that show high cell death (BXD48a, BXD100), two that show low cell death (BXD60, BXD71), and the two parental strains (C57BL/6 J (B6), DBA/2 J (D2)). On postnatal day 7, male and female neonatal pups were treated with ethanol (5.0 g/kg) or saline given in two equal doses 2 h apart. Adolescent behavior was assessed across multiple behavioral paradigms including the elevated plus maze, open field, Y-maze, and T-maze. Results Our results demonstrate that the effects of developmental ethanol exposure on adolescent behavioral responses are highly dependent on strain. The low cell death strains, BXD60 and BXD71, showed minimal effect of ethanol exposure on all behavioral measures but did present sex differences. The parental -B6 and D2-strains and high cell death strains, BXD48a and BXD100, showed ethanol-induced effects on activity-related or anxiety-like behaviors. Interestingly, the high cell death strains were the only strains that showed a significant effect of postnatal ethanol exposure on hippocampal-dependent spatial learning and memory behaviors. Discussion Overall, we identified effects of ethanol exposure, strain, and/or sex on multiple behavioral measures. Interestingly, the strains that showed the most effects of postnatal ethanol exposure on adolescent behavior were the BXD strains that show high ethanol-induced cell death in the neonatal hippocampus, consistent with our hypothesis. Additionally, we found evidence for interactions among strain and sex, demonstrating that these factors have a complex effect on alcohol responses and that both are important considerations.
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Affiliation(s)
- Jessica A. Baker
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
- Center for Behavioral Teratology, San Diego State University, San Diego, CA, United States
| | - Megan K. Mulligan
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Kristin M. Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States
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2
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Yao HL, Liu M, Wang WJ, Wang XL, Song J, Song QQ, Han J. Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells. Sci Rep 2019; 9:17876. [PMID: 31784561 PMCID: PMC6884461 DOI: 10.1038/s41598-019-54188-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.
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Affiliation(s)
- Hai Lan Yao
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, 2 YaBao Rd, Beijing, 100020, China
| | - Mi Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Wen Jun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Xin Ling Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Qin Qin Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China.
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China.
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3
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Théberge ET, Baker JA, Dubose C, Boyle JK, Balce K, Goldowitz D, Hamre KM. Genetic Influences on the Amount of Cell Death in the Neural Tube of BXD Mice Exposed to Acute Ethanol at Midgestation. Alcohol Clin Exp Res 2019; 43:439-452. [PMID: 30589433 DOI: 10.1111/acer.13947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/19/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Fetal alcohol spectrum disorders (FASD) have a strong genetic component although the genes that underlie this are only beginning to be elucidated. In the present study, one of the most common phenotypes of FASD, cell death within the early developing neural tube, was examined across a genetic reference population in a reverse genetics paradigm with the goal of identifying genetic loci that could influence ethanol (EtOH)-induced apoptosis in the early developing neural tube. METHODS BXD recombinant inbred mice as well as the parental strains were used to evaluate genetic differences in EtOH-induced cell death after exposure on embryonic day 9.5. Dams were given either 5.8 g/kg EtOH or isocaloric maltose-dextrin in 2 doses via intragastric gavage. Embryos were collected 7 hours after the initial exposure and cell death evaluated via TUNEL staining in the brainstem and forebrain. Genetic loci were evaluated using quantitative trait locus (QTL) analysis at GeneNetwork.org. RESULTS Significant strain differences were observed in the levels of EtOH-induced cell death that were due to genetic effects and not confounding variables such as differences in developmental maturity or cell death kinetics. Comparisons between the 2 regions of the developing neural tube showed little genetic correlation with the QTL maps exhibiting no overlap. Significant QTLs were found on murine mid-chromosome 4 and mid-chromosome 14 only in the brainstem. Within these chromosomal loci, a number of interesting candidate genes were identified that could mediate this differential sensitivity including Nfia (nuclear factor I/A) and Otx2 (orthodenticle homeobox 2). CONCLUSIONS These studies demonstrate that the levels of EtOH-induced cell death occur in strain- and region-dependent manners. Novel QTLs on mouse Chr4 and Chr14 were identified that modulate the differential sensitivity to EtOH-induced apoptosis in the embryonic brainstem. The genes underlying these QTLs could identify novel molecular pathways that are critical in this phenotype.
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Affiliation(s)
- Emilie T Théberge
- Centre for Molecular Medicine and Therapeutics , British Columbia Children's Research Institution, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica A Baker
- Department of Anatomy and Neurobiology , University of Tennessee Health Science Center, Memphis, Tennessee
| | - Candis Dubose
- Department of Anatomy and Neurobiology , University of Tennessee Health Science Center, Memphis, Tennessee
| | - Julia K Boyle
- Centre for Molecular Medicine and Therapeutics , British Columbia Children's Research Institution, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristina Balce
- Centre for Molecular Medicine and Therapeutics , British Columbia Children's Research Institution, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics , British Columbia Children's Research Institution, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristin M Hamre
- Department of Anatomy and Neurobiology , University of Tennessee Health Science Center, Memphis, Tennessee
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4
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Gunduz-Cinar O, Brockway E, Lederle L, Wilcox T, Halladay LR, Ding Y, Oh H, Busch EF, Kaugars K, Flynn S, Limoges A, Bukalo O, MacPherson KP, Masneuf S, Pinard C, Sibille E, Chesler EJ, Holmes A. Identification of a novel gene regulating amygdala-mediated fear extinction. Mol Psychiatry 2019; 24:601-612. [PMID: 29311651 PMCID: PMC6035889 DOI: 10.1038/s41380-017-0003-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/08/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022]
Abstract
Recent years have seen advances in our understanding of the neural circuits associated with trauma-related disorders, and the development of relevant assays for these behaviors in rodents. Although inherited factors are known to influence individual differences in risk for these disorders, it has been difficult to identify specific genes that moderate circuit functions to affect trauma-related behaviors. Here, we exploited robust inbred mouse strain differences in Pavlovian fear extinction to uncover quantitative trait loci (QTL) associated with this trait. We found these strain differences to be resistant to developmental cross-fostering and associated with anatomical variation in basolateral amygdala (BLA) perineuronal nets, which are developmentally implicated in extinction. Next, by profiling extinction-driven BLA expression of QTL-linked genes, we nominated Ppid (peptidylprolyl isomerase D, a member of the tetratricopeptide repeat (TPR) protein family) as an extinction-related candidate gene. We then showed that Ppid was enriched in excitatory and inhibitory BLA neuronal populations, but at lower levels in the extinction-impaired mouse strain. Using a virus-based approach to directly regulate Ppid function, we demonstrated that downregulating BLA-Ppid impaired extinction, while upregulating BLA-Ppid facilitated extinction and altered in vivo neuronal extinction encoding. Next, we showed that Ppid colocalized with the glucocorticoid receptor (GR) in BLA neurons and found that the extinction-facilitating effects of Ppid upregulation were blocked by a GR antagonist. Collectively, our results identify Ppid as a novel gene involved in regulating extinction via functional actions in the BLA, with possible implications for understanding genetic and pathophysiological mechanisms underlying risk for trauma-related disorders.
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Affiliation(s)
- Ozge Gunduz-Cinar
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, USA.
| | - Emma Brockway
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Lauren Lederle
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Troy Wilcox
- 0000 0004 0374 0039grid.249880.fThe Jackson Laboratory, Bar Harbor, ME USA
| | - Lindsay R. Halladay
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Ying Ding
- Joint Carnegie Mellon University–University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA USA
| | - Hyunjung Oh
- 0000 0004 1936 9000grid.21925.3dDepartment of Psychiatry, University of Pittsburgh, Pittsburgh, PA USA ,0000 0001 2157 2938grid.17063.33Departments of Psychiatry and Pharmacology & Toxicology, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Toronto, Canada
| | - Erica F. Busch
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Katie Kaugars
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Shaun Flynn
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Aaron Limoges
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Olena Bukalo
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Kathryn P. MacPherson
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Sophie Masneuf
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Courtney Pinard
- 0000 0004 0481 4802grid.420085.bLaboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD USA
| | - Etienne Sibille
- 0000 0004 1936 9000grid.21925.3dDepartment of Psychiatry, University of Pittsburgh, Pittsburgh, PA USA ,0000 0001 2157 2938grid.17063.33Departments of Psychiatry and Pharmacology & Toxicology, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Toronto, Canada
| | - Elissa J. Chesler
- 0000 0004 0374 0039grid.249880.fThe Jackson Laboratory, Bar Harbor, ME USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD, USA.
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5
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Arnau-Soler A, Adams MJ, Hayward C, Thomson PA. Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder. PLoS One 2018; 13:e0209160. [PMID: 30571770 PMCID: PMC6301766 DOI: 10.1371/journal.pone.0209160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/02/2018] [Indexed: 01/31/2023] Open
Abstract
Individual response to stress is correlated with neuroticism and is an important predictor of both neuroticism and the onset of major depressive disorder (MDD). Identification of the genetics underpinning individual differences in response to negative events (stress-sensitivity) may improve our understanding of the molecular pathways involved, and its association with stress-related illnesses. We sought to generate a proxy for stress-sensitivity through modelling the interaction between SNP allele and MDD status on neuroticism score in order to identify genetic variants that contribute to the higher neuroticism seen in individuals with a lifetime diagnosis of depression compared to unaffected individuals. Meta-analysis of genome-wide interaction studies (GWIS) in UK Biobank (N = 23,092) and Generation Scotland: Scottish Family Health Study (N = 7,155) identified no genome-wide significance SNP interactions. However, gene-based tests identified a genome-wide significant gene, ZNF366, a negative regulator of glucocorticoid receptor function implicated in alcohol dependence (p = 1.48x10-7; Bonferroni-corrected significance threshold p < 2.79x10-6). Using summary statistics from the stress-sensitivity term of the GWIS, SNP heritability for stress-sensitivity was estimated at 5.0%. In models fitting polygenic risk scores of both MDD and neuroticism derived from independent GWAS, we show that polygenic risk scores derived from the UK Biobank stress-sensitivity GWIS significantly improved the prediction of MDD in Generation Scotland. This study may improve interpretation of larger genome-wide association studies of MDD and other stress-related illnesses, and the understanding of the etiological mechanisms underpinning stress-sensitivity.
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Affiliation(s)
- Aleix Arnau-Soler
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Pippa A. Thomson
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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6
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Zhou D, Zhao Y, Hook M, Zhao W, Starlard-Davenport A, Cook MN, Jones BC, Hamre KM, Lu L. Ethanol's Effect on Coq7 Expression in the Hippocampus of Mice. Front Genet 2018; 9:602. [PMID: 30564271 PMCID: PMC6288283 DOI: 10.3389/fgene.2018.00602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/16/2018] [Indexed: 01/16/2023] Open
Abstract
Coenzyme Q (CoQ) is a well-studied molecule, present in every cell membrane in the body, best known for its roles as a mitochondrial electron transporter and a potent membrane anti-oxidant. Much of the previous work was done in vitro in yeast and more recent work has suggested that CoQ may have additional roles prompting calls for a re-assessment of its role using in vivo systems in mammals. Here we investigated the putative role of Coenzyme Q in ethanol-induced effects in vivo using BXD RI mice. We examined hippocampal expression of Coq7 in saline controls and after an acute ethanol treatment, noting enriched biologic processes and pathways following ethanol administration. We also identified 45 ethanol-related phenotypes that were significantly correlated with Coq7 expression, including six phenotypes related to conditioned taste aversion and ethanol preference. This analysis highlights the need for further investigation of Coq7 and related genes in vivo as well as previously unrecognized roles that it may play in the hippocampus.
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Affiliation(s)
- Diana Zhou
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Yinghong Zhao
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, China
| | - Michael Hook
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Melloni N Cook
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Psychology, The University of Memphis, Memphis, TN, United States
| | - Byron C Jones
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Kristin M Hamre
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
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7
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Luo J, Xu P, Cao P, Wan H, Lv X, Xu S, Wang G, Cook MN, Jones BC, Lu L, Wang X. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses. Front Mol Neurosci 2018; 11:102. [PMID: 29674951 PMCID: PMC5895640 DOI: 10.3389/fnmol.2018.00102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.
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Affiliation(s)
- Jie Luo
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Zhejiang Academy of Agricultural Sciences Hangzhou, China.,Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences Hangzhou, China.,State Key Laboratory Breeding Base for Sustainable Control of Plant Pest and Disease, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC Zhengzhou, China
| | - Hongjian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Xiaonan Lv
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Shengchun Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Gangjun Wang
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Zhejiang Academy of Agricultural Sciences Hangzhou, China
| | - Melloni N Cook
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center Memphis, TN, United States.,Department of Psychology, University of Memphis Memphis, TN, United States
| | - Byron C Jones
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center Memphis, TN, United States.,Department of Neurology, Affiliated Hospital of Nantong University Nantong, China
| | - Xusheng Wang
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital Memphis, TN, United States
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8
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Abstract
Identifying genes and pathways that contribute to differences in neurobehavioural traits is a key goal in psychiatric research. Despite considerable success in identifying quantitative trait loci (QTLs) associated with behaviour in laboratory rodents, pinpointing the causal variants and genes is more challenging. For a long time, the main obstacle was the size of QTLs, which could encompass tens if not hundreds of genes. However, recent studies have exploited mouse and rat resources that allow mapping of phenotypes to narrow intervals, encompassing only a few genes. Here, we review these studies, showcase the rodent resources they have used and highlight the insights into neurobehavioural traits provided to date. We discuss what we see as the biggest challenge in the field - translating QTLs into biological knowledge by experimentally validating and functionally characterizing candidate genes - and propose that the CRISPR/Cas genome-editing system holds the key to overcoming this obstacle. Finally, we challenge traditional views on inbred versus outbred resources in the light of recent resource and technology developments.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095-1761, USA
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9
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Analyses of differentially expressed genes after exposure to acute stress, acute ethanol, or a combination of both in mice. Alcohol 2017; 58:139-151. [PMID: 28027852 DOI: 10.1016/j.alcohol.2016.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 12/31/2022]
Abstract
Alcohol abuse is a complex disorder, which is confounded by other factors, including stress. In the present study, we examined gene expression in the hippocampus of BXD recombinant inbred mice after exposure to ethanol (NOE), stress (RSS), and the combination of both (RSE). Mice were given an intraperitoneal (i.p.) injection of 1.8 g/kg ethanol or saline, and subsets of both groups were exposed to acute restraint stress for 15 min or controls. Gene expression in the hippocampus was examined using microarray analysis. Genes that were significantly (p < 0.05, q < 0.1) differentially expressed were further evaluated. Bioinformatic analyses were predominantly performed using tools available at GeneNetwork.org, and included gene ontology, presence of cis-regulation or polymorphisms, phenotype correlations, and principal component analyses. Comparisons of differential gene expression between groups showed little overlap. Gene Ontology demonstrated distinct biological processes in each group with the combined exposure (RSE) being unique from either the ethanol (NOE) or stress (RSS) group, suggesting that the interaction between these variables is mediated through diverse molecular pathways. This supports the hypothesis that exposure to stress alters ethanol-induced gene expression changes and that exposure to alcohol alters stress-induced gene expression changes. Behavior was profiled in all groups following treatment, and many of the differentially expressed genes are correlated with behavioral variation within experimental groups. Interestingly, in each group several genes were correlated with the same phenotype, suggesting that these genes are the potential origins of significant genetic networks. The distinct sets of differentially expressed genes within each group provide the basis for identifying molecular networks that may aid in understanding the complex interactions between stress and ethanol, and potentially provide relevant therapeutic targets. Using Ptp4a1, a candidate gene underlying the quantitative trait locus for several of these phenotypes, and network analyses, we show that a large group of differentially expressed genes in the NOE group are highly interrelated, some of which have previously been linked to alcohol addiction or alcohol-related phenotypes.
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10
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Putman AH, Wolen AR, Harenza JL, Yordanova RK, Webb BT, Chesler EJ, Miles MF. Identification of quantitative trait loci and candidate genes for an anxiolytic-like response to ethanol in BXD recombinant inbred strains. GENES BRAIN AND BEHAVIOR 2017; 15:367-81. [PMID: 26948279 DOI: 10.1111/gbb.12289] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 11/29/2022]
Abstract
Genetic differences in acute behavioral responses to ethanol contribute to the susceptibility to alcohol use disorder and the reduction of anxiety is a commonly reported motive underlying ethanol consumption among alcoholics. Therefore, we studied the genetic variance in anxiolytic-like responses to ethanol across the BXD recombinant inbred (RI) mouse panel using the light-dark transition model of anxiety. Strain-mean genetic mapping and a mixed-model quantitative trait loci (QTL) analysis replicated several previously published QTL for locomotor activity and identified several novel anxiety-related loci. Significant loci included a chromosome 11 saline anxiety-like QTL (Salanq1) and a chromosome 12 locus (Etanq1) influencing the anxiolytic-like response to ethanol. Etanq1 was successfully validated by studies with BXD advanced intercross strains and fine-mapped to a region comprising less than 3.5 Mb. Through integration of genome-wide mRNA expression profiles of the mesocorticolimbic reward circuit (prefrontal cortex, nucleus accumbens and ventral midbrain) across the BXD RI panel, we identified high priority candidate genes within Etanq1, the strongest of which was Ninein (Nin), a Gsk3β-interacting protein that is highly expressed in the brain.
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Affiliation(s)
- A H Putman
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - A R Wolen
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - J L Harenza
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - R K Yordanova
- Institute of Mathematics and Informatics, Bulgarian Academy of Science, Sofia, Bulgaria
| | - B T Webb
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | | | - M F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA.,Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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Urquhart KR, Zhao Y, Baker JA, Lu Y, Yan L, Cook MN, Jones BC, Hamre KM, Lu L. A novel heat shock protein alpha 8 (Hspa8) molecular network mediating responses to stress- and ethanol-related behaviors. Neurogenetics 2016; 17:91-105. [PMID: 26780340 DOI: 10.1007/s10048-015-0470-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/10/2015] [Indexed: 12/15/2022]
Abstract
Genetic differences mediate individual differences in susceptibility and responses to stress and ethanol, although, the specific molecular pathways that control these responses are not fully understood. Heat shock protein alpha 8 (Hspa8) is a molecular chaperone and member of the heat shock protein family that plays an integral role in the stress response and that has been implicated as an ethanol-responsive gene. Therefore, we assessed its role in mediating responses to stress and ethanol across varying genetic backgrounds. The hippocampus is an important mediator of these responses, and thus, was examined in the BXD family of mice in this study. We conducted bioinformatic analyses to dissect genetic factors modulating Hspa8 expression, identify downstream targets of Hspa8, and examined its role. Hspa8 is trans-regulated by a gene or genes on chromosome 14 and is part of a molecular network that regulates stress- and ethanol-related behaviors. To determine additional components of this network, we identified direct or indirect targets of Hspa8 and show that these genes, as predicted, participate in processes such as protein folding and organic substance metabolic processes. Two phenotypes that map to the Hspa8 locus are anxiety-related and numerous other anxiety- and/or ethanol-related behaviors significantly correlate with Hspa8 expression. To more directly assay this relationship, we examined differences in gene expression following exposure to stress or alcohol and showed treatment-related differential expression of Hspa8 and a subset of the members of its network. Our findings suggest that Hspa8 plays a vital role in genetic differences in responses to stress and ethanol and their interactions.
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Affiliation(s)
- Kyle R Urquhart
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Yinghong Zhao
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jessica A Baker
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Ye Lu
- The International Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Lei Yan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Melloni N Cook
- Department of Psychology, University of Memphis, Memphis, TN, 38152, USA
| | - Byron C Jones
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Kristin M Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Lu Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA. .,Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA. .,Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Medical College of Nantong University, Nantong, China.
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