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Genes with particular expression in the Parastrial nucleus. Data represent fold expression difference in structure versus grey matter average expression.
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Fibrinogen levels. The EFO term fibrinogen measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
PS de Vries, DI Chasman, M Sabater-Lleal, MH Chen, JE Huffman, M Steri, W Tang, A Teumer, RE Marioni, V Grossmann, JJ Hottenga, S Trompet, M Müller-Nurasyid, JH Zhao, JA Brody, ME Kleber, X Guo, JJ Wang, PL Auer, JR Attia, LR Yanek, TS Ahluwalia, J Lahti, C Venturini, T Tanaka, LF Bielak, PK Joshi, A Rocanin-Arjo, I Kolcic, P Navarro, LM Rose, C Oldmeadow, H Riess, J Mazur, S Basu, A Goel, Q Yang, M Ghanbari, G Willemsen, A Rumley, E Fiorillo, AJ de Craen, A Grotevendt, R Scott, KD Taylor, GE Delgado, J Yao, A Kifley, C Kooperberg, R Qayyum, LM Lopez, TL Berentzen, K Räikkönen, M Mangino, S Bandinelli, PA Peyser, S Wild, DA Trégouët, AF Wright, J Marten, T Zemunik, AC Morrison, B Sennblad, G Tofler, MP de Maat, EJ de Geus, GD Lowe, M Zoledziewska, N Sattar, H Binder, U Völker, M Waldenberger, KT Khaw, B Mcknight, J Huang, NS Jenny, EG Holliday, L Qi, MG Mcevoy, DM Becker, JM Starr, AP Sarin, PG Hysi, DG Hernandez, MA Jhun, H Campbell, A Hamsten, F Rivadeneira, WL Mcardle, PE Slagboom, T Zeller, W Koenig, BM Psaty, T Haritunians, J Liu, A Palotie, AG Uitterlinden, DJ Stott, A Hofman, OH Franco, O Polasek, I Rudan, PE Morange, JF Wilson, SL Kardia, L Ferrucci, TD Spector, JG Eriksson, T Hansen, IJ Deary, LC Becker, RJ Scott, P Mitchell, W März, NJ Wareham, A Peters, A Greinacher, PS Wild, JW Jukema, DI Boomsma, C Hayward, F Cucca, R Tracy, H Watkins, AP Reiner, AR Folsom, PM Ridker, CJ O'Donnell, NL Smith, DP Strachan, A Dehghan
List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Multiple sclerosis. The EFO term multiple sclerosis was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Authors:
S Sawcer, G Hellenthal, M Pirinen, CC Spencer, NA Patsopoulos, L Moutsianas, A Dilthey, Z Su, C Freeman, SE Hunt, S Edkins, E Gray, DR Booth, SC Potter, A Goris, G Band, AB Oturai, A Strange, J Saarela, C Bellenguez, B Fontaine, M Gillman, B Hemmer, R Gwilliam, F Zipp, A Jayakumar, R Martin, S Leslie, S Hawkins, E Giannoulatou, S D'alfonso, H Blackburn, F Martinelli Boneschi, J Liddle, HF Harbo, ML Perez, A Spurkland, MJ Waller, MP Mycko, M Ricketts, M Comabella, N Hammond, I Kockum, OT McCann, M Ban, P Whittaker, A Kemppinen, P Weston, C Hawkins, S Widaa, J Zajicek, S Dronov, N Robertson, SJ Bumpstead, LF Barcellos, R Ravindrarajah, R Abraham, L Alfredsson, K Ardlie, C Aubin, A Baker, K Baker, SE Baranzini, L Bergamaschi, R Bergamaschi, A Bernstein, A Berthele, M Boggild, JP Bradfield, D Brassat, SA Broadley, D Buck, H Butzkueven, R Capra, WM Carroll, P Cavalla, EG Celius, S Cepok, R Chiavacci, F Clerget-Darpoux, K Clysters, G Comi, M Cossburn, I Cournu-Rebeix, MB Cox, W Cozen, BA Cree, AH Cross, D Cusi, MJ Daly, E Davis, PI de Bakker, M Debouverie, MB D'hooghe, K Dixon, R Dobosi, B Dubois, D Ellinghaus, I Elovaara, F Esposito, C Fontenille, S Foote, A Franke, D Galimberti, A Ghezzi, J Glessner, R Gomez, O Gout, C Graham, SF Grant, FR Guerini, H Hakonarson, P Hall, A Hamsten, HP Hartung, RN Heard, S Heath, J Hobart, M Hoshi, C Infante-Duarte, G Ingram, W Ingram, T Islam, M Jagodic, M Kabesch, AG Kermode, TJ Kilpatrick, C Kim, N Klopp, K Koivisto, M Larsson, M Lathrop, JS Lechner-Scott, MA Leone, V Leppä, U Liljedahl, IL Bomfim, RR Lincoln, J Link, J Liu, AR Lorentzen, S Lupoli, F Macciardi, T Mack, M Marriott, V Martinelli, D Mason, JL McCauley, F Mentch, IL Mero, T Mihalova, X Montalban, J Mottershead, KM Myhr, P Naldi, W Ollier, A Page, A Palotie, J Pelletier, L Piccio, T Pickersgill, F Piehl, S Pobywajlo, HL Quach, PP Ramsay, M Reunanen, R Reynolds, JD Rioux, M Rodegher, S Roesner, JP Rubio, IM Rückert, M Salvetti, E Salvi, A Santaniello, CA Schaefer, S Schreiber, C Schulze, RJ Scott, F Sellebjerg, KW Selmaj, D Sexton, L Shen, B Simms-Acuna, S Skidmore, PM Sleiman, C Smestad, PS Sørensen, HB Søndergaard, J Stankovich, RC Strange, AM Sulonen, E Sundqvist, AC Syvänen, F Taddeo, B Taylor, JM Blackwell, P Tienari, E Bramon, A Tourbah, MA Brown, E Tronczynska, JP Casas, N Tubridy, A Corvin, J Vickery, J Jankowski, P Villoslada, HS Markus, K Wang, CG Mathew, J Wason, CN Palmer, HE Wichmann, R Plomin, E Willoughby, A Rautanen, J Winkelmann, M Wittig, RC Trembath, J Yaouanq, AC Viswanathan, H Zhang, NW Wood, R Zuvich, P Deloukas, C Langford, A Duncanson, JR Oksenberg, MA Pericak-Vance, JL Haines, T Olsson, J Hillert, AJ Ivinson, PL De Jager, L Peltonen, GJ Stewart, DA Hafler, SL Hauser, G McVean, P Donnelly, A Compston
Differential gene expression in nucleus accumbens somatostatin interneurons_cocaine_mice_pvalue
Description:
To characterize transcriptional alterations that cocaine induces in these cells, we perform cell type-specific RNA-sequencing on FACS-isolated nuclei of somatostatin interneurons and identified 1100 DETs enriched for processes related to neural plasticity. To profile the entire (non poly-A selected) transcriptome of NAc somatostatin interneurons, we generated a transgenic reporter line (SST-TLG498 mice) to label the nuclei of these cells with a modified form of EGFP that is retained in the nuclear membrane (EGFP-F)22, enabling their isolation from NAc dissections using FACS. We succeeded in FACS-isolating nuclei suitable for RNA-sequencing from individual SST-TLG498 mice. We proceeded with differential expression analysis of the RNA-sequencing data to identify differentially expressed transcripts (DETs) in NAc somatostatin interneurons in response to repeated cocaine exposure: 778 transcripts were upregulated by cocaine and 322 were downregulated.
Authors:
Efrain A Ribeiro, Marine Salery, Joseph R Scarpa, Erin S Calipari, Peter J Hamilton, Stacy M Ku, Hope Kronman, Immanuel Purushothaman, Barbara Juarez, Mitra Heshmati, Marie Doyle, Casey Lardner, Dominicka Burek, Ana Strat, Stephen Pirpinias, Ezekiell Mouzon, Ming-Hu Han, Rachael L Neve, Rosemary C Bagot, Andrew Kasarskis, Ja Wook Koo, Eric J Nestler
Genes identified as expressed higher (up) in the AJ strain than in the NOD strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the NOD strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
We investigated the role of microglia in a mouse model of alcohol dependence using a colony stimulating factor 1 receptor inhibitor (PLX5622) to deplete microglia and a chronic intermittent ethanol vapor two-bottle choice drinking procedure. Additionally, we examined anxiety-like behavior during withdrawal. We then analyzed synaptic neuroadaptations in the central nucleus of the amygdala (CeA) and gene expression changes in the medial prefrontal cortex (mPFC) and CeA from the same animals used for behavioral studies.
Genes identified as expressed higher (up) in the AJ strain than in the AJ strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the AJ strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Microglia depletion and alcohol gene expression logFC
Description:
Alcohol abuse induces changes in microglia morphology and immune function, but whether microglia initiate or simply amplify the harmful effects of alcohol exposure is still a matter of debate. Here, we determine microglia function in acute and voluntary drinking behaviors using a colony-stimulating factor 1 receptor inhibitor (PLX5622). We show that microglia depletion does not alter the sedative or hypnotic effects of acute intoxication. Microglia depletion also does not change the escalation or maintenance of chronic voluntary alcohol consumption. Transcriptomic analysis revealed that although many immune genes have been implicated in alcohol abuse, down regulation of microglia genes does not necessitate changes in alcohol intake. Instead, microglia depletion and chronic alcohol result in compensatory upregulation of alcohol-responsive, reactive astrocyte genes, indicating astrocytes may play a role in regulation of these alcohol behaviors. Taken together, our behavioral and transcriptional data indicate that microglia are not theprimary effector cell responsible for regulation of acute and voluntary alcohol behaviors. Because microglia depletion did not regulate acute or voluntary alcohol behaviors, we hypothesized that these doses were insufficient to activate microglia and recruit them to an effector phenotype. Therefore, we used a model of repeated immune activation using polyinosinic:polycytidylic acid
Alcohol transcriptome changes in mice microglia total homogenate p-value
Description:
Microglia are fundamentally important immune cells within the central nervous system (CNS) that respond to environmental challenges to maintain normal physiological processes. Alterations in steady-state cellular function and over-activation of microglia can facilitate the initiation and progression of neuropathological conditions such as Alzheimer’s disease, Multiple Sclerosis, and Major Depressive Disorder. Alcohol consumption disrupts signaling pathways including both innate and adaptive immune responses that are necessary for CNS homeostasis. Coordinate expression of these genes is not ascertained from an admixture of CNS cell-types, underscoring the importance of examining isolated cellular populations to reveal systematic gene expression changes arising from mature microglia. Unbiased RNA-Seq profiling was used to identify gene expression changes in isolated prefrontal cortical microglia in response to recurring bouts of voluntary alcohol drinking behavior. The voluntary ethanol paradigm utilizes long-term consumption ethanol that results in escalated alcohol intake and altered cortical plasticity that is seen in humans. Gene coexpression analysis identified a coordinately regulated group of genes, unique to microglia, that collectively are associated with alcohol consumption. Genes within this group are involved in toll-like receptor signaling and transforming growth factor beta signaling. Network connectivity of this group identified Siglech as a putative hub gene and highlighted the potential importance of proteases in the microglial response to chronic ethanol. In conclusion, we identified a distinctive microglial gene expression signature for neuroimmune responses related to alcohol consumption that provides valuable insight into microglia-specific changes underlying the development of substance abuse, and possibly other CNS disorders.
Authors:
Gizelle M McCarthy, Sean P Farris, Yuri A Blednov, R Adron Harris, R Dayne Mayfield
Alcohol Microglia depletion in the medial prefrontal cortex q-value
Description:
dependence using a colony stimulating factor 1 receptor inhibitor (PLX5622) to deplete microglia and a chronic intermittent ethanol vapor two-bottle choice drinking procedure. Additionally, we examined anxiety-like behavior during withdrawal. We then analyzed synaptic neuroadaptations in the central nucleus of the amygdala (CeA) and gene expression changes in the medial prefrontal cortex (mPFC) and CeA from the same animals used for behavioral studies.
Alcohol Use Disorder (AUD) is a chronic, relapsing syndrome diagnosed by a heteroge- neous set of behavioral signs and symptoms. There are no laboratory tests that provide direct objective evidence for diagnosis. Microarray and RNA-Seq technologies enable genome-wide transcriptome profiling at low costs and provide an opportunity to identify bio- markers to facilitate diagnosis, prognosis, and treatment of patients. However, access to brain tissue in living patients is not possible. Blood contains cellular and extracellular RNAs that provide disease-relevant information for some brain diseases. We hypothesized that blood gene expression profiles can be used to diagnose AUD. We profiled brain (prefrontal cortex, amygdala, and hypothalamus) and blood gene expression levels in C57BL/6J mice using RNA-seq one week after chronic intermittent ethanol (CIE) exposure, a mouse model of alcohol dependence. We found a high degree of preservation (rho range: [0.50, 0.67]) between blood and brain transcript levels. There was small overlap between blood and brain DEGs, and considerable overlap of gene networks perturbed after CIE related to cell- cell signaling (e.g., GABA and glutamate receptor signaling), immune responses (e.g., anti- gen presentation), and protein processing / mitochondrial functioning (e.g., ubiquitination, oxidative phosphorylation). Blood gene expression data were used to train classifiers (logis- tic regression, random forest, and partial least squares discriminant analysis), which were highly accurate at predicting alcohol dependence status (maximum AUC: 90.1%). These results suggest that gene expression profiles from peripheral blood samples contain a bio- logical signature of alcohol dependence that can discriminate between CIE and Air subjects.
Authors:
Laura B Ferguson, Amanda J Roberts, R Dayne Mayfield, Robert O Messing
Alcohol use disorder (AUD) is a complex psychiatric disorder with strong genetic and environmental risk factors. We studied the molecular perturbations underlying risky drinking behavior by measuring transcriptome changes across the neurocircuitry of addiction in a genetic mouse model of binge drinking. Sixteen generations of selective breeding for high blood alcohol levels after a binge drinking session produced global changes in brain gene expression in alcohol-naïve High Drinking in the Dark (HDID-1) mice. Using gene expression profiles to generate circuit-level hypotheses, we developed a systems approach that integrated regulation of gene coexpression networks across multiple brain regions, neuron-specific transcriptional signatures, and knowledgebase analytics. Whole-cell, voltage-clamp recordings from nucleus accumbens shell neurons projecting to the ventral tegmental area showed differential ethanol-induced plasticity in HDID-1 and control mice and provided support for one of the hypotheses. There were similarities in gene networks between HDID-1 mouse brains and postmortem brains of human alcoholics, suggesting that some gene expression patterns associated with high alcohol consumption are conserved across species. This study demonstrated the value of gene networks for data integration across biological modalities and species to study mechanisms of disease.
Authors:
Laura B Ferguson, Lingling Zhang, Daniel Kircher, Shi Wang, R Dayne Mayfield, John C Crabbe, Richard A Morrisett, R Adron Harris, Igor Ponomarev
Genes identified as expressed higher (up) in the AJ strain than in the CAST strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the CAST strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Microglia depletion and alcohol gene expression p-value
Description:
Alcohol abuse induces changes in microglia morphology and immune function, but whether microglia initiate or simply amplify the harmful effects of alcohol exposure is still a matter of debate. Here, we determine microglia function in acute and voluntary drinking behaviors using a colony-stimulating factor 1 receptor inhibitor (PLX5622). We show that microglia depletion does not alter the sedative or hypnotic effects of acute intoxication. Microglia depletion also does not change the escalation or maintenance of chronic voluntary alcohol consumption. Transcriptomic analysis revealed that although many immune genes have been implicated in alcohol abuse, down regulation of microglia genes does not necessitate changes in alcohol intake. Instead, microglia depletion and chronic alcohol result in compensatory upregulation of alcohol-responsive, reactive astrocyte genes, indicating astrocytes may play a role in regulation of these alcohol behaviors. Taken together, our behavioral and transcriptional data indicate that microglia are not theprimary effector cell responsible for regulation of acute and voluntary alcohol behaviors. Because microglia depletion did not regulate acute or voluntary alcohol behaviors, we hypothesized that these doses were insufficient to activate microglia and recruit them to an effector phenotype. Therefore, we used a model of repeated immune activation using polyinosinic:polycytidylic acid
Alcohol use disorder (AUD) is a complex psychiatric disorder with strong genetic and environmental risk factors. We studied the molecular perturbations underlying risky drinking behavior by measuring transcriptome changes across the neurocircuitry of addiction in a genetic mouse model of binge drinking. Sixteen generations of selective breeding for high blood alcohol levels after a binge drinking session produced global changes in brain gene expression in alcohol-naïve High Drinking in the Dark (HDID-1) mice. Using gene expression profiles to generate circuit-level hypotheses, we developed a systems approach that integrated regulation of gene coexpression networks across multiple brain regions, neuron-specific transcriptional signatures, and knowledgebase analytics. Whole-cell, voltage-clamp recordings from nucleus accumbens shell neurons projecting to the ventral tegmental area showed differential ethanol-induced plasticity in HDID-1 and control mice and provided support for one of the hypotheses. There were similarities in gene networks between HDID-1 mouse brains and postmortem brains of human alcoholics, suggesting that some gene expression patterns associated with high alcohol consumption are conserved across species. This study demonstrated the value of gene networks for data integration across biological modalities and species to study mechanisms of disease.
Authors:
Laura B Ferguson, Lingling Zhang, Daniel Kircher, Shi Wang, R Dayne Mayfield, John C Crabbe, Richard A Morrisett, R Adron Harris, Igor Ponomarev
Genes associated with Mus musculus that interact with the MeSH term 'Tetrachlorodibenzodioxin' (D013749). Incorporates data from 2 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Mus musculus that interact with the MeSH term 'Tetracaine' (D013748). Incorporates data from 12365 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Mus musculus that interact with the MeSH term 'Acetaminophen' (D000082). Incorporates data from 2 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Alcohol transcriptome changes in mice microglia p-value
Description:
Microglia are fundamentally important immune cells within the central nervous system (CNS) that respond to environmental challenges to maintain normal physiological processes. Alterations in steady-state cellular function and over-activation of microglia can facilitate the initiation and progression of neuropathological conditions such as Alzheimer’s disease, Multiple Sclerosis, and Major Depressive Disorder. Alcohol consumption disrupts signaling pathways including both innate and adaptive immune responses that are necessary for CNS homeostasis. Coordinate expression of these genes is not ascertained from an admixture of CNS cell-types, underscoring the importance of examining isolated cellular populations to reveal systematic gene expression changes arising from mature microglia. Unbiased RNA-Seq profiling was used to identify gene expression changes in isolated prefrontal cortical microglia in response to recurring bouts of voluntary alcohol drinking behavior. The voluntary ethanol paradigm utilizes long-term consumption ethanol that results in escalated alcohol intake and altered cortical plasticity that is seen in humans. Gene coexpression analysis identified a coordinately regulated group of genes, unique to microglia, that collectively are associated with alcohol consumption. Genes within this group are involved in toll-like receptor signaling and transforming growth factor beta signaling. Network connectivity of this group identified Siglech as a putative hub gene and highlighted the potential importance of proteases in the microglial response to chronic ethanol. In conclusion, we identified a distinctive microglial gene expression signature for neuroimmune responses related to alcohol consumption that provides valuable insight into microglia-specific changes underlying the development of substance abuse, and possibly other CNS disorders.
Authors:
Gizelle M McCarthy, Sean P Farris, Yuri A Blednov, R Adron Harris, R Dayne Mayfield
GeneWeaver