Effects of Genetics and Sex on Hippocampal Gene Expression and Adolescent Behaviors Following Neonatal Ethanol Exposure in BXD Recombinant Inbred Mice

Author(s):  
◽  
Jessica Baker ◽  

Fetal alcohol spectrum disorders (FASD) are the leading preventable neurodevelopmental disorders in the western world. A hallmark symptom of FASD is cognitive and learning deficits that present in early childhood and continue throughout adulthood. Teratogenic effects of alcohol include increased cell death in the hippocampus, a brain region critically important in learning and memory. Genetics have been shown to have a role in the severity of alcohol’s teratogenic effect on the developing brain. Previous work in our lab identified differential vulnerability to ethanol-induced call death in the hippocampus using fourteen BXD strains and the two parental strains. The goal of the present study was to examine the effect of genetics and sex on differential gene expression changes and behavioral responses in animals exposed to postnatal ethanol. To test this, we examined multiple BXD strains that showed increased susceptibility to ethanol-induced cell death in the hippocampus, multiple BXD strains that were resistant to ethanol’s effect on hippocampal cell death, and the parental B6 and D2 strains which showed moderate levels of cell death in the hippocampus after ethanol exposure. Neonatal mice were treated on postnatal day 7 (third trimester equivalent in humans). Animals received a subcutaneous injection of either 5.0g/kg ethanol in saline solution or isovolumetric saline given in two equal doses two hours apart. Animals were sacrificed 7 hours after initial ethanol exposure. Differential gene expression was examined using the Affymetrix Microarray platform across the strains. In another subset of animals exposed to the same alcohol paradigm, we investigated the long-term effects of developmental alcohol exposure on cognition and behavior in select BXD strains and parental strains. Adolescent animals exposed to postnatal ethanol were tested across the following behavioral tests: elevated plus maze, open field, Y-maze, and T-maze. We identified gene expression changes after postnatal ethanol exposure in all BXD and parental strains with little overlap between males and females in the same strain. However, there were limited gene expression changes that showed a sex x treatment interaction. Sex-specific ethanol-induced gene expression changes were limited within each strain and these changes were not carried over across strains. Multiple genes showed a significant interaction between strain x treatment and/or strain x sex x treatment. Enrichment analysis of these genes revealed a number of significant over-represented biological categories involved in cell death and apoptosis. Genes that met our criteria and were also highly correlated with a number of apoptosis and learning and memory behaviors included Bcl2l11, Jun, Txnip, Chka, and Tgfb3. Interestingly, Tgfb3 has been previously linked to a significant QTL mediating strain-specific differences in hippocampal cell death after exposure to postnatal ethanol in BXD mice. When comparing ethanol-induced gene expression changes in high cell death strains (HCD) and low cell death strains (LCD), we observed almost double the number of differentially ethanol-induced gene expression changes in the HCD strains compared to the LCD strains. Enrichment analysis revealed some overlap in significant over-represented categories between the HCD and LCD strains, though HCD showed more cell death and apoptosis categories. Significant ethanol-induced gene expression changes in the HCD and LCD strains were always regulated in the same direction suggesting 1) more perturbed effects of ethanol-induced gene expression changes in the HCD strains compared to LCD strains and 2) limited gene expression changes that confer resistance to ethanol-induced cell death in the hippocampus in the LCD strains. In our behavioral study, our results demonstrate that the effects of developmental alcohol exposure on adolescent behavioral responses are highly dependent on strain, though the strains that showed the most behavioral alterations after exposure to postnatal alcohol were the B6 and D2 parental strains and the BXD100 and BXD48a HCD strains. In these four strains, we observed many anxiety-like and activity-related behaviors that were significantly affected by postnatal ethanol exposure and in many of these measures there were sex-specific differences within the strain. The LCD strains, BXD60 and BXD71, showed minimal effect of treatment in all behavioral tests. Interestingly, the HCD strains, BXD100 and BXD48a, were the only strains that showed significant effect of postnatal ethanol exposure in hippocampal-dependent spatial learning and memory assessment. These results suggest that there are long-term effects of developmental alcohol exposure on adolescent behavior and that these effects are highly strain specific. Overall, our study aimed to better understand genetic variation in ethanol-induced susceptibility to ethanol’s teratogenic effects. Our results accomplish this by identifying differential gene expression changes and behavioral responses in animals exposed to postnatal ethanol using the BXD RI mice and parental strains. Additionally, our study identified sex differences in both ethanol-induced gene expression changes and adolescent behaviors in mice exposed to postnatal ethanol, though sex-specific effects were highly dependent on strain. To our knowledge, this is the first study using the BXD RI strains to examine the effects of genetics and sex on 1) ethanol-induced gene expression changes during development, and 2) adolescent behaviors in mice exposed to postnatal ethanol.

2015 ◽  
Vol 309 (7) ◽  
pp. L677-L686 ◽  
Author(s):  
Georgios D. Vavougios ◽  
Evgeniy I. Solenov ◽  
Chrissi Hatzoglou ◽  
Galina S. Baturina ◽  
Liubov E. Katkova ◽  
...  

The aim of our study was to assess the differential gene expression of Parkinson protein 7 (PARK7) interactome in malignant pleural mesothelioma (MPM) using data mining techniques to identify novel candidate genes that may play a role in the pathogenicity of MPM. We constructed the PARK7 interactome using the ConsensusPathDB database. We then interrogated the Oncomine Cancer Microarray database using the Gordon Mesothelioma Study, for differential gene expression of the PARK7 interactome. In ConsensusPathDB, 38 protein interactors of PARK7 were identified. In the Gordon Mesothelioma Study, 34 of them were assessed out of which SUMO1, UBC3, KIAA0101, HDAC2, DAXX, RBBP4, BBS1, NONO, RBBP7, HTRA2, and STUB1 were significantly overexpressed whereas TRAF6 and MTA2 were significantly underexpressed in MPM patients ( network 2). Furthermore, Kaplan-Meier analysis revealed that MPM patients with high BBS1 expression had a median overall survival of 16.5 vs. 8.7 mo of those that had low expression. For validation purposes, we performed a meta-analysis in Oncomine database in five sarcoma datasets. Eight network 2 genes (KIAA0101, HDAC2, SUMO1, RBBP4, NONO, RBBP7, HTRA2, and MTA2) were significantly differentially expressed in an array of 18 different sarcoma types. Finally, Gene Ontology annotation enrichment analysis revealed significant roles of the PARK7 interactome in NuRD, CHD, and SWI/SNF protein complexes. In conclusion, we identified 13 novel genes differentially expressed in MPM, never reported before. Among them, BBS1 emerged as a novel predictor of overall survival in MPM. Finally, we identified that PARK7 interactome is involved in novel pathways pertinent in MPM disease.


F1000Research ◽  
2018 ◽  
Vol 5 ◽  
pp. 1384 ◽  
Author(s):  
Bernd Klaus ◽  
Stefanie Reisenauer

In this article, we walk through an end-to-end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current "Gene'' type arrays, e.g.the HuGene or MoGene arrays, but can easily be adapted to similar platforms. The data analyzed here is a typical clinical microarray data set that compares inflamed and non-inflamed colon tissue in two disease subtypes. For each disease, the differential gene expression between inflamed- and non-inflamed colon tissue was analyzed. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis.


2021 ◽  
Vol 12 ◽  
Author(s):  
Sneha S. Mokashi ◽  
Vijay Shankar ◽  
Rebecca A. MacPherson ◽  
Rachel C. Hannah ◽  
Trudy F. C. Mackay ◽  
...  

Fetal alcohol exposure can lead to developmental abnormalities, intellectual disability, and behavioral changes, collectively termed fetal alcohol spectrum disorder (FASD). In 2015, the Centers for Disease Control found that 1 in 10 pregnant women report alcohol use and more than 3 million women in the USA are at risk of exposing their developing fetus to alcohol. Drosophila melanogaster is an excellent genetic model to study developmental effects of alcohol exposure because many individuals of the same genotype can be reared rapidly and economically under controlled environmental conditions. Flies exposed to alcohol undergo physiological and behavioral changes that resemble human alcohol-related phenotypes. Here, we show that adult flies that developed on ethanol-supplemented medium have decreased viability, reduced sensitivity to ethanol, and disrupted sleep and activity patterns. To assess the effects of exposure to alcohol during development on brain gene expression, we performed single cell RNA sequencing and resolved cell clusters with differentially expressed genes which represent distinct neuronal and glial populations. Differential gene expression showed extensive sexual dimorphism with little overlap between males and females. Gene expression differences following developmental alcohol exposure were similar to previously reported differential gene expression following cocaine consumption, suggesting that common neural substrates respond to both drugs. Genes associated with glutathione metabolism, lipid transport, glutamate and GABA metabolism, and vision feature in sexually dimorphic global multi-cluster interaction networks. Our results provide a blueprint for translational studies on alcohol-induced effects on gene expression in the brain that may contribute to or result from FASD in human populations.


F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1384 ◽  
Author(s):  
Bernd Klaus

In this article, we walk through an end–to–end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current “Gene” type arrays, e.g. the HuGene or MoGene arrays but can easily adapted to similar platforms. The data re–analyzed is a typical clinical microarray data set that compares inflammed and non–inflammed colon tissue in two disease subtypes. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis. As experimental designs can be complex, a self contained introduction to linear models is also part of the workflow.


2020 ◽  
Vol 11 ◽  
Author(s):  
Patrick Douglas Corrêa Pereira ◽  
Ediely Pereira Henrique ◽  
Danillo Monteiro Porfírio ◽  
Caio César de Sousa Crispim ◽  
Maitê Thaís Barros Campos ◽  
...  

2009 ◽  
Vol 23 (6) ◽  
pp. 1869-1879 ◽  
Author(s):  
Carlos Penaloza ◽  
Brian Estevez ◽  
Shari Orlanski ◽  
Marianna Sikorska ◽  
Roy Walker ◽  
...  

2010 ◽  
Vol 126 (4) ◽  
pp. 497-505 ◽  
Author(s):  
Virginia Sánchez Monroy ◽  
Ma. Olivia Medel Flores ◽  
José D’Artagnan Villalba-Magdaleno ◽  
Consuelo Gómez Garcia ◽  
David Guillermo Pérez Ishiwara

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