Ethanol induced transcriptional and translational changes in Aldh1l1-EGFP/Rpl10a cortical astrocyte cultures
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ABSTRACT:
PROVIDER: PRJNA947241 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23934006_1.fastq.gz | Fastqsanger.gz | |||
| SRR23934006_2.fastq.gz | Fastqsanger.gz | |||
| SRR23934007_1.fastq.gz | Fastqsanger.gz | |||
| SRR23934007_2.fastq.gz | Fastqsanger.gz | |||
| SRR23934008_1.fastq.gz | Fastqsanger.gz |
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Project description:The role astrocytes play in brain development and function has come under increased focus as the diversity of roles they are involved in has become apparent. We have previously shown ethanol exposed astrocytes alter neuronal neurite outgrowth in an in vitro co-culture system and that ethanol alters the astrocyte produced extracellular matrix (ECM) in vitro, with similar alterations in vivo. Here we utilize the translating ribosome affinity purification (TRAP) procedure in Aldh1l1-EGFP/Rpl10a transgenic mouse primary cortical astrocyte cultures to transcriptionally and translationally profile the astrocyte response to ethanol. We found large differences in the total RNA pool in comparison to the translating RNA pool while the ethanol response within each pool showed a large degree of overlap. Comparisons to published datasets indicate the in vitro model used here are most similar to PD1-PD7 in vivo cortical astrocytes and the ethanol regulated genes showed significant overlap with models of chronic ethanol exposure in astrocytes and a model of third-trimester ethanol exposure in the hippocampus and cerebellum. These findings will further our understanding of the effects of ethanol on astrocyte gene expression and protein translation and how these changes alter brain development.
2023-06-21 | GSE227891 | GEO
Project description:Background: Fetal Alcohol Spectrum Disorders (FASD) cause life-long cognitive and behavioral impairment and are highly prevalent across the world. The effects of developmental ethanol exposure on astrocyte functions in vivo are poorly understood. To fill this gap, we assessed changes in the astrocyte translatome following in vivo developmental ethanol exposure and mechanistically linked some of these changes to altered neuronal development. Methods: The translating RNA from hippocampal astrocytes of neonatal Aldh1l1-EGFP-Rpl10a mice exposed to ethanol was isolated by Translating Ribosomal Affinity Purification and sequenced; neuronal dendritic morphology was assessed by Golgi-Cox staining and morphometric analysis; chondroitin sulfate glycosaminoglycan (CS-GAG) disaccharides were measured by Liquid Chromatography/Mass Spectrometry; neurite outgrowth was assessed in in vitro hippocampal neurons incubated in the presence of astrocyte-conditioned medium prepared from control and Chpf2-silenced astrocytes. Results: Translatome results suggested that ethanol alters mechanisms of astrocyte-neuron interactions involved in neuronal development. Moreover, ethanol increased dendritic arborization in hippocampal pyramidal neurons, inhibited the astrocyte translation of enzymes involved in the biosynthesis of inhibitory CS-GAGs, and decreased the levels of disaccharides forming CS-GAGs in vivo. Lastly, the silencing of CS-GAG biosynthetic enzyme Chpf2 in astrocyte cultures increased neurite branching of hippocampal neuron in vitro. Conclusions: Translatome analysis revealed novel effects of developmental ethanol exposure on astrocytes and provided mechanistic insights into altered brain development possibly relevant to the pathophysiology of FASD. We also identified a novel mechanism by which ethanol-induced reduction of astrocyte-produced inhibitory extracellular matrix components CS-GAGs increases dendritic arborization.
2024-09-30 | GSE272272 | GEO
Project description:The CCM endothelium is hypersensitive to angiogenesis and can induce a hypoxic program associated with changes in angiogenesis, inflammation, and endothelial-cell metabolism under normoxic conditions. However, the role of active drivers of angiogenesis as CCM disease modifiers in human disease remains unclear. To assess whether CCM reactive astrocytes with neuroinflammatory capacity respond to hypoxia-induced CCM exacerbation, we employed the astrocyte-specific (Aldh1l1-EGFP/Rpl10a) Translational Ribosome Affinity Purification (TRAP) system in combination with a CCM mouse model (Pdcd10BECKO;Aldh1l1-EGFP/Rpl10a). TRAP protocol was performed using Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice to isolate ribosomes from astrocytes as previously described. Astrocyte-TRAP mRNAs were from cerebral tissue of mice age P50 exposed to hypoxia or normoxia conditions.
2024-09-23 | GSE236162 | GEO
Project description:The role astrocytes play in brain development and function has garnered greater attention as the diversity of roles they are involved in has become apparent. We have previously shown that ethanol-exposed astrocytes alter neuronal neurite outgrowth in an in vitro co-culture system and that ethanol alters the astrocyte-produced extracellular matrix (ECM) in vitro, with similar alterations in vivo. In this study, we utilized the translating ribosome affinity purification (TRAP) procedure in Aldh1l1-EGFP/Rpl10a transgenic mouse primary cortical astrocyte cultures to transcriptionally and translationally profile the astrocyte response to ethanol. We found a large number of differences between the total RNA pool and the translating RNA pool, indicating that the transcriptional state of astrocytes may not always reflect the translational state of astrocytes. In addition, there was a considerable overlap between ethanol-dysregulated genes in the total RNA pool and the translating RNA pool. Comparisons to published datasets indicate the in vitro model used here is most similar to PD1 or PD7 in vivo cortical astrocytes, and the ethanol-regulated genes showed a significant overlap with models of chronic ethanol exposure in astrocytes, a model of third-trimester ethanol exposure in the hippocampus and cerebellum, and an acute model of ethanol exposure in the hippocampus. These findings will further our understanding of the effects of ethanol on astrocyte gene expression and protein translation and how these changes may alter brain development and support the use of in vitro astrocyte cultures as models of neonatal astrocytes.
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Project description:BAC array purification of hippocampus astroglial ribosome-bound transcriptome in astrocytes from Aldh1l1:Rpl10a eGFP/ Cx43 KO and Aldh1l1:Rpl10a eGFP/ Cx43FL mice
2019-05-22 | GSE110721 | GEO
Project description:Comparing the expression of FACS wildtype forebrain P7 Aldh1l1-EGFP cells with mutant (hGFAP-Cre:dicer1/dicer1) forebrain P7 Aldh1l1-EGFP cells and Ald1l1-EGFP positive primary astrocytes
2014-10-09 | E-MTAB-2995 | biostudies-arrayexpress
Project description:Gene expression analysis was performed in Gfap+/+, Gfap+/R236H, and mGFAPTg170-2 transgenic mice, using the Aldh1l1-eGFP-L10a transgenic line (JD130) to isolate translating ribosomes and purify astrocyte specific transcripts for RNAseq.
2023-01-17 | GSE198817 | GEO
Project description:Aldh1l1-EGFP cells were FACS and isolated from postnatal day 7 mouse forebrains. Total RNAs were then isolated and analyzed for microRNA expression.
2015-02-24 | E-MTAB-3336 | biostudies-arrayexpress
Project description:The Khakh laboratory sequenced RNA from both whole and astrocyte specific RNAs from mouse prefrontal cortex and visual cortex by using Aldh1l1-CreERT2 - RiboTag mice. RNA was purified from controls and LPS injected mice, 1, 2 and 14 days after the injection.
2021-08-10 | GSE135110 | GEO
Project description:The cytoskeletal protein tubulin plays an integral role in the functional specialization of many cell types. In the central nervous system, post-translational modifications and the expression of specific tubulin isotypes in neurons have been analyzed in greater detail than in their astrocytic counterparts. In this study, we characterized post-translational specifications of tubulin in human astrocytes using the normal human astrocyte (NHA; Lonza) commercial cell line of fetal origin. Immunocytochemical techniques were implemented in conjunction with confocal microscopy to image class III ?-tubulin (?III-tubulin), acetylated tubulin, and polyglutamylated tubulin using fluorescent antibody probes. Fluorescent probe intensity differences and colocalization were quantitatively assessed with the 'EBImage' package for the statistical programming language R. Colocalization analysis revealed that, although both acetylated tubulin and polyglutamylated tubulin showed a high degree of correlation with ?III-tubulin, the correlation with acetylated tubulin was stronger. Quantification and statistical analysis of fluorescence intensity demonstrated that the fluorescence probe intensity ratio for acetylated tubulin/?III-tubulin was greater than the ratio for polyglutamylated tubulin/?III-tubulin. The open source GEODATA set GSE819950, comprising RNA sequencing data for the NHA cell line, was mined for the expression of enzymes responsible for tubulin modifications. Our analysis uncovered greater expression at the mRNA level for enzymes reported to function in acetylation and deacetylation as compared to enzymes implicated in glutamylation and deglutamylation. Taken together, the results represent a step toward unraveling the tubulin isotypic expression profile and post-translational modification patterns in astrocytes during human brain development.
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