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BacTRAP profiling of astrocytes in five mouse brain regions in wildtype controls and hippocampus region in a Alzheimer's disease mouse model

ABSTRACT: We experimentally generated astrocyte gene expression profiles in five major brain regions in mouse: prefrontal cortex (P), hippocampus (H), amygdala (A), caudate nucleus (C) and ventral striatum (V) (Figure 1A, Methods), with more than three biological replicates in each region. To derive the differences between the regional transcriptional profiles, we utilized TRAP-seq, a method that enables detailed profiling of actively translated mRNA, rather than just transcribed mRNA, thus better capturing the functional state of the cell. This approach enables us to generate ex vivo region-specific astrocyte signatures.

ORGANISM(S): Mus musculus

PROVIDER: GSE310518 | GEO | 2025/12/20

REPOSITORIES: GEO

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Project description:Neurotoxicology is hampered by the inability to predict regional and cellular targets of toxicant-induced damage. Evaluating astrogliosis overcomes this problem because reactive astrocytes highlight the location of toxicant-induced damage. While enhanced expression of glial fibrillary acidic protein is a hallmark of astrogliosis, few other biomarkers have been identified. However, bacterial artificial chromosome - translating ribosome affinity purification (bacTRAP) technology allows for characterization of the actively translating transcriptome of a particular cell type; use of this technology in aldehyde dehydrogenase 1 family member L1 (ALDH1L1) bacTRAP mice can identify genes selectively expressed in astrocytes. The aim of this study was to characterize additional biomarkers of neurotoxicity-induced astrogliosis using ALDH1L1 bacTRAP mice. The known dopaminergic neurotoxicant 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP; 12.5 mg/kg s.c.) was used to induce astrogliosis. Striatal tissue was obtained 12, 24, and 48 h following exposure for the isolation of actively translating RNA. Subsequently, MPTP-induced changes in this RNA pool were analyzed by microarray and 184 statistically significant, differentially expressed genes were identified. The dataset was interrogated by gene ontology, pathway, and co-expression network analyses, which identified novel genes, as well as those with known immune and inflammatory functions. Using these analyses, we were directed to several genes associated with reactive astrocytes. Of these, TIMP1 and miR-147 were identified as candidate biomarkers because of their robust increased expression following both MPTP and trimethyl tin exposures. Thus, we have demonstrated that bacTRAP can be used to identify new biomarkers of astrogliosis and aid in the characterization of astrocyte phenotypes induced by toxicant exposures. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/. Cover Image for this issue: doi: 10.1111/jnc.14518.

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BacTRAP profiling of astrocytes in five mouse brain regions in wildtype controls and hippocampus region in a Alzheimer's disease mouse model

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