Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression data of cultured primary microglia from neonatal control and Cstb-/- mice.

ABSTRACT: Cystain B (Cstb) is a ubiquitously expressed cysteine protease inhibitor and mutations of the CSTB gene lead to the neurodegenerative disease progressive myoclonus epilepsy of Unverricht-Lundorg type (EPM1). We are interested in the microglia-specific, Cstb-dependent gene-expression changes in mice and in this data set, we include gene-level expression data from cultured primary microglia of control and Cstb-/- mice extracted from neonatal mice at P5 and we identified 156 differentially-expressed genes in Cstb-/- microglia. We analyzed 8 samples in total and we compared 4 control microglia samples to 4 Cstb-/- microglia samples. Genes with a fold change > 1.3 and with p < 0.05 in T-test with BH correction were considered differentially expressed.

ORGANISM(S): Mus musculus

SUBMITTER: Inken KÃ¶rber

PROVIDER: E-GEOD-64823 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Objective: Brain tumors (gliomas) contain large populations of infiltrating macrophages and recruited microglia, which in experimental murine glioma models promote tumor formation and progression. Among the barriers to understanding the contributions of these stromal elements to high-grade glioma (glioblastoma; GBM) biology is the relative paucity of tools to characterize infiltrating macrophages and resident microglia. In this study, we leveraged multiple RNA analysis platforms to identify new monocyte markers relevant to GBM patient outcome. Methods: High-confidence lists of mouse resident microglia- and bone marrow-derived macrophage-specific transcripts were generated using converging RNA-seq and microarray technologies and validated using qRT-PCR and flow cytometry. Expression of select cell surface markers was analyzed in brain-infiltrating macrophages and resident microglia in an induced GBM mouse model, while allogeneic bone marrow transplantation was performed to trace the origins of infiltrating and resident macrophages. Glioma tissue microarrays were examined by immunohistochemistry, and the Gene Expression Omnibus (GEO) database was queried to determine the prognostic value of identified microglia biomarkers in human GBM. Results: We generated a unique catalog of differentially-expressed bone marrow-derived monocyte and resident microglia transcripts, and demonstrated that brain-infiltrating macrophages acquire F11R expression in GBM and following bone-marrow transplantation. Moreover, mononuclear cell F11R expression positively correlates with human high-grade glioma and additionally serves as a biomarker for GBM patient survival, regardless of GBM molecular subtype. Significance: These studies establish F11R as a novel monocyte prognostic marker for GBM critical for defining a subpopulation of stromal cells for future potential therapeutic intervention. Total RNA was isolated from three independently-generated sets of flow sorted bone marrow monocytes (CD11b+ CD45high CD115+ Ly6G- cells) and brainstem microglia (CD11b+ CD45low CD115low Ly6G- cells) for Illumina RNA-Seq, and two additional pools were subsequently generated and submitted for Affymetrix Mouse Exon 1.0ST microarray. Two of the RNA-Seq samples were additionally analyzed by the microarray, for a total of 6 samples (3 monocyte, 3 microglia) in each platform. Data outputs were analyzed by two analysis methods each (RNA-Seq data: ALEXA-Seq and Cufflinks; microarray data: Partek and Aroma). All four lists were merged into a new high-confidence gene list of transcripts that were significantly differentially expressed (DE) in three out of the four analyses. In this dataset, we include exon expression data obtained from flow sorted mouse bone marrow monocytes and brainstem microglia.

Dataset Information

Gene expression data of cultured primary microglia from neonatal control and Cstb-/- mice.

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