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RNA-seq analysis of diabetes induced changes in macrophage transcriptome

ABSTRACT: Macrophage dysfunction and polarization plays key role in chronic inflammation associated with diabetes and its complications. However, the effect of diabetes on macrophage transcriptome including long non-coding RNAs is not known. Here, we analyzed global changes in transcriptome of bone marrow macrophages isolated from type 2 diabetic db/db mice and control littermates db/+ mice using high throughput RNA-seq technique. Data analysis showed that expression of genes relevant to fibrosis, cell adhesion and inflammation were altered in diabetic db/db mice relative to control db/+ mice. Furthermore, expression of several known and novel long non coding RNAs and nearby genes was altered in db/db mice. Gene ontology and IPA showed activation of signaling netwroks relevant to fibrosis, cell adhesion and inflammatory pathways . This study for the first time demonstrated that diabetes profoundly affects macrophage transcriptome including expression of long non coding RNAs and altered the levels of genes relevant to diabetes complications.

ORGANISM(S): Mus musculus

PROVIDER: GSE54154 | GEO | 2014/09/15

SECONDARY ACCESSION(S): PRJNA235308

REPOSITORIES: GEO

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Project description:Objective: Macrophages play key roles in inflammation and diabetic vascular complications. Emerging evidence implicates long noncoding RNAs (lncRNAs) in inflammation, but their role in macrophage dysfunction associated with inflammatory diabetic complications is unclear and was therefore investigated in this study. Approach and Results: RNA-sequencing and RT-qPCR demonstrated that a lncRNA Dynamin 3 opposite strand (Dnm3os) is upregulated in bone marrow derived macrophages from type2 diabetic (T2D) db/db mice, diet-induced insulin-resistant mice and diabetic ApoE-/- mice, as well as in monocytes from T2D patients relative to controls. Diabetic conditions (High glucose and palmitic acid) induced Dnm3os in mouse macrophages and THP1 human monocytes. Promoter reporter analysis and chromatin-immunoprecipitation (ChIP) assays demonstrated that diabetic conditions induce Dnm3os via NF-kB activation. RNA-FISH and RT-qPCRs of sub-cellular fractions demonstrated nuclear localization and chromatin enrichment of Dnm3os in macrophages. Stable overexpression of Dnm3os in macrophages altered global histone modifications and upregulated inflammation and immune response genes, and phagocytosis. Conversely, siRNA mediated knockdown of Dnm3os attenuated these responses. RNA pull-down assays with macrophage nuclear lysates identified nucleolin and ILF-2 as protein binding partners of Dnm3os, which was further confirmed by RNA-IP and RNA-FISH-immunofluorescence. Furthermore, nucleolin levels were decreased in diabetic conditions, and its knockdown enhanced Dnm3os-induced inflammatory gene expression and histone H3K9-acetylation at their promoters. Conclusions: These results demonstrate novel mechanisms involving upregulation of lncRNA Dnm3os, disruption of its interaction with nucleolin, and epigenetic modifications at target genes that promote macrophage inflammatory phenotype in diabetes. The data could lead to lncRNA-based therapies for inflammatory diabetes complications.

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RNA-seq analysis of diabetes induced changes in macrophage transcriptome

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