Identification of LPS-Induced Enhancers in Human Mesenchymal Stromal Cells

Human mesenchymal stromal cells (hMSCs) are multipotent stromal cells that hold great therapeutic promise, in part because of their immunomodulatory and migratory response to pathogen-associated molecular patterns such as lipopolysaccharide (LPS). We have previously described the LPS-induced hMSCS gene expression profiles using RNA-seq. Among alternated genes, IFITM1 showed a higher induction of gene expression and enrichment for H3K27ac than other migration-related genes, and RNA interference directed against IFITM1 suppressed LPS-stimulated hMSC migration. LPS treatment led to increased eRNA synthesis and increased H3K27 acetylation in region R2 (2 kb upstream of the IFITM1 gene). Reporter gene analysis confirmed the enhancer activity of this region. Chromatin immunoprecipitation assays revealed increased binding of the transcription factors NF-κB and IRF1 to R2; pharmacological inhibition of NF-κB binding and RNA interference directed against IRF1 prevented the increased IFITM1 expression. Further, inhibition of NF-κB binding prevented the increased expression of eRNAs in R2. In summary, we found that increased expression of IFITM1 is important for LPS-stimulated hMSC migration, and we uncovered molecular mechanisms underlying this increased expression, most notably the NF-κB mediated activation of enhancer region R2.