A multi-omics analysis of the regulatory changes induced by miR-223 in a monocyte/macrophage cell line

Highlights

• We used a multi-omics approach to study the impact of miR-223 in the RAW cell line.

• We evidenced changes linked to cell death, histone acetylation, bone remodeling, RNA regulation.

• Changes in miR-223 expression altered the metabolic profile of cells including nucleotides.

• miR-223 impacted NF-kB levels, macrophage differentiation and osteoclastogenesis.

Abstract

We used a multi-omics approach to study the impact of over-expression and inhibition of the microRNA miR-223, a pleiotropic regulator of metabolic-related disease, in a monocyte-macrophage cell line. We analyzed the levels of proteins, mRNAs, and metabolites in order to identify candidate molecules involved in miR-223 regulation, to determine disease biomarkers and potential therapeutic targets. Microarray-based transcriptomics evidenced a change in 120 genes that were linked predominantly to histone acetylation, bone remodeling and RNA regulation. In addition, 30 out the 120 genes encoded long noncoding RNAs. The nanoLC-MS/MS experiment revealed that 52 proteins were significantly altered when comparing treatments. Gene Ontology analyses evidenced association with cell death, splicing and stability of mRNAs, bone remodeling and metabolism. Among targets, miR-223 alteration changed the expression of CARM-1, Ube2g2, Cactin and Ndufaf6 during macrophage differentiation and osteoclastogenesis, indicating that these genes are potential biomarkers of these processes. The most important discriminant metabolites found in the metabolomics study were found to be hydrophilic amino acids, carboxylic acids linked to metabolism and pyrimidine nucleotides, indicating that changes in miR-223 expression alter the metabolic profile of cells, and may affect their apoptotic and proliferative state.