Genome-wide gene expression profiling of macrophages treated with novel 1,2,4-oxadiazole scaffold-based compounds

Background: Anti-tuberculosis drugs, mainly developed more than 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy (HDT) has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, we evaluated the impact of two host-directed compounds, namely MC3465 and MC3209, on the response of human monocytes-derived macrophages infected with Mycobacterium tuberculosis (MTB). Results: The expression of 181 genes was differentially regulated following MC3465 treatment (p-value < 0.05, log FC = 0.5 and = -0.5) after 4 h, with 53 being upregulated and 128 being downregulated. The expression of more genes was affected after 24h of treatment. 224 genes were upregulated and 652 genes downregulated. (p value < 0.05, log FC = 0.5 and = -0.5). We classified those differentially expressed genes by performing gene-set enrichment analysis using ClueGO cluster analysis. The gene set downregulated by MC3465 at 4 h was significantly enriched for genes associated with chemotaxis and cellular zinc ion homeostasis and cell chemotaxis. At 24 h, most of the downregulated genes belongs to the innate immune response and the cytokine response, with many genes belonging to the type I IFN pathway. Conclusions: Our results indicate that MC3465 alters zinc homeostasis in human macrophages. Overall design: CD14+ monocytes were isolated from 4 blood donors (named D1, D2, D3 and D4) by positive selection using CD14 microbeads (Miltenyi Biotec). Cells were cultured at 37°C and 5% CO2 in RPMI-1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Dutscher), and 2 mM L-glutamine (Gibco) with macrophage colony stimulating factor (M-CSF, 20 ng/mL; Miltenyi Biotec). After six days of differentiation, the resulting macrophageswere infected with Mycobacterium tuberculosis (H37Rv strain, multiplicity of infection: one bacterium-per two cell). Naive macrophages and M. tuberculosis infected macrophages were treated with MC3465 (40) or MC3209 (a1). After 4 h and 24 h of treatment, we characterized the genome-wide gene expression profiles of macrophages by RNAseq, with DMSO-treated cells serving as a control.