Fig. 1

TX and CQ co-treatments alter mRNA levels of genes involved in response to inflammation. MIAMI cells were treated with 500 U/ml IFN-γ alone or in combination with 10 μM CQ or 5 μM TX. Total RNA was isolated and subjected to RNAseq. Sequencing data were processed as described in the “Material and methods” section. IPA gene expression analysis was performed to determine signaling pathways that are involved in MIAMI cell’s response to IFN-γ alone or in combination with TX or CQ (a). Representative heatmaps for genes belonging to antigen presentation (b) and Th1 and Th2 activation pathways (c) are shown. Upstream pathway analysis was performed to determine putative upstream regulators (d)