Sustained Transcriptional Response to Lipopolysaccharide and Interleukin-4 in an Immortalized Mouse Microglial Cell Line

In an attempt to identify markers that better characterize microglial states and to search for potential therapeutic targets, we performed a study using the IMG cell line as an in vitro microglial model. Specifically, we tested its response to several pro-inflammatory stimuli (lipopolysaccharide, interferon gamma, and tumor necrosis factor) and an anti-inflammatory stimulus (Interleukin-4) after 12 and 24 h of incubation. We performed RNA sequencing to identify genes modified at both incubation times (i.e., genes with sustained changes in the window between 12 and 24 h) that could reflect sustained microglial transcriptional responses. We also used Gene Ontology (GO) analysis to identify the most relevant pathways modified by these stimuli. RNA sequencing revealed four gene sets: (1) common genes that respond similarly to IL-4 and LPS, (2) specific LPS responders, (3) specific IL-4 responders, and (4) genes that exhibit LPS-induced upregulation and IL-4-induced downregulation, and vice versa (opposite responders). We hypothesize that the common gene set represents a general microglia response to pathological conditions, while the LPS- and IL-4-responder gene sets define specific microglial states under pro- and anti-inflammatory stimuli, respectively. We further propose that opposite responder genes act as metabolic switches between certain microglial states. The GO analysis indicated that LPS strongly upregulates biological processes related to the innate immune response, while IL-4 upregulates pathways related to repair, metabolic reprogramming, and cellular cooperation. Finally, the transcriptional response of IMG cells closely mirrored that of primary microglia, revealing highly similar gene expression and GO term profiles under LPS stimulation.