A genome-wide CRISPR screen identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling

Interleukin-1ß (IL-1ß) is dysregulated in chronic inflammatory diseases, yet the genetic factors influencing IL-1ß production remain largely unknown. Myeloid-derived cells are the primary producers of IL-1ß, which prompted a genome-wide CRISPR knockout screen in the human myeloid-derived U937 cell model treated with lipopolysaccharide (LPS) to mimic inflammatory conditions and sorted for high and low intracellular IL-1ß levels. A total of 295 genes were identified as regulators of IL-1ß production, including known mediators such as TLR4, JAK-STAT and IL-10 receptor. Notably, 57 out of the 295 genes overlapped with loci associated with human inflammatory diseases, including the TNRC18 gene locus associated with multiple diseases in the Finnish population. U937 cells engineered with the Finnish-enriched rs748670681 risk allele demonstrated decreased levels of mRNA for TNRC18 and an adjacent gene WIPI2, reduction in LPS-dependent gene activation and cytokine production, but elevation of interferon-responsive gene programs. Transcriptomic profiles for individual knockouts of TNRC18 and WIPI2 attributed the loss of LPS-dependent signaling primarily to TNRC18, which occurs through the modulation of H3K27 acetylation around inflammatory regulatory regions via TNRC18 and its protein interaction network. In contrast, the loss of WIPI2 is characterized by an exacerbation of interferon signaling. Collectively, these findings delineate the global regulatory mechanisms of IL-1ß production and provide molecular insights to the role of the rs748670681 variant as a pleiotropic risk factor for inflammatory diseases. Overall design: To investigate the downstream effects of the TNRC18 and WIPI2 gene knockouts on global gene expression in differentiated U937 myeloid cells, and the effects of the Finnish-enriched risk variant rs748670681 at the WIPI2/TNRC18 gene locus associated with immune-mediated diseases. Genes were knocked out using the CRISPR Cas9 or Cas12a enzymes. The risk alelle T of the rs748670681 SNP was inserted into U937 cells by the HDR-mediated CRISPR/Cas9 editing method. We performed gene expression profiling analysis using data obtained from RNA-seq of U937 cells treated with LPS or vehicle for 24 hours. Comparative gene expression analysis of RNA-seq data were performed between WT and KO cells, and rs748670681-TT and rs748670681-CC cells.