YBX1 regulates cellular homeostasis to prevent inflammation

Tolerance of endogenous nucleic acids is crucial for cellular homeostasis and when perturbed can lead to immune dysregulation. RNA-binding proteins (RBPs) bind, modify and compartmentalize endogenous RNAs to prevent their recognition by the innate immune system. We discovered that loss of a highly abundant RBP, the cold shock domain containing Y-box binding protein 1 (YBX1), results in the spontaneous induction of an IL6/STAT3 inflammatory response and the upregulation of interferon-stimulated genes (ISGs). Overall design: CRISPR Cas9 technology was used to generate hepatocellular carcinoma cell lines (Huh7) depleted of YBX1 protein. Partental (wildtype WT) Huh7 cells and two independently generated YBX1 KO clonal cell lines (YBX1 KO1, YBX1 KO3) were grown for two days in 10cm dishes before harvesting for RNA isolation and sequencing.