UC San Diego

Mammalian cells are surrounded by fluctuations of various cytokines, small proteins that control a broad range of cellular signaling. In order to survive, cells must respond appropriately to these different dynamics of these signaling molecules. This thesis work presents partial answers to how human epithelial cells decode information encoded in the dynamics of the external stimuli and successfully execute proper responses. We focus on interferon (IFN) pathway which is important for viral infection as well as tumorigenesis. We employed CRISPR/Cas9 technology to generate reporter cell lines, time-lapse microscopy, microfluidics, single cell analysis and computational modeling to dissect the molecular mechanism governing the cytokine responses. In chapter 1, we studied how IFN-a pretreatment could lead to two contradictive effects: priming and desensitization. We discovered that short pretreatment duration produced priming effect while prolonged IFN treatment caused activation of delayed negative feedback, USP18, responsible for desensitization. Intriguingly, USP18 induction was duration and cell-cycle dependent. Understanding this regulation paves ways to improve the usage of IFN in virus infection such as SARS-CoV-2 and cancer therapy.

In chapter 2, we systemically studied the cellular response to different type of IFN. We found that three types of IFN process distinct dynamic responses. Type I IFN (IFN-I) was a potent IRF9 inducer than type III but succumb to desensitization. Single cells analysis showed heterogenous response to IFN-III stimulation. Type II was strong STAT1 activator but was unable to induce IRF9. Interestingly, combination of IFN-II and -III generated a synergy effect mimicking IFN-I response but without USP18 induction and therefore no desensitization. Short pulses of low IFN-II dose were sufficient to maintain the synergy. We believe that this will provide alternative methods to deliver IFN to patients especially against virus infection.