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Abstract

The cell intrinsic innate immune response serves as the first line of defense of a host cell against microbial invasions. It initiates with the activation of pattern recognition receptors (PRRs) by various pathogen-associated molecular patterns (PAMPs), through complex signaling pathways, resulting in the expression of Interferons (IFNs) and numerous Interferon-stimulated genes (ISGs) to eliminate invading pathogens. The key players in this process are well-established, however, increasing numbers of regulatory factors have also been discovered in recent years, playing vital roles in tuning the innate immune response. Some of these factors are exclusively expressed in certain tissue or cell-types, shaping the specific responses there. Toll-like receptor 3 (TLR3) is a PRR residing in the endosome of certain cell types, including endothelial cells and hepatocytes. To identify host factors involved in TLR3 pathway of hepatocytes, my colleagues initiated a CRISPR/Cas screening in two liver cell lines, Huh7-Lunet-TLR3 and PH5CH cells, and identified 55 candidate genes potentially affecting TLR3 responses. After a large-scale siRNA validation, they finally narrowed down the candidates to three genes, protein tyrosine phosphatase receptor type T (PTPRT), lysine demethylase 2A (KDM2A) and RNA binding motif protein 39 (RBM39). Since PTPRT and KDM2A showed off-target effects, my thesis mainly focused on the analysis of the innate immune function of RBM39. RBM39 is an RNA binding protein involved in transcriptional regulation and splicing of many genes, mainly contributing to cell cycle control and metabolic pathways. In this study, I found that RBM39 furthermore plays a role in innate immunity signaling, including TLR3, RIG-I, MDA5 and IFN pathways. Upon poly(I:C) stimulation, loss of RBM39 significantly attenuated these pathways not only in liver-based cell lines but also in human alveolar epithelial cell, A549. This role was further confirmed during virus infections where RBM39 also affected virus-induced ISG expression. Furthermore, knockdown of RBM39 specifically inhibited the type III IFN but not type I IFN pathway, due to a down-regulation of the type III IFN receptor subunit IL10RB. In addition, I observed that RBM39 affected mainly IRF3-dependent ISG induction but not the production NF-κB-induced inflammatory cytokines, IL6 and TNFAIP3, pointing to an IRF3-related regulation by RBM39, at least upon TLR3 activation. Indeed, further investigation uncovered that deletion of RBM39 significantly reduced IRF3 expression, partly resulting from its co-transcriptional function and highly associated with its role as alternative splicing factor. RNA sequencing (RNA-seq) analysis in PH5CH revealed that downregulation of RBM39 results in a switch from the functional IRF3 isoform to dysfunctional ones, leading to a reduction of IRF3 protein expression and thus a suppression of the IFN response. This analysis further identified other important innate immune factors regulated by RBM39 either at the transcription level or by alternative splicing, such as RIG-I, MDA5, IL10RB, STAT1 and STAT2. A proteomic analysis confirmed the reduction of RIG-I, STAT1 and STAT2, collectively highlighting the role of RBM39 in cell intrinsic innate immunity. In addition, Indisulam, a sulfonamide drug mediating RBM39 degradation and used for cancer treatment in clinical trials, was found to act as an innate immune inhibitor, reducing IRF3 expression and ISGinduction. This data suggests that targeting of RBM39 might be a strategy to tune down exaggerating innate immune responses, e.g. for the therapy of autoimmune disorders. To comprehensively understand the role of TLR3 in liver-specific antiviral immunity, I also collected 14 TLR3 single nucleotide polymorphisms (SNPs), and investigated their functionality in Huh7.5 cells, an immune-incompetent liver hepatoma cell line lacking TLR expression. The function of TLR3 SNPs L360P, P680L, L742F, G743S were severely impaired while R811S, R867Q, M870V were partly reduced. However, further in-depth analysis going beyond the scope of this thesis are required to draw conclusions on the mechanisms underlying the functional defects.