Comprehensive proteomics identification of IFN-λ3-regulated antiviral proteins in HBV-transfected cells

Abstract

Interferon (IFN)-λ is a relatively unexplored, yet promising anti-viral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B, with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA. Quantitative proteomic analysis of HBV-transfected cells was performed following 24-hour IFN-λ3 treatment, with parallel IFN-α2a and PBS treatments for comparison using a dimethyl labeling method. The depth of the study allowed us to map the induction of anti-viral proteins to multiple points of the viral life cycle, as well as facilitating the identification of anti-viral proteins not previously known to be elicited upon HBV infection. This study also shows up-regulation of many effectors involved in antigen processing/presentation indicating that this cytokine exerted immunomodulatory effects through a number of essential molecules for these processes. Interestingly, immunoproteasome caps were up-regulated while cap components of the constitutive proteasome were down-regulated upon IFN-λ3 treatment, suggesting coordinated modulation towards the antigen processing/presentation mode. Furthermore, we reveal that IFN-λ3 restored levels of RIG-I and RIG-G, proteins known to be suppressed by HBV. Enrichment analysis demonstrated that several biological processes including RNA metabolism, translation, and ER-targeting were differentially regulated upon treatment with IFN-λ3 vs. IFN-α2a. Our proteomic data suggests that IFN-λ3 regulates an array of cellular processes to control HBV replication.