Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line

Abstract

Interferons are commonly utilized in the treatment of chronic hepatitis B virus (HBV) infection but are not effective for all patients. A deep understanding of the limitations of interferon treatment requires delineation of its activity at multiple “omic” levels. While myriad studies have characterized the transcriptomic effects of interferon treatment, surprisingly, few have examined interferon-induced effects at the proteomic level. To remedy this paucity, we stimulated HepG2 cells with both IFN-α and IFN-λ and performed proteomic analysis versus unstimulated cells. Alongside, we examined the effects of HBV transfection in the same cell line, reasoning that parallel IFN and HBV analysis might allow determination of cases where HBV transfection counters the effects of interferons. More than 6000 proteins were identified, with multiple replicates allowing for differential expression analysis at high confidence. Drawing on a compendium of transcriptomic data, as well as proteomic half-life data, we suggest means by which transcriptomic results diverge from our proteomic results. We also invoke a recent multiomic study of HBV-related hepatocarcinoma (HCC), showing that despite HBV’s role in initiating HCC, the regulated proteomic landscapes of HBV transfection and HCC do not strongly align. Special focus is applied to the proteasome, with numerous components divergently altered under IFN and HBV-transfection conditions. We also examine alterations of other protein groups relevant to HLA complex peptide display, unveiling intriguing alterations in a number of ubiquitin ligases. Finally, we invoke genome-scale metabolic modeling to predict relevant alterations to the metabolic landscape under experimental conditions. Our data should be useful as a resource for interferon and HBV researchers.

Proteomic Profiling and Artificial Intelligence for Hepatocellular Carcinoma Translational Medicine

“…Among them were survival-associated proteins including proliferating cell nuclear antigen (PCNA), MutS homolog 6 (MSH6), cyclin-dependent kinase 1 (CDK1), and asparagine synthetase (ASNS) ( Figure 5 ). Additionally, using high pH fractionation and LC-MS/MS analysis, more than 6000 DEPs were identified in IFN-α and INF-λ-stimulated HepG2 cell line under HBV transfection condition [ 185 ]. Among these proteins were those involved in interferon signaling, metabolic processes, antiviral response, ubiquitin-proteasomal degradation, and vesicle-mediated transportation.…”

Review of Lambda Interferons in Hepatitis B Virus Infection: Outcomes and Therapeutic Strategies

“…Although the effect of IFNLs on cccDNA have been less well-characterized, overexpressing or inducing expression of IFNLs in hepatocyte cell lines and murine infection models results in ISG induction and inhibition of HBV replication [38,117,[129][130][131][132][133]. IFNL3 treatment reduced HBV transcripts and intracellular DNA in HepG2 2.2.15 cells that have clonally integrated HBV, a phenotype linked to changes in the host transcriptome and proteome [132,134,135]. Exposure of primary human hepatocytes or HepaRG cells to type-I IFNs or IFNLs reduced open-circle and cccDNA by causing cccDNA deamination and degradation, a phenotype attributed to induction of APOBEC deaminases [136].…”