System-Based Approaches to Delineate the Antiviral Innate Immune Landscape

Abstract

Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and how infected cells react to the virus on a molecular level. Invading viruses are commonly sensed by components of the innate immune system, which is composed of a highly effective yet complex network of proteins that, in most cases, mediate efficient virus inhibition. Central to this process is the activity of interferons and other cytokines that coordinate the antiviral response. So far, numerous methods have been used to identify how viruses interact with cellular processes and revealed that the innate immune response is highly complex and involves interferon-stimulated genes and their binding partners as functional factors. Novel approaches and careful experimental design, combined with large-scale, high-throughput methods and cutting-edge analysis pipelines, have to be utilized to delineate the antiviral innate immune landscape at a global level. In this review, we describe different currently used screening approaches, how they contributed to our knowledge on virus–host interactions, and essential considerations that have to be taken into account when planning such experiments.

CRISPR Screening: Molecular Tools for Studying Virus–Host Interactions

“…Unlike CRISPR-ko, CRISPRi markedly suppresses target gene transcription by epigenetic mechanisms, eliminating the risk of producing truncated proteins and genotoxicity. Additionally, RNA interference, the canonical method for loss-of-function screens, results in less efficient gene knock-down and typically has higher rates of non-specific effects than CRISPRi [34,35].…”

Type I and III IFN-mediated antiviral actions counteracted by SARS-CoV-2 proteins and host inherited factors

“…Such heterogeneity in the IFN-I response is also sustained by dissimilar cellular metabolism, translational and transcriptional states at the activation time that influences the level of sensors, adaptors, and receptors. The dissimilar timing of the IFN response upon viral replication is crucial to define its efficacy in controlling viral spread [ [36] , [37] , [38] , [39] , [40] ]. The preferential distribution of IFNLR on epithelial cells suggests functional differences between IFN-I and IFN-III at epithelial surfaces, despite their redundant functions.…”

What sequencing technologies can teach us about innate immunity*

“…[162][163][164] There have been many pooled CRISPR screens performed to try and better understand host-viral interactions which is reviewed in. 165 Perturb-seq is an approach in which CRISPR screening is combined with single-cell sequencing readouts allowing for both target identification and mechanistic insights in one experiment. Dixit et al, used this approach to target 24 transcription factors in bone marrowderived dendritic cells and reconstruct the complex interplay between positive and negative regulators within the LPS signaling pathway.…”