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.

Keywords: gene regulation; genetic screens; innate immunity; interferon-stimulated genes; knockout; overexpression; virus–host interactions.

Figure 1

The antiviral innate immune response is orchestrated by signaling cascades and the synergistic activity of numerous factors that are converging in a complex regulatory network. Pathogen-associated molecular patterns such as viral nucleic acids (viral NAs) are sensed by cytoplasmic pattern recognition receptors (PRRs), which in turn, activate signaling cascades of the innate immune system. This leads to the expression of regulatory function (Regulator) and proteins with antiviral effector proteins (Effector), which is controlled on transcriptional and translational level. Paracrine and autocrine interferon (IFN) signaling synergistically modulate these signaling cascades. The activity of numerous contributing factors puts the cell into an antiviral state, inhibiting virus replication at multiple stages of the viral life cycle. To avoid overshooting immune reactions and adverse effects on cellular fitness, negative regulators eventually shut down the IFN response.

Figure 2

An extensive portfolio of genetic perturbation approaches (1) can be used to modify the protein expression levels to study the contextual function of specific gene products. With a suitable infection model system (2) (e.g., reporter viruses) and a fitting screening format (3), a large number of target genes can be studied on a large scale. Several different methods can then be used as a readout for gene/protein functionality (4). Different datasets can then be merged and fed into meta- and network-analysis algorithms (5). Gathering detailed insights from different experimental settings, a global picture of the innate immunity landscape can be drawn. It is critical to understand virus–host interactions in detail to develop novel antiviral drugs and treatments at the time they are needed.