Interrogating Host Antiviral Environments Driven by Nuclear DNA Sensing: A Multiomic Perspective

Abstract

Nuclear DNA sensors are critical components of the mammalian innate immune system, recognizing the presence of pathogens and initiating immune signaling. These proteins act in the nuclei of infected cells by binding to foreign DNA, such as the viral genomes of nuclear-replicating DNA viruses herpes simplex virus type 1 (HSV-1) and human cytomegalovirus (HCMV). Upon binding to pathogenic DNA, the nuclear DNA sensors were shown to initiate antiviral cytokines, as well as to suppress viral gene expression. These host defense responses involve complex signaling processes that, through protein-protein interactions (PPIs) and post-translational modifications (PTMs), drive extensive remodeling of the cellular transcriptome, proteome, and secretome to generate an antiviral environment. As such, a holistic understanding of these changes is required to understand the mechanisms through which nuclear DNA sensors act. The advent of omics techniques has revolutionized the speed and scale at which biological research is conducted and has been used to make great strides in uncovering the molecular underpinnings of DNA sensing. Here, we review the contribution of proteomics approaches to characterizing nuclear DNA sensors via the discovery of functional PPIs and PTMs, as well as proteome and secretome changes that define a host antiviral environment. We also highlight the value of and future need for integrative multiomic efforts to gain a systems-level understanding of DNA sensors and their influence on epigenetic and transcriptomic alterations during infection.

Keywords: DNA sensing; IFI16; cGAS; innate immunity; mass spectrometry; post-translational modifications; protein interactions; proteomics; transcriptomics; virus–host interactions.

Figure 1

Nuclear DNA sensors bind to viral DNA and activate antiviral cytokine signaling. (A) Domain maps for each nuclear DNA sensor. IFI16 and IFIX belong to the PYHIN family of proteins and each contain an N-terminal pyrin domain that mediates protein interactions and one or two HIN-200 domains that bind dsDNA in a sequence-independent manner. cGAS consists of overlapping Ntase core (cGAMP production) and Mab21 (DNA binding) domains. hnRNPA2B1 possesses two RNA recognition motifs, the first of which has been proposed to also contain the DNA binding site. Each protein contains a nuclear localization signal (red bars). (B) Model for the intrinsic and innate immune activity of IFI16, IFIX, cGAS, and hnRNPA2B1. During infection, IFI16 and IFIX bind viral DNA entering the nucleus through a nuclear pore complex. After binding to viral DNA via their HIN domains (blue), these proteins each form homo-oligomers mediated by the PYD in order to build antiviral signaling scaffolds necessary for the repression of viral transcription and induction of IFNß. cGAS was shown to stabilize nuclear IFI16 levels during HSV-1 infection to promote immune signaling. In the cytoplasm, cGAS binds to foreign DNA and produces cGAMP, which in turn activates the STING–TBK1–IRF3 signaling axis to induce IFNß. hnRNPA2B1 binds viral DNA and is then demethylated by JMJD6. This is required for hnRNPA2B1 dimerization and subsequent translocation into the cytosol, where it activates the STING–TBK1–IRF3 axis. In each case, IFNß protein is secreted from the cell in order to communicate with and initiate antiviral programs in neighboring cells.

Figure 2

Yearly research articles investigating nuclear DNA sensors. Research papers focused on each nuclear DNA sensor, obtained from PubMed search when considering published research articles each year since 1990. The sum of each year’s articles for each protein is represented by line graphs (left Y axis) while articles specifically utilizing proteomics approaches to investigate proteome changes, protein–protein interactions, post-translational modifications, etc., are shown as stacked bars (right Y axis). Of note, the black line represents the number of articles concerning all kinds of DNA sensing, including non-nuclear sensors such as the cytoplasmic AIM2 and endosomal TLR9. The red dashed line marks the discovery of IFI16 as the first nuclear DNA sensor.

Figure 3

Protein–protein interactions contribute to the activation or inhibition of DNA sensor. Over the course of viral infection and immune signaling, DNA sensors interact with other cellular and viral proteins. Several of these cellular proteins are important for the function of the DNA sensors for both suppressing virus replication by repressing viral transcription and inducing antiviral cytokines. Protein interactions are also used to regulate DNA sensor function. Viruses have evolved distinct mechanisms to facilitate immune evasion and cells must also possess mechanisms to prevent excessive immune signaling. Although localized to both the nucleus and cytoplasm, protein interactions with cGAS are best characterized in the cytoplasm. Nuclear proteins are shown here as rectangles and cytoplasmic interactions as hexagons.