Noncanonical DNA virus sensing via an IKK-alpha-driven interferon signaling cascade

The National Institute of Allergy and Infectious Diseases awarded Western University of Health Sciences $200,600 on August 7, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to investigate noncanonical DNA virus sensing through an IKK-alpha-driven interferon signaling cascade.

The research project maps a previously unrecognized antiviral signaling pathway that bypasses the canonical cGAS-STING-TBK1-IRF3 axis and instead utilizes IKK-alpha to drive type I interferon responses in gammaherpesvirus-infected cells. The work employs knockout mouse cells, RNA-sequencing, biochemical interaction studies, and reporter assays to identify upstream viral DNA sensors, define critical transcription factors, and characterize how gammaherpesviruses such as murine gammaherpesvirus 68, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus engage this pathway. The discovery would demonstrate that antiviral interferon responses can persist even when canonical pathways are blocked by viral evasion mechanisms, potentially explaining how hosts maintain immune surveillance under viral pressure and pointing to novel therapeutic strategies targeting this alternate system.

Performance occurs at Western University of Health Sciences in Pomona, California, with a period of performance from August 7, 2026, through July 31, 2028. The funding is classified as a Project Grant.

Abstract

Innate immune recognition of viral DNA is a cornerstone of antiviral defense, primarily mediated through the cgas-sting-TBK1-IRF3 signaling axis. This canonical pathway leads to type i interferon (IFN-i) production and restricts viral replication. However, gammaherpesviruses such as murine gammaherpesvirus 68 (MHV- 68), epstein-barr virus (EBV), and kaposi's sarcoma-associated herpesvirus (kshv) have evolved mechanisms to subvert these pathways, raising the question of how IFN-i is still produced in infected cells. Our preliminary data reveal a surprising finding: robust IFN-i responses to MHV-68 infection persist in cells lacking both TBK1 and ikki, but are completely dependent on the kinase ikkα. This observation suggests a previously unrecognized, noncanonical DNA-sensing pathway that bypasses TBK1/ikki and instead utilizes ikkα, which is traditionally associated with TLR7/9-MYD88 signaling in plasmacytoid dendritic cells, to drive IFN-i responses in broader cell types. This R21 proposal seeks to uncover the molecular basis of this alternate antiviral signaling axis. We hypothesize that viral DNA is sensed by conventional receptors, but signals downstream through ikkα rather than TBK1, leading to IFN-i activation. We will employ a combination of knockout mouse cells, RNA- sequencing, biochemical interaction studies, and reporter assays to map the upstream sensors, define the critical transcription factors, and determine how gammaherpesvirus DNA engages with this pathway. The discovery of an ikkα-dependent IFN pathway in non-immune cells would shift the current paradigm in antiviral innate immunity by demonstrating that antiviral IFN responses can be maintained even when canonical pathways are blocked by viruses. This could explain how hosts retain immune surveillance under viral pressure and point to novel strategies that exploit this "backup" system to bolster immunity against persistent viruses. By revealing new mechanistic insights into immune redundancy and pathway plasticity, this work will advance our understanding of host-virus interactions during DNA viral infection.