Dual roles for influenza A protein PA-X: limiting inflammatory response and disrupting MHC I antigen presentation in human respiratory epithelium

The mechanisms of immune evasion of influenza A virus are key to its success as an infectious agent. To replicate effectively, influenza A virus must suppress both early innate immune responses, like antiviral type I and III interferons, and adaptive immune responses. The latter is particularly important during infections of animals and humans with pre-existing immunity and explains the continued circulation of influenza A viruses. Here we report how influenza A virus employes a single immunomodulatory protein, the endoribonuclease PA-X, to control both arms of the immune responses. To define how influenza A virus uses PA-X to evade immune responses, we characterized its impact on the host response to infection in the infected and bystander cells of the airway epithelium using a 3D ex vivo model and primary cells from multiple human donors. PA-X significantly decreases secretion of multiple cytokines from airway epithelium, including IFN- λ, inflammatory cytokines, and growth factors related to lung damage, which likely plays a role in its ability to modulate inflammation and lung pathology in vivo. In addition, we discovered that PA-X also decreases and delays MHC I antigen presentation from infected cells. This reduction likely aids influenza A virus in hiding from antigen-specific T cells and allows the virus to successfully replicate prior to immune detection. These new functions for PA-X highlight how influenza A virus employs active mechanisms to block not only innate immune but also adaptive immune detection, in addition to tolerating high levels of antigen mutations to escape it. Significance Statement Influenza viruses must evade both innate and adaptive immune responses to infect, replicate, and transmit to new hosts. Through innate immunity, infected cells activate proteins to disrupt viral replication and alert surrounding cells. Through adaptive immunity, antigen-specific T cells recognize specific viral peptides and kill infected cells. We studied how influenza overcomes immune responses. Using a model of human airway tissue, we found that influenza viruses use a single protein PA-X, to counteract both innate and adaptive responses. PA-X decreases innate immune signaling between infected and surrounding cells and interferes with presentation of viral peptides to antigen-specific T cells. Thus, PA-X helps the virus continue to circulate and infect new hosts, even in populations with prior exposure to the flu.