Long-term surviving influenza infected cells evade CD8 ⁺ T cell mediated clearance

Abstract

Influenza A virus (IAV) is a seasonal pathogen with the potential to cause devastating pandemics. IAV infects multiple epithelial cell subsets in the respiratory tract, eliciting damage to the lungs. Clearance of IAV is primarily dependent on CD8 ⁺ T cells, which must balance control of the infection with immunopathology. Using a virus expressing Cre recombinase to permanently label infected cells in a Cre-inducible reporter mouse, we previously discovered infected club cells that survive both lytic virus replication and CD8 ⁺ T cell-mediated clearance. In this study, we demonstrate that ciliated epithelial cells, type I and type II alveolar cells can also become survivor cells. Survivor cells are stable in the lung long-term and demonstrate enhanced proliferation compared to uninfected cells. When we investigated how survivor cells evade CD8 ⁺ T cell killing we observed that survivor cells upregulated the inhibitory ligand PD-L1, but survivor cells did not use PD-L1 to evade CD8 ⁺ T cell killing. Instead our data suggest that survivor cells are not inherently resistant to CD8 ⁺ T cell killing, but instead no longer present IAV antigen and cannot be detected by CD8 ⁺ T cells. Finally, we evaluate the failure of CD8 ⁺ T cells to kill these previously infected cells. This work demonstrates that additional cell types can survive IAV infection and that these cells robustly proliferate and are stable long term. By sparing previously infected cells, the adaptive immune system may be minimizing pathology associated with IAV infection.

Author summary

Influenza A virus is a seasonal respiratory pathogen that can cause severe lung damage and death. We previously made the discovery that cells infected with influenza virus do not have a death sentence. An infected cell can survive both influenza virus infection and the immune response to eliminate the virus, specifically CD8 ⁺ T cells which are required for virus clearance. Here, we investigated how an infected cell could survive the CD8 ⁺ T cell immune response. We used an influenza virus expressing a recombinant protein that permanently labels infected cells in inducible reporter mice. This system allowed us to detect actively infected cells, as well as cells that had survived influenza virus infection and CD8 ⁺ T cell-mediated killing, called survivor cells. We demonstrate that survivor cells do not actively block CD8 ⁺ T cell effector function and are not inherently resistant to CD8 ⁺ T cell-mediated killing. Our data suggest that survivor cells have lost influenza virus antigen and are rendered invisible to virus-specific CD8 ⁺ T cells. Our research provides important new insight into the mechanism of how survivor cells can be generated. This could be a mechanism by which the host is protecting the lung from greater pathology during influenza virus infection.