Nasal Mucosal Antiviral Immunity Following Vaccination or Influenza Infection

Abstract

The respiratory tract is a critical but challenging barrier to protect against invading pathogens. Lower respiratory tract infections are among the leading causes of death globally. However, it is the upper respiratory tract that is typically first infected by pathogens that disseminate to the lungs and other organs to cause significant disease. It is critical to understand the immune defense system of the upper respiratory tract and how immune memory is established and maintained in this distinct barrier tissue. To broadly characterize nasal mucosal immunity, we performed a single-cell RNA sequencing analysis of the tissue over the course of an acute Influenza A virus infection and validated key observations. We revealed that the nasal mucosa has distinct epithelial and immune cell compartments corresponding with the different functional roles of respiration, immune defense, and olfaction. Influenza infection was largely restricted to the respiratory mucosa which had the greatest influx of monocytes that differentiated into resident macrophages. A robust population of neutrophils was identified before and during infection, some with unique features not observed in other tissues. Lymphocyte populations expanded towards the end of the viral infection and were maintained after viral clearance as memory populations, such as CD8 tissue-resident memory T cells (Trm). CD8 Trm can serve as a first line of defense against pathogens, but it is unclear what their role is in protecting the nasal mucosa and how they are established. Utilizing a variety of vaccination strategies, we demonstrated that CD8 T cells are recruited to the nasal mucosa following intranasal vaccination or a peripheral vaccination coupled with a nasal recruitment step driven by an inflammatory adjuvant or a cognate antigen-IFNg recruitment cascade. Nasal CD8 T cell trafficking depended on VCAM-1, ICAM-1, and CXCR3. Whereas CXCR6 supported Trm maintenance and protection against influenza infection. CD8 Trm rapidly cleared influenza within a timeframe that systemic memory CD8 T cells had no impact on viral load. Overall, this work provides a stepwise portrait of antiviral nasal immunity, and establishes a significant role for CD8 Trm in protecting the nasal mucosa from viral challenge and key mechanisms for their recruitment and maintenance.