Vaccine-Induced Mucosal T-Cell Immunity to Respiratory Viruses in Dirty Mice

Abstract: Respiratory infections have been among the top three leading causes of global deaths for decades. Their

importance is reinforced by the emergence of novel highly transmissible respiratory pathogens, as witnessed in the current SARS-CoV-2 and past influenza pandemics. Current influenza and SARS-CoV-2 vaccines are focused on eliciting

antibodies to highly mutable viral surface proteins, and frequent vaccine reformulations are needed to match the antigenicity

of constantly evolving viral strains or variants that evade vaccine-elicited antibodies. Therefore, elicitation of lung tissue-

resident memory T cells (TRMs), which recognize epitopes that are conserved across viral variants is critical to elicit broad anti-viral immunity. We have developed combination adjuvant-based subunit mucosal vaccine formulations that elicit exceptionally strong and functionally diverse lung/airway CD8 and CD4 TRMs and provide effective and broad

protection against influenza A virus (IAV) and SARS-CoV-2 in specific-pathogen-free (SPF) mice. However, a central question is whether vaccine efficacy studies in SPF mice are translatable to humans, who are exposed to diverse microbial species. In recent years, Dirty mice (SPF mice cohoused with pet store mice), have been used to model human

immune responses. Significantly, TRM numbers are greatly increased in Dirty mice, but the underlying mechanisms are unknown. We have exciting preliminary data that the lungs and spleen of Dirty mice have markedly elevated number of Granzyme BHI/CD44HI CD8 T cells with transcriptional attributes (T-betLO/EOMESLO/TCF-1LO) reminiscent of precursor

TRMs, which are poised for a TRM cell fate. The overarching goal is to exploit the high resolution of our combination adjuvant-based vaccine approach and the Dirty mouse model to elucidate the effects of diverse microbial exposure on the

development of pre-TRMs and their subsequent differentiation into TRMs that protect against respiratory viruses. Specific

Aim 1 will test the hypothesis that diverse microbial exposure influences the development and protective functions of lung TRMs against IAV and SARS-CoV-2. Here, we will compare the development and transcriptional programming of lung TRMs induced by two combination adjuvant vaccine formulations and protective immunity to IAV and SARS-CoV-2 in SPF and

Dirty mice. Specific Aim 2 will test the hypothesis that diverse microbial exposure promotes the conditioning of

circulating/lymphoid pre-TRMs, leading to enhanced differentiation of TRMs in lungs of vaccinated Dirty mice. Here, in Dirty and SPF mice, we will incisively dissect whether diverse microbial exposure enhances the pre-conditioning of naïve CD8 or CD4 T cells prior to vaccination and/or antigen-activated effector T cells during vaccination, to a TRM cell fate.

Impact:. Proposed studies will leverage microbial exposure to improve the rigor of mouse models to predict human immune response to vaccines, and provide mechanistic insights into the development of TRMs in the lung under conditions

of diverse microbial exposure. Hence, this exploratory ‘high pay off’ R21 application blends significance and innovation to lay the conceptual framework for further mechanistic investigations that will pave the way for the development of a

biologically relevant and translatable pre-clinical animal model to learn how we can leverage microbiota to enhance vaccine- induced T-cell immunity to IAV and SARS-CoV-2, which are human respiratory viruses of public health importance.