Mechanisms of regulatory T cell-mediated recovery from severe viral pneumonia

PROJECT SUMMARY/ABSTRACT Severe viral pneumonia due to influenza A virus and SARS-CoV-2 injures the lung to cause the acute respiratory distress syndrome (ARDS). Viral pneumonia-induced ARDS carries a mortality rate approaching 40% despite advances in clinical management, with unrepaired lung injury placing patients at risk for fatal intensive care unit (ICU) complications. Therefore, we reason that activation of lung repair following severe viral pneumonia will spur the process of recovery to reduce the duration of time that patients require the ICU, mitigating the ICU's attendant morbidity and mortality. CD4+FOXP3+ regulatory T (Treg) cells are required for healthy repair of lung injury in mouse models of viral pneumonia and accumulate in the alveolar spaces of patients with severe pneumonia and ARDS. Within Treg cells, the DNA methylation pattern at specific genomic loci as well as mitochondrial metabolism determine their identity and function. Alveolar Treg cells in patients with severe pneumonia display DNA methylation and transcriptional profiles predicted by mouse experiments, credentialing Treg cells as a cellular therapy if several barriers are surmounted. Specifically, 1) metabolic challenges to Treg cell function hinder clinical Treg cell transfer protocols, and 2) induced (i)Treg cells, which derive from abundant conventional T cells following treatment with TGF-β ex vivo, exhibit transcriptional and functional instability in inflamed microenvironments, limiting their use as a cellular therapy. Preliminary data suggest that an energy- sensitive enzyme, AMPK, regulates DNA methylation to promote Treg cell lung-protective function in vivo and that a DNA methylation maintainer, UHRF1, stabilizes iTreg cell identity after adoptive transfer to mice with influenza A virus pneumonia. Accordingly, we hypothesize that AMPK optimizes Treg cell pro-repair function in the virus-injured lung and UHRF1 stabilizes iTreg cell pro-repair function to drive recovery from viral pneumonia. In our three Specific Aims, we will use innovative and rigorous approaches, including Treg cell- specific inducible systems in mice and a case-control study of patients with severe viral pneumonia. In Aim 1, we will determine whether AMPK is necessary to promote DNA methylation patterns that optimize mitochondrial and pro-repair function in Treg cells during recovery from influenza A virus pneumonia. In Aim 2, we will determine the necessity of UHRF1-mediated DNA methylation in stabilizing iTreg cell transcriptional programs and pro-repair function during recovery from influenza A virus pneumonia. In Aim 3, we will determine whether AMPK-associated transcriptional programs and the DNA methylation status of mitochondrial metabolism- promoting genes are correlated with 30-day mortality in alveolar Treg cells obtained from patients with severe viral pneumonia. Our proposal will establish causal evidence linking targetable mechanisms to detailed physiological readouts of Treg cell function. Elucidating these causal links will inform the development of Treg cell-based therapeutic approaches for patients with severe viral pneumonia and other causes of ARDS.