Kinetical scRNAseq Analysis Reveals Immune Mechanisms Underlying Hindered Lung Recovery following Influenza Virus Infection in Aged Hosts

Aging is a major risk factor for host morbidity and mortality upon acute respiratory virus infections. To better elucidate the immune determinants of viral pathogenesis during aging, we conducted a time-course single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry analysis on the pulmonary responses against influenza infection in young or aged mice. Notably, aged mice exhibited decreased populations of alveolar macrophages (AMs) and dendritic cells (DCs), alongside an increase in monocyte-derived macrophages (MoMs) and interstitial macrophages (IMs), which last weeks after acute viral infection. Additionally, there was enhanced accumulation of respiratory adaptive immune cell cells including tissue resident helper CD4 T cells (TRHs), CD8 tissue resident memory cells (TRMs) and a unique B cell population resembling age-associated B cells. Gene set enrichment analysis (GSEA) comparing lung transcriptomes of young and aged mice across time points highlighted persistent type I and type interferon signaling in aged hosts, especially in the macrophage population. Interestingly, inhibiting interferon signaling in aged mice after viral clearance led to ameliorated long-term sequelae, along with a decrease in IM and TRH populations. Our findings suggest that IFNa/? signaling, particularly in MoM/IM, is pivotal in the development of long-term sequelae following acute respiratory infections in aged hosts. Overall design: To distinguish tissue resident and circulating/vasculature-associated immune population, 2µg/ms anti-mouse biotin conjugated CD45 antibody (Biolegend, Clone: 30-F11) was injected intravascularly 5min before humanely euthanizing the animal. Single cell suspention from lung homogenate was stained with DNA-oligo conjugated streptavidin. Single Cell 5' Library & Gel Bead Kit with Feature Barcoding was then utilized for scRNAseq library construction.