Immune profiling of the lung in Influenza-Associated Pulmonary Aspergillosis using CITE-seq

Influenza-associated pulmonary aspergillosis (IAPA) is a severe fungal superinfection affecting critically ill influenza patients. Current treatments target pathogens but do not address the dysregulated host immune responses that drive morbidity. Host-directed immunotherapies could overcome this treatment gap. In this study, we used CITE-seq to compare transcriptional and surface antibody expression in immune cell populations within the lung tissue of mice with IAPA, influenza infection, Aspergillus infection, and healthy controls. This dataset provides comprehensive immune profiling, offering insights into the immune landscape of the lung during IAPA compared to single infections and healthy controls, which could aid in the development of targeted immunomodulatory therapies. These findings are part of a broader investigation, as detailed in the study "Anakinra restores the immunological misfiring that drives influenza-associated pulmonary aspergillosis." Here, we identified IL-1 inflammation, extensive neutrophil activation, and NET release as key features of IAPA pathogenesis. This inflammation led to an immunological imbalance that impaired neutrophil function, creating a permissive environment for Aspergillus. Blocking the IL-1 receptor with anakinra reduced inflammation, restored neutrophil function, and protected influenza-infected mice from invasive pulmonary aspergillosis and death. These results underscore the critical role of IL-1 inflammation in IAPA and suggest that anakinra could be a promising immunomodulatory therapy for IAPA patients. Overall design: To further refine the different immune cell populations in the lung, we performed CITE-seq on CD45+ sorted lung cells from Healthy control (HC) (n=3), Aspergillus (n=3), influenza (n=4) and IAPA (n=4) mice on day 7