Influenza virus causes distinct alterations in human and murine alveolar macrophages: a comparative analysis for a translational perspective – FLUMACRO

Influenza A virus (IAV) cause deadly epidemics but therapeutic strategies are lacking. Bacterial co-infection is commonly reported in critically ill patients admitted for influenza and promotes a greater severity of viral infection. Alveolar macrophages (AMs) are critical players of innate immunity but little is known about IAV-infected alveolar macrophages. A substantial reduction in the AM population is often seen in IAV–infected mice models. The prominent theory suggests that the IAV-induced AMs depletion results in an increased lung predisposition to bacterial co-infection. However, and as preliminary data, we demonstrated in clinical investigations that no AMs depletion was observed in human during IAV-related pneumonia. Moreover, we observed important mice-to-human differences in the local production of granulocyte macrophage-colony stimulating factor (GM-CSF), a potent regulator of AMs proliferation and function. Overall, these results evidence a clear contrast between IAV-infected humans and IAV-infected mice. We hypothesize that a better knowledge of human AMs pathophysiology during influenza infection, and the potential protective role of GM-CSF, will lift major barriers for understanding the severity of some influenza infections and bacterial superinfection phenomena. The objectives of the project are (i) to decipher the mechanism by which IAV infection alters human AMs function, taking in consideration both isolated cells and the lung micro-environment and, (ii) to provide evidence, in both mice and human, that GM-CSF could represent a promising therapy during influenza infection. To achieve these goals, the project is organized in two work packages (WP): WP1 aims to characterize the GM-CSF-dependent pathways in human AM during lung influenza infection by (i) using omics of human AMs collected during ex-vivo infection by IAV, (ii) using spatial transcriptomic analysis of human precision cut lung slice infected by IAV and (iii) using single-cell RNA-sequencing of endotracheal aspirates from patients with influenza infection. WP2 aims at deciphering the mechanisms of AM depletion in IAV-infected mice and its correction by GM-CSF or by trained immunity. We will compare IAV-induced cell death ex vivo in mice and human AMs, assess the effect of GM-CSF therapy on the ‘‘macrophage disappearance reaction’’ observed in mice, and evaluate if experiencing previous infections protect mice from IAV-induced AM depletion. We aim to get results that will provide the ultimate step for designing a clinical trial that will assess the benefit of GM-CSF administration to treat severe influenza infection and prevent bacterial super-infection. To optimize the chance of success, we have built a consortium that brings together complementary expertise in influenza infection, macrophage biology and intensivists specialized in respiratory infection. A continuous crosstalk between researchers and clinicians has been set-up to maximize the extraction of information from human biological samples and a constant effort has been made throughout this project to use physiological conditions to optimize the translational value of the experimental results.