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Deciphering the host and microbial grounds that license inflammasome-mediated execution

Periodic Reporting for period 4 - INFLAME (Deciphering the host and microbial grounds that license inflammasome-mediated execution)

Reporting period: 2023-06-01 to 2023-11-30

Inflammasomes are intracellular multi-protein complexes that play essential functions in immunity against microbial pathogens. Upon microbial sensing, inflammasomes induce protease caspase-1-dependent maturation and release of the pro-inflammatory cytokines interleukin (IL)-1β and IL-18 as well as gasdermin-D-dependent cell necrosis, called pyroptosis. While both pyroptosis and IL-1β/IL-18 release play key parts in controlling microbial infections, the host-regulated pathways that promote detection of microbial ligands by cytosolic inflammasome-forming sensors and the non-canonical functions of inflammasome-derived components, remain to be fully characterized.
Building on the group expertise in the field of inflammasome regulators during microbial infections, we propose to study several key, yet unexplored aspects of the functions of inflammasomes in immunity from different angles. In particular, we propose to 1/ identify and characterize new host interferon-inducible factors that mediate microbial sensing by the inflammasomes, and 2/ unravel new non-canonical functions of inflammasome-derived proteases and gasdermins.
To address these issues, we will use a combination of state-of-the-art and innovative technologies in biochemistry, molecular and cell biology, and immunology in various in vitro and in vivo models.
This multidisciplinary proposal will provide breakthroughs in the field of microbial pathogens detection by the host immune system. The results of this project will also provide strong bases for building innovative host-directed therapies for auto-inflammatory disorders and infectious diseases.
The overall aim of the project was to identify and characterize host and microbial factors that regulate inflammasome assembly or promote non-canonical functions of inflammasome-derived components. The project has led to several publications in leading scientific journals. We have demonstrated that additional host-derived and microbial-derived effectors can control and modulate microbial sensing by the cytosolic inflammasomes. Specifically, we could unveil that several host- and microbial-derived factors control the induction of the non-canonical inflammasome pathway in response to the Gram-negative component, namely the LPS. More precisely, we found that the non canonical inflammasome is kept under control thanks to the engameent of two host effectors, Irgm2 and Gate16, which limits its deletrious and uncontrolled response (Eren et al., EMBO Rep. 2020). We also determined that, among the large body of microbial ways of triggering the non canonical inflammasome pathway, pathogenic E. coli bacteria produce an hyper active type of outer membrane vesicles (OMVs) that promote a pathological inflammasome-dependent response (David. L et al., Autophagy. 2022). Furthermore, microbial studies also highlighted a surprising process by which P. aeruginosa pathogenic bacteria trigger an exacerbated and lethal infection through the induction of cellular necrosis, a process that we unveiled to require host basal phospholipid peroxidation-induced P. aeruginosa ExoU-dependent activation (Bagayoko and Meunier, FEBS J. 2022) and (Bagayoko et al., PLoS Pathog. 2021).
In another aspect, we deciphered that during SARS-CoV2 infection of airway respiratory cell, responsible of COVID19 disease, an innate immune receptor, namely NLRP1, was able to detect the virulence induced by the SARS-CoV2 protease 3CL (Planes et al., Mol Cell
. 2022). Specifically this sensor behaved as a decoy sensor of the protolytic activity of 3CL protease, which further promoted the formation fo the NRLP1 inflammasome and the death of the infected cell. We also unveiled that the 3CL protease was able to partly counteract this signalling pathway by directly cleaving and inactivating the pyroptosis effector, Gasdermin D. FInally, this work also highlighted that IL-16, a poorly understood and characterized cytokine, was also released upon apoptotic caspase-3-induced epithelial cell pyroptosis during viral infection. Interestingly, this characterization is also linked to a complementary study where we could unveil that neutrophils, critical immune cells, also release IL-16 in an inflammasome-dependent pyroptosis pathway upon P. aeruginosa bacterial infection, hence warranting for a deep charcaterization of the function of IL-16 on the immune response (Santoni et al., PLoS Pathog. 2022), (Santoni, Planes, Meunier Methods Mol Biol. 2022) and in collaboration (Chauhan et al., EMBO Rep. 2022).
Further studies also identified novel microbial, environmental and host signals that specifically regulate the human NLRP1 inflammasome response in various pathological contextes. For instance, we could determine that upon infection with P. aeruginosa bacteria, the human NLRP1 inflammasome is a sensor of the host translation inhibition induced by the P. aeruginosa virulence toxin, ExoA (Pinilla et al., J Exp Med. 2023). We also determined that mutations in the critical pathway involved in teh regulation of the EXOA target, confer resistance to EXOA-induced translation inhibition and subsequent NRLP1 inflammasome response. Related to this, an unexpected finding of this work is that we could detemrine that in non hematopietic cells, the NLRP1 inflammasome is also an innate immune complex that monitor for the intracellular levels of potassium, a critical ionic specie in our body (Rosario, Pinilla et al., Proc Natl Acad Sci U S A. 2024). Beyond this work, these studies required the development of specific human-derived structures, namely organoids, that allowed us to set up novel airway and lung organoids from donors and patients in order to charcaterize their response to infections and the associated signalling pathways involved (Iakobachvili, Leon-Icaza et al., Mol Microbiol. 2022) and (Leon-Icaza et al., PLoS Pathog. 2023).
All in one, the results presented above provide 1/ novel mechanistic insights in the host-driven and microbial-dependent reguation of inflammasome-induced response in macrophages, neutrophils and epithelial cells/organoids, 2/ highlight novel effectors as cell death-derived immune components (IL-16) and 3/ unveil gasdermins as targets of microbial proteases. The generated knowledge aims at serving as scientific ground for future studies but also in the frame of the development of host-targeted therapies.
Beyond our findings, we have observed a strong link between genetic polymoprhisms in NLRP1 and various infectious and non infectious pathologies. Here we also aim at evaluating the selective disadvantage/advantage of genetic polymorphisms in NLRP1 against various inflamamtory toxins/infections. To this regard, we are finishing a study of the characterization of detrimental dermatitis induced by exposure to algal blooms. In this process, we unveiled that this disease is fully driven by te NLRP1 inflammasome and provided two major additional findings: First, we used and charcterized a fully competent in vivo model for studying NLRP1 response (the zebrafish) and secondly, we highlight several human polymorphisms that confer host protection against dermatitis induced during algal blooms. This study is about to be submitted.
Main achivements of this year regarding the SARS-CoV2-2 research