Project description:The role of mucosal invariant T (MAIT) cells in the lung tumor microenvironment re-mains poorly understood, especially in the setting of immune checkpoint inhibitors. We identified intratumoral MAIT cells from paired single cell RNA and TCR sequencing datasets of tumor infil-trating CD3 T cells isolated from non-small cell lung cancer tumors in patients receiving neoadju-vant PD-1 blockade therapy. MAIT cells were subclustered to identify conventional MAIT-associ-ated TCR clonotypes, which were then tested for the recognition of bacteria using a MAIT TCR capture functional assay. Strikingly, surveillance of intratumoral bacteria in lung cancer patients revealed Enterococcus spp. that are not directly recognized by MAIT cells but, nevertheless can synergize with exogenous riboflavin biosynthesis-derived metabolites to induce expression of MR1 by antigen presenting cells (APC, dendritic cells, B cells and mononuclear phagocytes). Enhanced MR1 cell surface expression resulted from enterococcal-mediated perturbation of an endo-lysosomal vacuolar pathway with recycling of early endosomal MR1 to the APC cytoplasmic membrane. Riboflavin auxotrophic Enterococcus spp may therefore exercise their beneficial im-munomodulatory functions upon immune checkpoint blockade treatment, at least in part, by pro-moting intratumoral MR1 expression and innate-like T cell activation. Our results indicate that composition of the intratumoral microbiome during immune checkpoint inhibitor treatment has the potential to impact the function of human intratumoral MAIT cells.
Project description:We investigated the RNA-protein interactome of Enterococcus faecalis V583 and Enterococcus faecium Aus0004 by native gradient fractionation of complexes coupled to RNA-sequencing. Whole bacterial cell lysates were analysed by size and density in a glycerol gradient. At native conditions, RNA-protein complexes stay intact and sediment as a whole. Sedimentation profiles of individual RNAs appear correlated in case of interaction in a complex. The profile of KhpB caught our attention and we determined its RNA interactome by immunoprecipitation that suggests a role at the post-transcriptional level, binding notably several tRNAs, sRNAs, and 3’UTRs.
Project description:To further investigate the homeostatic response of E. faecalis to Fe exposure, we examine the whole-genome transcriptional response of wild-type (WT) exposed to non toxic Fe excess. This experiment correspond the work titled Transcriptomic response of Enterococcus faecalis to iron excess (work in preparation) A four chip study using total RNA recovered from four separate wild-type cultures of Enterococcus faecalis OG1RF, two controls samples (N medium growth) and two iron samples (N medium gowth with 0.5 mM Fe-NTA). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).