EOMES: A link between METABOLIC ADAPTATION and EPIGENETIC REMODELING? – EMETIC

The role of Eomes in the CD4+ T cells remains mostly unclear and differs regarding the disease, context and Th subsets. However, what seems consistent is the importance of Eomes in inflammation as suggested by genetic association studies. Our recent results revealed that Eomes controls chronic neuroinflammation by increasing survival of effector CD4 T cells infiltrating the CNS through the regulation of mitochondrial metabolism. This unappreciated function of Eomes in metabolic adaptation could also account for the accumulation of Eomes-expressing cells in inflamed tissues of patients with chronic inflammatory diseases or cancer. However, many questions about the molecular mechanisms at play remain to be answered.

Therefore, this project aims to decipher the role of Eomes in the complex cross-talk between metabolic adaptation and gene expression that is likely to play a central role in T-cell-mediated inflammatory diseases. To achieve this goal, we will use the EAE model induced upon transfer of 2D2 TCR transgenic cells specific for the myelin immunodominant peptide. Eomes role will be address by comparing WT versus Eomes-deficient 2D2 cells and the impact of the environment by comparing cells extracted from the CNS to cells from draining lymph nodes of the same mice. Using this model, we plan to:

1) Analyze the metabolomic pathways regulated by Eomes in CNS infiltrating CD4+ T cells. Mitochondrial bioenergetic profiles of ex vivo isolated cells will be characterized using SeaHorse technology and the Scenith method. Changes in both the rates of nutrient consumption and metabolic end-products will be measured and quantitative changes in the central metabolite pools evaluated by Mass Spectrometry methods and further validate by isotope labeling and profiling experiments.

2) Decipher the molecular function of Eomes at the transcriptomic and epigenetic level. We will identify genome-wide specific Eomes DNA-binding sites by CUT&RUN associated with RNA-seq and ATAC-seq assays to strengthen the list of true Eomes targets. Global change in histone modifications will be assess and epigenetically affected loci identified.
3) Integrate Multi-omics data and validation. Bioinformatic tools will be used to identify critical metabolic nodes and their functional transcriptomic and/or epigenetic consequences but also genes and networks that coordinated metabolic response. Selected candidate genes or metabolites will be validated using inhibitors, lentiviral-driven overexpression or a CRISPR-Cas9 system. Their relevance will be further confirmed in other inflammatory models and human samples of MS patients.
Deciphering the precise mode of action of this transcription factor is critical to gain insight into the specific metabolic programs necessary for CD4+ T cells to survive and accumulate in inflamed tissues. Our results should foster understanding of the mechanisms whereby metabolic remodeling alters gene expression and thereby T cell function. Beyond these scientific advances, this project will have direct relevance to human diseases. Indeed, results obtained here will lead to a more comprehensive understanding of the metabolic checkpoints regulating T cell persistence in tissues that has been shown to contribute to disease progression. Targeted manipulation of metabolism is a powerful tool to shape immune cell responses in diseases and our results should provide new insights in the dialog between metabolism regulation and gene expression of T cells involved in the inflammatory response and open new avenue for therapeutic strategies.

This multidisciplinary project is based on the collaboration between three partners that have complementary expertise encompassing metabolism (JES), epigenetic and transcriptomic (AV) and neuroimmunology (ASD). This consortium will benefit from the expertise of bioinformaticians from our centers and MetaToul and GenoToul specialized platforms.