T cell responses in vivo are highly heterogeneous and polyfunctional. Thus, to capture the diversity of T cell populations we are using single-cell methods. In addition of multiparameter flow cytometry, we perform single-cell RNAseq, ATACseq, CHIPseq to uncover new cell populations and gene programs of T cells responding to pathogens and tumors.
Imaging and Spacial Transcriptomics
To uncover the dynamics of T cell responses within tissues we are using new imaging and transcriptomics methods to investigate the spatial distribution and gene expression of T cell populations in the tumor and lymphoid organs.
Recent advances in gene editing methods allow us to target specific loci using CRISPR-Cas9 approaches. By creating new animal models this allow us to enhance, delete or track gene expression in T cells in vivo. In addition, we implemented this strategy to perform high throughput gene screening in T cells in vivo.
To analyze and integrate data generated from our study, we are developing new computational methods to further understand how the repertoire, gene expression and epigenetic landscape influence T cell responses.