Remin-T · Dissecting the molecular basis of immunological memory in human T cells

T lymphocytes are essential for immunity to pathogens and malignancies. Activated T cells can retain a memory imprint of their adversary (e.g. a virus), enabling them to respond more rapidly and vigorously to any subsequent encounters. While memory T cell formation is critical for successful vaccination and anti-tumor immunity, dysfunctional memory T cells are a common feature of human disease, including allergy, autoimmunity and cancer. T cell activation emerges from changes in gene expression dictated by intricate chromatin dynamics. Recently, 3D chromatin folding emerged as a key regulator of transcriptional control by ensuring correct communication between regulatory elements and their target genes. How memory T cells leverage three-dimensionally organized chromatin configurations to achieve rapid re-activation of specific inflammatory genes is unclear. Hence, the molecular mechanisms that control and maintain immunological memory remain poorly understood. To address this issue, I propose an innovative molecular strategy to dissect immunological memory in primary human CD4+ T cells that combines cutting-edge genome-wide analyses of gene expression, chromatin state and three-dimensional (3D) genome folding with CRISPR/Cas9-based functional assays. This approach will generate the first integrated multidimensional epigenome atlas of a human T cell memory recall response, yielding molecular circuits of genes, regulatory elements and biological pathways underlying human immunological memory. Multimodal single cell genomics assays will reveal the nature of transcriptome-epigenome crosstalk in individual T cells and the heterogeneity of memory recall. These insights will force a breakthrough in our understanding of how human immune cells maintain specific transcriptional programs for launching rapid and tailored responses upon re-activation, and how this feeds into susceptibility to develop disease.