Gene regulatory network determinants of rapid recall in human memory CD4+ T cells

Rapid recall is the hallmark of memory T cells. While naive cells require days to mount effector responses to new threats, antigen-experienced memory cells produce cytokines within hours of a repeat encounter. Compared to naive cells, memory cells exhibit enhanced chromatin accessibility proximal to rapid-recall genes, but the transcription factors (TFs) that establish, maintain, and utilize these putative regulatory elements are unknown. We leverage single-nuclei multiome sequencing (gene expression and chromatin accessibility) to characterize the dynamic activation responses of CD4⁺ T cells and reconstruct the underlying gene regulatory networks. Memory-associated TFs (MAF, PRDM1, RUNX2, SMAD3, and KLF6) are predicted to orchestrate rapid recall. KLF6 binding to its predicted target genes is confirmed by chromatin immunoprecipitation sequencing, while the memory-associated activities of all five factors replicate in independent single-cell RNA sequencing studies. Integrating genome-wide association study data, we nominate CD4⁺ T cell populations and gene regulatory mechanisms that might underlie genetic risk to immune-mediated diseases.