Profiling transcription factor-cofactor networks in various T cell states
OA Version
Citation
Abstract
Characterizing the gene regulatory mechanisms that define distinct T cell states is essential for understanding T cell biology in health and disease. Despite advances in identifying transcriptional and epigenetic differences across T cell states, the regulators of these changes remain poorly defined. Gene expression changes are primarily coordinated by transcription factors (TFs) that bind throughout the genome and recruit cofactor proteins (COFs) for gene regulation. These TF-COF interactions can be cell type-specific, change in response to signals, and be altered in various diseases. To understand how TF-COF interactions might control transcriptional and epigenetic differences in T cell states, we developed CoRec (Cofactor Recruitment), a high-throughput, protein-based method for characterizing TF-COF complexes in cells. Using CoRec, we profiled numerous COFs in resting, activated, and exhausted T cells. Preliminary work with Jurkat T cell lines revealed that COF-TF networks are highly dynamic, with 35% of initial interactions altered after 45 minutes of TCR stimulation. Additionally, integration of CoRec data with H3K27ac ChIP-seq suggested that specific TF-COF complexes regulate the placement and maintenance of this epigenetic mark. Expanding our analysis to primary CD4+ T cells, we examined resting memory, TCR-stimulated, and IL-15-stimulated T cells, uncovering distinct functional differences and widespread changes in TF-COF complexes across states. Furthermore, we used CoRec to profile COFs in T cell exhaustion, a dysfunctional state, and observed that key TF regulators of exhaustion interact with KATs, suggesting mechanisms by which these TFs drive T cell exhaustion. Finally, we developed an additional assay called the Cooperative Recruitment of Cofactors Assay (CCRA) to profile cooperative recruitment of COFs by TF pairs. Preliminary CCRA work in unstimulated Jurkat T cells indicated that cooperative recruitment is a widespread occurrence, with 65% of TF pairs showing cooperative COF recruitment. This widespread cooperative recruitment suggests that the combinatorial logic of multiple TFs may also regulate gene expression in different T cell states. Overall, our study provides valuable insights into the intricate mechanisms of gene regulation in T cells, emphasizing the dynamic nature of TF-COF interactions. This work also offers a foundation for future research that could be translated into targeted therapeutic strategies for immune modulation.
Description
2025
License
Attribution-NonCommercial-ShareAlike 4.0 International