Transcription factor collaboration enables precise T cell state engineering

Area of Science:

• Immunology
• Molecular Biology
• Systems Biology

Background:

• Transcription factors (TFs) orchestrate gene expression programs crucial for cell fate determination.
• CD8+ T cell exhaustion, a state of dysfunction, impairs immunity during chronic infections and cancer.
• Understanding TF collaboration is vital for deciphering cell state regulation.

Purpose of the Study:

• To identify cell state-specific TFs regulating CD8+ T cell exhaustion.
• To map TF-program connections and understand their collaborative roles.
• To explore the potential of TF engineering for therapeutic applications.

Main Methods:

• Pooled overexpression screens of 3,548 TF and TF isoforms in primary T cells.
• Perturb-seq (perturb-SHARE-seq) to link TF perturbations to chromatin accessibility and gene expression in single cells.
• Deep learning framework (seq2PRINT) to predict functional TF interactions.

Main Results:

• Identified 82 regulators collaborating with exhaustion-specific programs.
• Mapped 12,616 TF-program connections across CD8+ T cell states.
• Discovered RUNX as a master collaborator, with a specific RUNX2:KLF2 interaction driving exhaustion.
• Nominated KLF2 as a predictor of CAR-T therapy response.

Conclusions:

• The collaborative action of RUNX TFs significantly drives CD8+ T cell states.
• Targeting TF interactions, like RUNX2:KLF2, can modulate T cell exhaustion.
• TF tethering offers a strategy for engineering cell identity in cell and gene therapies.