Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision
Kathleen Abadie, Elisa C. Clark, Rajesh M. Valanparambil, Obinna Ukogu, Wei Yang, Riza M. Daza, Kenneth K.H. Ng, Jumana Fathima, Allan L. Wang, Judong Lee, Tahseen H. Nasti, Avinash Bhandoola, Armita Nourmohammad, Rafi Ahmed, Jay Shendure, Junyue Cao, Hao Yuan Kueh
Abstract
The immune system encodes information about the severity of a pathogenic threat in the quantity and type of memory cells it forms. This encoding emerges from lymphocyte decisions to maintain or lose self-renewal and memory potential during a challenge. By tracking CD8+ T cells at the single-cell and clonal lineage level using time-resolved transcriptomics, quantitative live imaging, and an acute infection model, we find that T cells will maintain or lose memory potential early after antigen recognition. However, following pathogen clearance, T cells may regain memory potential if initially lost. Mechanistically, this flexibility is implemented by a stochastic cis-epigenetic switch that tunably and reversibly silences the memory regulator, TCF1, in response to stimulation. Mathematical modeling shows how this flexibility allows memory T cell numbers to scale robustly with pathogen virulence and immune response magnitudes. We propose that flexibility and stochasticity in cellular decisions ensure optimal immune responses against diverse threats.