Atomistic TCR-ligand interactions instruct memory T-cell differentiation

Memory T cells endow the mammalian host with an essential form of adaptive immunity that generates durable and rapid protection following re-exposure to an infectious pathogen or a cancerous transformation^1-4. How naive CD8⁺ T cells develop into memory T cells that bifurcate into long-lived central (TCM) versus effector (TEM) subsets after such an antigen encounter remains ill-defined at the molecular level. To address this gap, here we dissect the functional T-cell receptor (TCR) repertoire of 242 murine CD8⁺ TCRαβ clonotypes specific for the peptide-major histocompatibility complex molecule (pMHC) comprising an immunodominant influenza A virus (IAV) oligopeptide epitope NP_366-374 presented by H-2D^{b 5,6}. Using single-cell transcriptomics with TCR sequencing, biophysical measurements of force-dependent TCR-pMHC interactions, in vivo memory development, and structural analyses, we integrate these data to define relationships between signaling polarity and memory fate. We find that T_CM and T_EM polarities are reflected in distinct subunit-related mechanotransduction biases: T_CM-associated TCRs favor TCRβ-driven pMHC engagement, whereas T_EM-associated TCRs preferentially favor TCRα-driven pMHC engagement. Moreover, "bipolar" clonotypes (T_BP) capable of generating both memory subsets exhibit more balanced signaling, the largest average clonal expansions, and broadest heterosubtypic crossreactivities. By contrast, variegated T_CM TCR sequences foster mostly clonal singlets with the greatest IAV mutant recognition potential within the overall memory repertoire, thus revealing two complementary memory niche crossreactivity strategies. Weak, force-sensitive TCR bonds are pervasive for this entire repertoire, being most conspicuous amongst T_CM clonotypes. At the atomic level, highly nuanced variation in TCRαβ bonding to either peptide and/or MHC modulates mechanical load transmission across the holoreceptor's ectodomains, transmembrane segments, and CD3 cytoplasmic tails to differentially influence downstream tyrosine phosphorylation and memory development. Collectively, TCR diversity anticipates epitope-specific pathogen evolution, whereas divergent TCR signaling regulates memory fate with implications for adoptive T-cell immunotherapies seeking to maximize persistence and minimize functional exhaustion.