Okazaki, I.-m. | bioRxiv Science

bioRxiv2026

Temporal Mechanisms of T-Cell Fate Decisions under Immune Checkpoint Blockade Resolved by CanonicalTockySeq

In cancer immunotherapy, T-cell functional states change dynamically, and no single marker or gene fully defines them. Static molecular profiles may therefore be insufficient to resolve these states. Capturing signalling history together with ongoing activity could provide a temporal framework for their dissection. Here, we developed CanonicalTockySeq, which integrates a molecular clock of T-cell receptor (TCR) signalling based on the Fluorescent Timer reporter Nr4a3-Tocky (Timer-of-cell-kinetics-and-activity) with scRNA-seq to establish an experimentally anchored temporal reference. Using landmark Tocky fractions as biological ground truths, CanonicalTockySeq constructs a transcriptomic manifold in canonical space with conical geometry. In a murine melanoma model treated with combination anti-PD-L1 and anti-CTLA-4, this framework separates temporal progression (geodesic angle) from signalling strength (radial intensity), enabling time-resolved analysis of gene-expression programmes at single-cell resolution. Application to scRNA-seq data from patients with melanoma further identifies distinct temporal programmes associated with clinical response. These analyses indicate that effective combination immunotherapy is associated with decreased persistence of antigen engagement, suppression of exhaustion-associated TCR signalling programmes, and maintenance of progenitor-like features linked to durable antitumour responses. Collectively, our findings identify temporal-state control as a key component of immunotherapy outcome and establish CanonicalTockySeq as a framework for resolving T-cell response states in vivo.

immunology↗

bioRxiv2022

Single-cell level temporal profiling of tumour-reactive T cells under immune checkpoint blockade

The blockade of the immune checkpoints PD-1 and CTLA-4 enhances T cell response. However, it is largely unknown how antigen-reactive T cells regulate their checkpoint expression in vivo and whether and how the checkpoint blockade can change activation dynamics of tumour-reactive T cells. To address this, here we used Nr4a3-Timer-of-cell-kinetics-and-activity (Tocky), which allows analysis of temporal changes of activated T cells following TCR signalling in vivo. By analysing melanoma-bearing Nr4a3 Tocky mice, we elucidate hidden dynamics of tumour-reactive T cells in the steady-state. Checkpoint blockade depleted highly activated effector Treg, while promoting unique effector T cell populations, and thus differentially modulating activation of tumour-reactive T cell populations. Furthermore, multidimensional analysis and seamless analysis of Tocky and scRNA-seq revealed a full spectrum of T cell dynamics in response to tumour burden and treatment with checkpoint blockade. Lastly, we propose a rational design of combinatorial therapy to further enhance T cell activities.

immunology↗