Machine learning predictions of T cell antigen specificity from intracellular calcium dynamics

Sci Adv. 2024 Mar 8;10(10):eadk2298. doi: 10.1126/sciadv.adk2298. Epub 2024 Mar 6.

Abstract

Adoptive T cell therapies rely on the production of T cells with an antigen receptor that directs their specificity toward tumor-specific antigens. Methods for identifying relevant T cell receptor (TCR) sequences, predominantly achieved through the enrichment of antigen-specific T cells, represent a major bottleneck in the production of TCR-engineered cell therapies. Fluctuation of intracellular calcium is a proximal readout of TCR signaling and candidate marker for antigen-specific T cell identification that does not require T cell expansion; however, calcium fluctuations downstream of TCR engagement are highly variable. We propose that machine learning algorithms may allow for T cell classification from complex datasets such as polyclonal T cell signaling events. Using deep learning tools, we demonstrate accurate prediction of TCR-transgenic CD8+ T cell activation based on calcium fluctuations and test the algorithm against T cells bearing a distinct TCR as well as polyclonal T cells. This provides the foundation for an antigen-specific TCR sequence identification pipeline for adoptive T cell therapies.

MeSH terms

  • Algorithms*
  • Animals
  • Animals, Genetically Modified
  • Calcium*
  • Machine Learning
  • Receptors, Antigen, T-Cell

Substances

  • Calcium
  • Receptors, Antigen, T-Cell