Signalome-wide mapping of the NFκB pathway in T-cells reveals novel targets for immunotherapy

Abstract

Cell signalling networks govern fundamental cellular processes yet remain incompletely defined. Moreover, what is known is biased toward a limited subset of well-characterised components. Phosphoprotein-based interrogation methods, including mass spectrometry and targeted phosphosite panels, have limited utility in physiological settings dependent on cell-cell interactions because the signalling fluxes can be difficult to detect despite producing robust functional responses. Here we developed a perturbation-based experimental framework that infers signalling pathway architecture using quantitative functional outputs rather than direct measurements of effector state, e.g., phosphorylation levels. Using antigen-specific, NF-{kappa}B-GFP reporter-expressing transformed T-cells co-cultured with cellular targets, we performed an arrayed CRISPR-Cas9 screen targeting a curated signalome of kinases, phosphatases, adaptor and scaffolding proteins, totalling 706 genes. Quantitative effect-size profiling recovered canonical T-cell receptor regulators and revealed unequal, family-specific patterns of control over NF-{kappa}B activation. Comparing T-cell stimulation with low- and high-affinity antigen uncovered signal-strength-dependent buffering of proximal signalling nodes, exemplified by reduced sensitivity to perturbation of LCK under high-intensity stimulation. Targeted perturbation in primary human CD8 T-cells validated our findings and identified TRRAP and CTDSPL2 as negative regulators of T-cell effector output, whose disruption enhanced cytotoxicity, degranulation, and cytokine production in both polyclonal and TCR-engineered T cells. Together, these results establish a scalable strategy for mapping signalling pathway architecture in the setting of physiological T-cell activation.