Systematic single-cell pathway analysis to characterize early T cell activation
Jack Bibby, Divyansh Agarwal, Tilo Freiwald, Natalia Kunz, Nicolas S. Merle, Erin E. West, Parul Singh, André Larochelle, Fariba Chinian, Somabha Mukherjee, Behdad Afzali, Claudia Kemper, Nancy R. Zhang
Abstract
Pathway analysis is a key analytical stage in the interpretation of omics data, providing a powerful method for detecting alterations in cellular processes. We recently developed a sensitive and distribution-free statistical framework for multisample distribution testing, which we implement here in the open-source R package single-cell pathway analysis (SCPA). We demonstrate the effectiveness of SCPA over commonly used methods, generate a scRNA-seq T cell dataset, and characterize pathway activity over early cellular activation. This reveals regulatory pathways in T cells, including an intrinsic type I interferon system regulating T cell survival and a reliance on arachidonic acid metabolism throughout T cell activation. A systems-level characterization of pathway activity in T cells across multiple tissues also identifies alpha-defensin expression as a hallmark of bone-marrow-derived T cells. Overall, this work provides a widely applicable tool for single-cell pathway analysis and highlights regulatory mechanisms of T cells.