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Systematic Single Cell Pathway Analysis (SCPA) reveals novel pathways engaged during early T cell activation

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 unexpected regulatory mechanisms of T cells.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE212270 | GEO | 2022/09/01

REPOSITORIES: GEO

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