Systematic single-cell pathway analysis to characterize early T cell activation.
Cell Rep
; 41(8): 111697, 2022 11 22.
Article
in En
| MEDLINE
| ID: mdl-36417885
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Single-Cell Analysis
Language:
En
Journal:
Cell Rep
Year:
2022
Document type:
Article
Affiliation country:
United States