Inferring pathway activity from single-cell and spatial transcriptomics data with PaaSc

Abstract

Recent advances in single-cell and spatial transcriptomics have revolutionized our understanding of cellular heterogeneity. However, translating high-dimensional data into functional pathway insights remains challenging. To address this obstacle, we developed PaaSc (Pathway activity analysis of Single-cell), a computational method for inferring pathway activity at single-cell resolution. PaaSc employs multiple correspondence analysis to simultaneously project cells and genes into a common latent space and selects pathway-associated dimensions through linear regression to infer pathway activity scores. We validated PaaSc across diverse benchmarking datasets, including those that jointly profiled protein and RNA levels, as well as large-scale cancer scRNA-seq cohorts. Compared with state-of-the-art methods, PaaSc demonstrated superior performance in multiple applications: scoring cell type-specific gene sets, identifying cell senescence-associated pathways, and exploring GWAS trait-associated cell types. Importantly, PaaSc maintained accuracy despite batch effects and demonstrated robust performance across different data modalities, including scATAC-seq and spatial transcriptomics data. Our results demonstrate that PaaSc accurately captures dynamic cellular states and spatial patterns, thereby advancing our understanding of cellular dynamics, aging, and disease mechanisms.