Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model.

ABSTRACT:

Motivation

Immune cells undergo cytokine-driven polarization in response to diverse stimuli, altering their transcriptional profiles and functional states. This dynamic process is central to immune responses in health and diseases, yet a systematic approach to assess cytokine-driven polarization in single-cell RNA sequencing data has been lacking.

Results

To address this gap, we developed single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization assessment. Scupa leverages data from the Immune Dictionary, which characterizes cytokine-driven polarization states across 14 immune cell types. By integrating cell embeddings from the single-cell foundation model Universal Cell Embeddings, Scupa effectively identi

SUBMITTER: Liu W 

PROVIDER: S-EPMC11893155 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature