
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.15.608093
preprint
1
Article
Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model
Liu Wendao http://orcid.org/0000-0002-5124-9338

Zhao Zhongming http://orcid.org/0000-0002-3477-0914

19 8 2024
2024.08.15.608093https://creativecommons.org/licenses/by-nc/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.15.608093
nihpp-2024.08.15.608093.pdf
Immune cells undergo cytokine-driven polarization in respond to diverse stimuli. This process significantly modulates their transcriptional profiles and functional states. Although single-cell RNA sequencing (scRNA-seq) has advanced our understanding of immune responses across various diseases or conditions, currently there lacks a method to systematically examine cytokine effects and immune cell polarization. To address this gap, we developed Single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization analysis. Scupa is trained on data from the Immune Dictionary, which characterizes 66 cytokine-driven polarization states across 14 immune cell types. By leveraging the cell embeddings from the Universal Cell Embeddings model, Scupa effectively identifies polarized cells in new datasets generated from different species and experimental conditions. Applications of Scupa in independent datasets demonstrated its accuracy in classifying polarized cells and further revealed distinct polarization profiles in tumor-infiltrating myeloid cells across cancers. Scupa complements conventional single-cell data analysis by providing new insights into immune cell polarization, and it holds promise for assessing molecular effects or identifying therapeutic targets in cytokine-based therapies.
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