Robust identification of perturbed cell types in single-cell RNA-seq data

• Published in: Nature communications 2024-09, Vol.15 (1), p.7610-14, Article 7610
• Main Authors: Nicol, Phillip B., Paulson, Danielle, Qian, Gege, Liu, X. Shirley, Irizarry, Rafael, Sahu, Avinash D.
• Format: Article
• Language: English
• Subjects: 631/114/2164; 631/114/2397; 631/114/2415; 631/1647/48; 631/208/212/2019; Computational Biology - methods; Computer applications; COVID-19; COVID-19 - genetics; COVID-19 - virology; Datasets; Dendritic cells; Dendritic Cells - metabolism; Disease; Gene Expression Profiling - methods; Humanities and Social Sciences; Humans; Immune system; Immunotherapy; Immunotherapy - methods; Killer Cells, Natural - metabolism; multidisciplinary; Perturbation; RNA-Seq - methods; Robustness; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Single-Cell Gene Expression Analysis; Software; Statistical analysis; Statistical methods; Transcriptome; Transcriptomics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-51649-3

Single-cell transcriptomics has emerged as a powerful tool for understanding how different cells contribute to disease progression by identifying cell types that change across diseases or conditions. However, detecting changing cell types is challenging due to individual-to-individual and cohort-to-cohort variability and naive approaches based on current computational tools lead to false positive findings. To address this, we propose a computational tool, scDist , based on a mixed-effects model that provides a statistically rigorous and computationally efficient approach for detecting transcriptomic differences. By accurately recapitulating known immune cell relationships and mitigating false positives induced by individual and cohort variation, we demonstrate that scDist outperforms current methods in both simulated and real datasets, even with limited sample sizes. Through the analysis of COVID-19 and immunotherapy datasets, scDist uncovers transcriptomic perturbations in dendritic cells, plasmacytoid dendritic cells, and FCER1G+NK cells, that provide new insights into disease mechanisms and treatment responses. As single-cell datasets continue to expand, our faster and statistically rigorous method offers a robust and versatile tool for a wide range of research and clinical applications, enabling the investigation of cellular perturbations with implications for human health and disease. Single-cell RNA-seq experiments often aim to identify cell types that have significant transcriptional differences between two or more biological conditions. Here, authors introduce scDist, a statistical approach to identify perturbed cell types that controls for common confounders in these data.