A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. Issue 1 (11th January 2023)

• Record Type: Journal Article
• Authors: Deng, Wenxuan; Li, Bolun; Wang, Jiawei; Jiang, Wei; Yan, Xiting; Li, Ningshan; Vukmirovic, Milica; Kaminski, Naftali; Wang, Jing; Zhao, Hongyu
• Is Part Of: Briefings in bioinformatics. Volume 24:Issue 1(2023)
• Publication Date: 2023-01-11
• Subjects: cell type deconvolution -- scRNA-seq -- reference signature matrix -- harmonize information; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac616
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Computational cell type deconvolution on bulk transcriptomics data can reveal cell type proportion heterogeneity across samples. One critical factor for accurate deconvolution is the reference signature matrix for different cell types. Compared with inferring reference signature matrices from cell lines, rapidly accumulating single-cell RNA-sequencing (scRNA-seq) data provide a richer and less biased resource. However, deriving cell type signature from scRNA-seq data is challenging due to high biological and technical noises. In this article, we introduce a novel Bayesian framework, tranSig, to improve signature matrix inference from scRNA-seq by leveraging shared cell type-specific expression patterns across different tissues and studies. Our simulations show that tranSig is robust to the number of signature genes and tissues specified in the model. Applications of tranSig to bulk RNA sequencing data from peripheral blood, bronchoalveolar lavage and aorta demonstrate its accuracy and power to characterize biological heterogeneity across groups. In summary, tranSig offers an accurate and robust approach to defining gene expression signatures of different cell types, facilitating improved in silico cell type deconvolutions.