RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types



Monaco, Gianni, Lee, Bernett, Xu, Weili, Mustafah, Seri, Hwang, You Yi, Carré, Christophe, Burdin, Nicolas, Visan, Lucian, Ceccarelli, Michele, Poidinger, Michael
et al (show 3 more authors) (2019) RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types. Cell Reports, 26 (06). 1627 - 1640.E7.

Access the full-text of this item by clicking on the Open Access link.

Abstract

The molecular characterization of immune subsets is important for designing effective strategies to understand and treat diseases. We characterized 29 immune cell types within the peripheral blood mononuclear cell (PBMC) fraction of healthy donors using RNA-seq (RNA sequencing) and flow cytometry. Our dataset was used, first, to identify sets of genes that are specific, are co-expressed, and have housekeeping roles across the 29 cell types. Then, we examined differences in mRNA heterogeneity and mRNA abundance revealing cell type specificity. Last, we performed absolute deconvolution on a suitable set of immune cell types using transcriptomics signatures normalized by mRNA abundance. Absolute deconvolution is ready to use for PBMC transcriptomic data using our Shiny app (https://github.com/giannimonaco/ABIS). We benchmarked different deconvolution and normalization methods and validated the resources in independent cohorts. Our work has research, clinical, and diagnostic value by making it possible to effectively associate observations in bulk transcriptomics data to specific immune subsets.

Item Type: Article
Uncontrolled Keywords: immune system, flow cytometry, transcriptome, RNA-seq, gene modules, housekeeping, mRNA composition, mRNA abundance, mRNA heterogeneity, deconvolution
Depositing User: Symplectic Admin
Date Deposited: 11 Mar 2019 14:18
Last Modified: 06 Oct 2022 05:38
DOI: 10.1016/j.celrep.2019.01.041
Open Access URL: https://doi.org/10.1016/j.celrep.2019.01.041
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3034061