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.
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: | 19 Jan 2023 00:57 |
| 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 |
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