RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

Cell Rep. 2019 Feb 5;26(6):1627-1640.e7. doi: 10.1016/j.celrep.2019.01.041.

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.

Keywords: RNA-seq; deconvolution; flow cytometry; gene modules; housekeeping; immune system; mRNA abundance; mRNA composition; mRNA heterogeneity; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • B-Lymphocytes / classification
  • B-Lymphocytes / cytology
  • B-Lymphocytes / immunology*
  • Basophils / classification
  • Basophils / cytology
  • Basophils / immunology
  • Benchmarking
  • Cell Lineage / genetics*
  • Cell Lineage / immunology
  • Dendritic Cells / classification
  • Dendritic Cells / cytology
  • Dendritic Cells / immunology*
  • Female
  • Flow Cytometry
  • Healthy Volunteers
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunophenotyping
  • Killer Cells, Natural / classification
  • Killer Cells, Natural / cytology
  • Killer Cells, Natural / immunology
  • Male
  • Monocytes / classification
  • Monocytes / cytology
  • Monocytes / immunology
  • Neutrophils / classification
  • Neutrophils / cytology
  • Neutrophils / immunology
  • Organ Specificity
  • RNA, Messenger / genetics*
  • RNA, Messenger / immunology
  • Stem Cells / classification
  • Stem Cells / cytology
  • Stem Cells / immunology
  • T-Lymphocytes / classification
  • T-Lymphocytes / cytology
  • T-Lymphocytes / immunology*
  • Transcriptome*

Substances

  • RNA, Messenger