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Identification of innate lymphoid cells in single-cell RNA-Seq data

Suffiotti, Madeleine
Carmona, Santiago J
Gfeller, David
Published in Immunogenetics. 2017, vol. 69, no. 7, p. 439-450
Abstract Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process. Here we propose and validate a novel framework for studying ILCs at the transcriptomic level using single-cell RNA-Seq data. Our approach combines unsupervised clustering and a new cell type classifier trained on mouse ILC gene expression data. We show that this approach can accurately identify different ILCs, especially ILC2 cells, in human lymphocyte single-cell RNA-Seq data. Our new model relies only on genes conserved across vertebrates, thereby making it in principle applicable in any vertebrate species. Considering the rapid increase in throughput of single-cell RNA-Seq technology, our work provides a computational framework for studying ILC2 cells in single-cell transcriptomic data and may help exploring their conservation in distant vertebrate species.
Keywords AnimalsDatabasesGeneticGene Expression ProfilingHigh-Throughput Nucleotide Sequencing/methodsHumansImmunityInnate/genetics/immunologyKiller CellsNatural/immunology/metabolismLymphocytes/classification/immunology/metabolismMiceSequence AnalysisRNA/methodsSingle-Cell Analysis/methods
PMID: 28534222
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Article (Published version) (974 Kb) - document accessible for UNIGE members only Limited access to UNIGE
Research group Ciblage des lymphocytes sécrétant des cytokines (1015)
Project FNS: Ambizione PZOOP3_161459
(ISO format)
SUFFIOTTI, Madeleine et al. Identification of innate lymphoid cells in single-cell RNA-Seq data. In: Immunogenetics, 2017, vol. 69, n° 7, p. 439-450. doi: 10.1007/s00251-017-1002-x

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Deposited on : 2020-03-17

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