Single-cell RNA sequencing to explore immune cell heterogeneity

Nat Rev Immunol. 2018 Jan;18(1):35-45. doi: 10.1038/nri.2017.76. Epub 2017 Aug 7.


Advances in single-cell RNA sequencing (scRNA-seq) have allowed for comprehensive analysis of the immune system. In this Review, we briefly describe the available scRNA-seq technologies together with their corresponding strengths and weaknesses. We discuss in depth how scRNA-seq can be used to deconvolve immune system heterogeneity by identifying novel distinct immune cell subsets in health and disease, characterizing stochastic heterogeneity within a cell population and building developmental 'trajectories' for immune cells. Finally, we discuss future directions of the field and present integrated approaches to complement molecular information from a single cell with studies of the environment, epigenetic state and cell lineage.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Animals
  • B-Lymphocytes / immunology
  • B-Lymphocytes / metabolism
  • Cell Differentiation
  • Cell Lineage
  • Dendritic Cells / immunology
  • Dendritic Cells / metabolism*
  • Epigenomics
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Killer Cells, Natural / immunology
  • Killer Cells, Natural / metabolism
  • Lymphocytes / immunology
  • Lymphocytes / metabolism*
  • Macrophages / immunology
  • Macrophages / metabolism*
  • Monocytes / immunology
  • Monocytes / metabolism*
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • T-Lymphocytes / immunology
  • T-Lymphocytes / metabolism