Single-cell technologies to study the immune system

Immunology. 2016 Feb;147(2):133-40. doi: 10.1111/imm.12553. Epub 2015 Dec 27.


The immune system is composed of a variety of cells that act in a coordinated fashion to protect the organism against a multitude of different pathogens. The great variability of existing pathogens corresponds to a similar high heterogeneity of the immune cells. The study of individual immune cells, the fundamental unit of immunity, has recently transformed from a qualitative microscopic imaging to a nearly complete quantitative transcriptomic analysis. This shift has been driven by the rapid development of multiple single-cell technologies. These new advances are expected to boost the detection of less frequent cell types and transient or intermediate cell states. They will highlight the individuality of each single cell and greatly expand the resolution of current available classifications and differentiation trajectories. In this review we discuss the recent advancement and application of single-cell technologies, their limitations and future applications to study the immune system.

Keywords: CD4+ T helper cells; immune cells; single-cell RNA-sequencing; single-cell technology.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • CD4-Positive T-Lymphocytes / immunology*
  • CD4-Positive T-Lymphocytes / metabolism
  • Cell Differentiation
  • Cell Lineage
  • Diffusion of Innovation
  • Forecasting
  • Gene Expression Profiling* / trends
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immune System / cytology
  • Immune System / immunology*
  • Immune System / metabolism
  • Immunologic Techniques* / trends
  • Immunophenotyping
  • Phenotype
  • RNA / genetics
  • Sequence Analysis, RNA
  • Single-Cell Analysis* / trends
  • Transcriptome


  • RNA