Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells

Nat Commun. 2021 Mar 19;12(1):1737. doi: 10.1038/s41467-021-21994-8.


Innate lymphoid cells (ILCs) emerge in the last few years as important regulators of immune responses and biological processes. Although ILCs are mainly known as tissue-resident cells, their precise localization and interactions with the microenvironment are still unclear. Here we combine a multiplexed immunofluorescence technique and a customized computational, open-source analysis pipeline to unambiguously identify CD127+ ILCs in situ and characterize these cells and their microenvironments. Moreover, we reveal the transcription factor IRF4 as a marker for tonsillar ILC3, and identify conserved stromal landmarks characteristic for ILC localization. We also show that CD127+ ILCs share tissue niches with plasma cells in the tonsil. Our works thus provide a platform for multiparametric histological analysis of ILCs to improve our understanding of ILC biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cluster Analysis
  • Connective Tissue / diagnostic imaging
  • Connective Tissue / pathology
  • Humans
  • Image Processing, Computer-Assisted
  • Immunity, Innate
  • Interferon Regulatory Factors / metabolism
  • Interleukin-7 Receptor alpha Subunit / metabolism
  • Lymphocytes / immunology*
  • Lymphocytes / pathology*
  • Machine Learning
  • Palatine Tonsil / diagnostic imaging
  • Palatine Tonsil / pathology
  • Phenotype*
  • Spatial Analysis*


  • Interferon Regulatory Factors
  • Interleukin-7 Receptor alpha Subunit
  • interferon regulatory factor-4