Early-life compartmentalization of immune cells in human fetal tissues revealed by high-dimensional mass cytometry

Na Li, Vincent van Unen, Nannan Guo, Tamim Abdelaal, Antonios Somarakis, Jeroen Eggermont, Ahmed Mahfouz, Susana M. Chuva de Sousa Lopes, Boudewijn P.F. Lelieveldt, Frits Koning

Research output: Contribution to journalArticleScientificpeer-review

6 Citations (Scopus)
19 Downloads (Pure)


The human fetal immune system must protect the infant against the sudden exposure to a large variety of pathogens upon birth. While it is known that the fetal immune system develops in sequential waves, relatively little is known about the composition of the innate and adaptive immune system in the tissues. Here, we applied high-dimensional mass cytometry to profile the immune system in human fetal liver, spleen, and intestine. With Hierarchical Stochastic Neighbor Embedding (HSNE) we distinguished 177 distinct immune cell clusters, including both previously identified and novel cell clusters. PCA analysis indicated substantial differences between the compositions of the immune system in the different organs. Through dual t-SNE we identified tissue-specific cell clusters, which were found both in the innate and adaptive compartment. To determine the spatial location of tissue-specific subsets we developed a 31-antibody panel to reveal both the immune compartment and surrounding stromal elements through analysis of snap-frozen tissue samples with imaging mass cytometry. Imaging mass cytometry reconstructed the tissue architecture and allowed both the characterization and determination of the location of the various immune cell clusters within the tissue context. Moreover, it further underpinned the distinctness of the immune system in the tissues. Thus, our results provide evidence for early compartmentalization of the adaptive and innate immune compartment in fetal spleen, liver, and intestine. Together, our data provide a unique and comprehensive overview of the composition and organization of the human fetal immune system in several tissues.

Original languageEnglish
Article number1932
Pages (from-to)1-13
Number of pages13
JournalFrontiers in Immunology
Publication statusPublished - 2019


  • Fetal intestine
  • Fetal liver
  • Fetal spleen
  • High-dimensional analysis
  • Imaging mass cytometry (IMC)
  • Immune composition
  • Mass cytometry (CyTOF)

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