For the first time, scientists from the VIB Center for Inflammation Research, Ghent University, The Wellcome Sanger Institute (UK), and Newcastle University (UK) have composed a complete map of the cells in the developing human thymus. This novel approach with single cell resolution allowed them to identify more than 50 different cell states in the human thymus which dynamically change in abundance during life.

A collaboration to map the vital thymus
The thymus is a vital organ for the establishment of the immune system.  Its main function is to support the maturation of T cells, which are essential white blood cells and part of the adaptive immune system that protects us from infections and tumor cells. Up to now, it was not precisely clear how these T cells develop from early immune precursor cells in the thymus over the course of a human life.

Researchers from the labs of Tom Taghon (Ghent University) and Yvan Saeys (VIB Center for Inflammation Research) played a crucial role in the story of mapping all the cells in the thymus. This single-cell transcriptomic atlas comprises more than 250,000 cells.

Yvan Saeys explains: “A few years ago, we kicked off the first project on single-cell technologies at Ghent University.  This collaboration has proven very fruitful, and through the team of Tom Taghon, which has a longstanding expertise in T cell development, we got involved in the human Thymus Cell Atlas project of the Chan Zuckerberg initiative. The current publication is the first result of that collaboration.” 

The value of single cell research
Niels Vandamme, who coordinates the single-cell platform at Saeys’ lab, adds: “The thymus atlas project provided essential data to set up our single-cell infrastructure, the Singularity platform, which allows researchers to perform single-cell analysis from wet lab experiments up to analysis and visualization within one workflow.”

 “The thymus atlas project will provide a great resource for the community,” says Tom Taghon, a co-senior author on the study. "We now have a very detailed understanding of how T cells are generated in healthy tissue and this helps us understand how immunity develops. Since we now know which genes need to be activated to generate T cells, we can exploit this information to engineer T cells with, for instance, a desired specificity to target tumor cells."

An atlas to discover new therapies
The thymus cell atlas project establishes a firm foundation for new clinical applications and therapies. It also helps scientists better understand diseases that affect T cell development, such as severe combined immunodeficiency (SCID) and T cell leukemia. In addition, the knowledge of all thymus cell types will help researchers to possibly generate an artificial thymus for regenerative medicine.​


Park et al., 2020. A cell atlas of human thymic development defines T cell repertoire formation. Science, 2020; 367 (6480): eaay3224

Chan Zuckerberg initiative
This project received funding from Ghent University through a GOA project
Fund for Scientific Research Flanders​