Rediscovering the human thymus through cutting-edge technologies

Abstract

Recent technological advances have transformed our understanding of the human thymus. Innovations such as high-resolution imaging, single-cell omics, and organoid cultures, including thymic epithelial cell (TEC) differentiation and culture, and improvements in biomaterials, have further elucidated the thymus architecture, cellular dynamics, and molecular mechanisms underlying T cell development, and have unraveled previously unrecognized levels of stromal cell heterogeneity. These advancements offer unprecedented insights into thymic biology and hold promise for the development of novel therapeutic strategies for immune-related disorders.

Figure 1.

Main advancements on human thymus from single-cell omics and spatial analysis. The left panel highlights significant findings obtained through single-cell omics studies performed on dissociated thymic tissue, including scRNA-seq, CITE-seq, TCR-seq, and ATAC-seq. (A) Thymus seeding progenitors based on Cordes et al. (2022). (B) Unconventional T cells based on Billiet et al. (2023); Roels et al. (2020). (C) T(agonist), Treg, and CD8αα based on Heimli et al. (2023). (D) TEC populations based on Bautista et al. (2021); Campinoti et al. (2020); Park et al. (2020). (E) Non-TEC stromal cells based on Heimli et al. (2023); Park et al. (2020); Ragazzini et al. (2023). The right panel shows novel insight into thymus biology deriving from studies using spatial transcriptomics and multiplex imaging. (A) CMA based on Yayon et al. (Yayon et al., 2023, Preprint). (B) Sex differences based on Stankiewicz et al. (Stankiewicz et al., 2023, Preprint). (C) HC’s niche based on Stankiewicz et al. (Stankiewicz et al., 2023, Preprint) and Yayon et al. (Yayon et al., 2023, Preprint). (D) T cell developmental pathway based on Yayon et al. (Yayon et al., 2023, Preprint). (E) Differences in fibroblast localization in fetal and pediatric thymus based on Yayon et al. (Yayon et al., 2023, Preprint).

Figure 2.

In vitro modeling of T cell and stromal cell development and potential applications. The figure shows that TEP, mesenchymal cells, and CD34/ProT cells can be generated by direct differentiation from iPSCs or ESCs, while mature T cells can be obtained using 3D aggregation of iPSCs or CD34⁺ cells with stromal cell lines expressing Notch ligands (MS5- or OP9-DL4/DL1). A combination of hematopoietic progenitors, mesenchymal cells, and epithelial cells in 3D structures that can be based on hydrogel, scaffolds, or bioprinted materials are being tested to create all-human thymi in a dish. All these models can be used to perform a variety of studies and could be the base for the development of novel therapeutic approaches.