Journal: Nature Communications
Article Title: Combinatory differentiation of human induced pluripotent stem cells generates functional thymic epithelium driving dendritic cell and CD4/CD8 T cell development
doi: 10.1038/s41467-026-68675-y
Figure Lengend Snippet: a Differentiation itinerary of the thymic epithelium showing DE (Definitive Endoderm), AFE (Anterior Foregut Endoderm), 3PPE (Third Pharyngeal Pouch Endoderm) and TEP (Thymic Epithelial Progenitor) stages (Created in BioRender. Guillonneau, C. (2025) https://BioRender.com/r5v7uln ). b Factors tested in DOE (abbreviations), their associated pathways and the timings corresponding to each tested stage transition (D5-D7: DE-to-AFE, D7-D11: AFE-to-3PPE and D11-D13: 3PPE-to-TEP). Plackett–Burman designs were used to estimate factor effects on differentiation at the three transitions, with two dose levels (−1/+1) per factor. c UMAP representations of early ( Left ) and late ( Right ) pharyngeal development scRNA-seq reference datasets, with clusters corresponding to stages of the thymic differentiation trajectory shown in color. Reference datasets: Han et al. (E8.5–E9.5) and Magaletta et al. (E9.5–E12.5). d Bulk RNA-seq results for each sample (vertical) treated with combinations of factors tested in DOE in four experiments (D5-D7, Han E8.5; D7-D11, Han and Magaletta E9.5; D11-D13, Magaletta E11.5/12.5) showing expression scores of marker genes for pharyngeal development clusters (horizontal). Cluster names corresponding to the thymic differentiation trajectory are highlighted in bold. The upper part of each heatmap shows the factor combinations applied, with high doses highlighted in orange. Statistical significance was assessed by ANOVA (Supplementary Fig. ). Significant factors are shown in red or blue, indicating those to be supplemented or excluded in the optimized protocol. Han et. al. dataset: D5 to D7: p = 0.02338 (Noggin); 4.246e-05 (IWR1); 0.05526 (LY3); 4.345.e-07 (RA)/D7 to D11: p = 5.233.e-05 (CHIR99); 0.0002875 (FLI06); 0.0015895 (IWR1). Magaletta et. al. dataset: D7 to D11: p = 1.877.e-05 (CHIR99); 1.877.e-05 (FLI06); 0.0003179 (IRW1)/D11 to D13: dots indicate suggestive p values, p = 0.089927 (BMP4); 0.079926 (IGF1); 0.086185 (RANKL). e Summary of pathway modulation: black, DOE-identified pathways to be activated (+) or inhibited (−); blue, pathways neutral in DOE but enhancing FOXN1 expression (BMP/FGF) or proliferation (FGF/EGF) at the TEP stage; green, the FGF pathway (not tested in DOE, post-DOE), activating FOXN1 at the TEP stage. DE Definitive Endoderm, AFE Anterior Foregut Endoderm, 3PPE Third Pharyngeal Pouch Endoderm, TEP Thymic Epithelial Progenitor. See corresponding factor names in ( b ) (Created in BioRender. Guillonneau, C. (2025) https://BioRender.com/ht4edy0 ). f Summary of the optimized protocol with full factor list, doses and exposure windows, DE Definitive Endoderm, AFE Anterior Foregut Endoderm, 3PPE Third Pharyngeal Pouch Endoderm, TEP Thymic Epithelial Progenitor.
Article Snippet: The supplementation included Activin A, CHIR99, BMP4 (Miltenyi, 130-111-167), retinoic acid (Sigma Aldrich, 302-79-4), FGF8 (BiotechneR&D, 423-F8), Noggin (Miltenyi 130-103-455), LY-364947 (Sigma Aldrich L6293-5MG), FGF10 (Miltenyi, 130-127-858), IGF1 (Miltenyi, 130-093-886), EGF (Miltenyi, 130-097-751), and RANK-L (BiotechneR&D: 6449-TEC).
Techniques: RNA Sequencing, Expressing, Marker