Fig. 6: In silico quantitative perturbation for cell reprogramming and differentiation.

a Diagram of in silico cell fate transition. In silico knockout or overexpression experiment is performed by removing or shifting the highlighted gene in red forward within the ranking genes. b In silico low-level or high-level overexpression of OSKM is performed in human (upper) or mouse (bottom) fibroblasts to calculate the cosine similarity of the simulated cell states with iPSCs. In silico overexpression of four other random genes is used as control. In each simulation group, all embedding pairs between perturbed fibroblast cells and iPSCs are used to compute the cosine similarity. The cosine similarity of all pairs in each group is simultaneously presented using probability density and box plots. c Distribution of candidate genes that drive the shift of cell embeddings towards Leydig cell status and gonadal progenitor status in response to in silico overexpression in human ESC cells. Top 50 genes shifting towards Leydig cell (lower) or gonadal progenitor (upper) status and away from the ESC status are presented. Five genes in the intersection set of Venn diagram are selected as candidate genes for gonadal differentiation. d Protein co-immunofluorescence staining for markers of interstitial/Leydig lineage and Sertoli cells with GATA4 (GATA4⁺, red; TCF21⁺, green; NR2F2/NR2F1⁺, cyan),). Scale bars: 100\({{\rm{\mu }}}{{\rm{m}}}\) e The identification of upregulated gonadal lineage-related marker genes in the GATA4 overexpression group compared to cells derived from wild-type ESCs, with fold changes exceeding 2-fold. f Gene ontology (GO) enrichment analysis was performed using DAVID for the total up-regulated genes with a 2-fold change in the GATA4 overexpression group compared to cells derived from wild-type ESCs. (*P < 0.05, Wilcoxon-test).