Fig. 2

MDMi organize in subpopulations that exhibit the highest pathway enrichment in 3D co-culture. A Volcano plot representation of the top 100 most differentially expressed genes in monocytes and MDMi (2D, 3D, and 3D co-culture). B Pathway enrichment analysis of monocytes and MDMi (2D, 3D, and 3D co-culture) shows different biological processes across all models, with the greatest diversity in biological functions observed in 3D co-culture. The statistical test used was the hypergeometric test, and the correction methods for multiple testing were Benjamini–Hochberg and FDR. Significance level: P-value threshold of 0.05. (Detailed analysis pipeline can be found in Methods). C UMAP plots of the monocyte and MDMi single-cell transcriptomes identified three clusters in monocytes, five clusters in 2D MDMi and 3D co-culture, and six clusters in 3D MDMi. Total number of cells analyzed were 9521 for monocytes; 5608 for 2D MDMi; 5667 for 3D MDMi and 4543 for 3D co-culture. D Top 38 variable genes expressed in MDMi (2D, 3D, and 3D co-culture), with the most variable genes listed at the bottom and the most constant genes at the top of the list. Each row represents the level of expression of a selected key gene. The color of the dot represents the average expression z-score of the cells within the given cluster, while the size of the dot represents the % of cells within that cluster