Fig. 6: Activity programmes.
From: Club cells employ regeneration mechanisms during lung tumorigenesis
a UMAP embedding of combined RNA velocity and PAGA. Connections between clusters are established based on PAGA, while the direction of the arrows is inferred from the RNA velocity analysis. b Heatmap of the module scores of each cluster (Y axis) for the identified activity programmes (cNMF modules, “Methods”). The top 10 genes were used to calculate the module score. c Activity of the transcription programmes identified by the cNMF analysis for each identified cluster. The heatmap colours represent the z-score of the gene expression for the top 10 marker genes for each activity programme. d RNA velocity and gene expression of candidate genes Ltf (upper) and Trp63 (lower). The left side of the plots shows the current gene expression levels. The right side of the plots shows the RNA velocity. The green colour represents a high velocity, therefore upregulation, while the red colour denotes downregulation. e Immunohistochemistry of Ltf in Ad-Cas9 control samples and in representative Eml4-Alk lung sections at different time points after adenoviral instillation. Scale bar 20 μm. Below, a quantification of the number of Ltf positive cells mm−2 of bronchi of the animals. Each dot represents a bronchus. Mann–Whitney test, two-tailed. Data are presented as mean values +/− SEM. n = 3 mice per group were analysed except Ad-Cas9 2 weeks and Ad-EA 4 weeks (n = 4) and Ad-Cas9 6 endpoint (n = 2). f Schematic representation of the two routes followed by Club cells upon Eml4-Alk transformation.
