Journal: bioRxiv

Article Title: PI3K/mTOR activity sensitizes cancer cells to nucleolar stress

doi: 10.1101/2025.11.12.688066

Figure Lengend Snippet: (A) Functional enrichment analysis for the top and bottom 100 expressed genes (TPM > 1; p < 0.01) for each treatment (ActD, BMH-21) at early and late timepoints. To the right, the percentage of significant genes localized to the nucleolus (Human Protein Atlas Subcellular Compartment database) and the fraction classified in the COSMIC Cancer Gene Census (CGC) are shown, with absolute gene counts indicated within each cell. (B) UpSet plot illustrating the unique and shared top 100 significant genes across treatments and timepoints. Genes depleted upon ActD and BMH-21 treatment are shown in red and orange, while enriched genes are shown in blue and teal, respectively. Gray bars represent the 62 common top 100 significant genes shared between ActD and BMH-21 at different timepoints, highlighting their differential regulatory patterns. (C) STRING network analyses of interaction patterns among mutations unique to ActD or BMH-21. Thicker lines indicate higher confidence. Nodes with a black border denote COSMIC cancer driver genes, further annotated by their functional class (oncogene, tumor suppressor, or fusion gene). (D) Sankey plot depicting the 62 common top 100 significant genes from (B), indicating their roles as common sensitizers or resistance factors. Connections reflect whether genes display concordant (e.g., depleted in both treatments) or divergent regulatory patterns. Fractions indicate the proportion of common genes consistently observed across all conditions. COSMIC-listed genes are highlighted by their classification (oncogene, tumor suppressor, or fusion driver). (E) Enrichment analysis of pathways commonly enriched or depleted across ActD and BMH-21 treatments. Dot size reflects gene counts per term, and the −log10(adjusted p-value) indicates enrichment significance. Gene ratios (hits/total term genes) are annotated on the plots. (F) STRING network analyses of genes in (E) indicating key complexes including. Edges are scaled by STRING confidence, and grey sub-lines indicate experimentally validated physical interactions within a complex. Nodes with a black outline mark COSMIC cancer drivers, emphasizing their potential contribution to the enriched biological themes. (G) A lollipop enrichment plot illustrating the overrepresentation of chromatin regulators, transcriptional modulators, DNA repair factors, splicing components, and proteolytic machinery among genes enriched in ActD but depleted in BMH-21. Dot size corresponds to the number of genes, and −log10(adjusted p-value) reflects statistical significance. Gene ratios are annotated within the plot. (H) STRING network visualization of enriched chromatin remodeling complexes (SAGA, SWI/SNF), transcriptional regulators (Mediator complex), and DNA repair regulators among ActD-enriched/BMH-21-depleted genes. Edges are scaled by STRING confidence, with thicker lines denoting higher confidence of association. Grey sub-lines mark direct physical interactions within defined complexes. Nodes outlined in black denote COSMIC cancer driver genes, such as SMARCD1 (SWI/SNF), CREBBP, and MED12 (Mediator).

Article Snippet: Finally, significant hits were annotated for protein localization to the nucleolus using the Human Protein Atlas subcellular compartment database ( Thul et al ., 2017 ) and cross-referenced with the COSMIC Cancer Gene Census ( Sondka et al ., 2018 ), which also provided functional classifications of oncogenes, tumor suppressors, and fusion drivers.

Techniques: Functional Assay