(A) Scheme (left) showing WaGa and MKL-1 cells were treated with DMSO, KTX-049, or DS-3032 followed by TMT profiling. Heatmaps showing the log₂(fold change) from MKL-1 and WaGa cells treated with KTX-049 or DS-3032 highlight the most significantly regulated proteins with Gene Ontology Biological Process (GOBP) cell cycle process annotation (middle) or with the KEGG p53 signaling annotation (right). The cell cycle process heatmap was filtered to include only proteins with log₂(fold change) > 1 or < –1, while the p53 signaling heatmap was filtered to include only proteins with log₂(fold change) > 0.5 or < –0.5. NOTCH1 is not a KEGG p53 signaling pathway protein but is a direct p53 target (38) and was also included in the heatmap. A pathway analysis was performed for WaGa and MKL-1 cells, and the enrichment factors for identified GOBP and KEGG terms common to both cell lines were plotted as a scatterplot (right). (B) Mice implanted with PDX 48396 were treated with vehicle or KT-253 for 24 h before tumor harvesting, processing, and analysis by DIA-based global proteomics (left). The corresponding heatmaps highlight the most regulated proteins with the GOBP cell cycle process annotation (middle) or KEGG p53 signaling annotation (right), with log₂(fold change) filtering criteria as described above. Both heatmaps show the direct comparison of log₂(fold change) between WaGa cells and PDX 48396 (referred to as MCC PDX) treated with KT-253. As above, a pathway analysis was performed to determine significantly enriched GOBP and KEGG annotation terms, and the enrichment factors for terms identified for WaGa and the PDX 48396 model were plotted as a scatterplot (B, below). Terms associated with mitosis or cell cycle are in blue, those associated with p53 signaling are in red, and all others are purple.