Ribosomal Biogenesis Hyperactivation and ErbB signalling Mediated Network Rewiring Causes Adaptive Resistance to FGFR2 Inhibition

Abstract Fibroblast Growth Factor Receptor 2 inhibition presents a promising therapeutic approach for restraining the growth and survival of cancer cells, particularly in breast tumours. However, the emergence of resistance to FGFR2 inhibitors like PD173074 highlights the importance of understanding the molecular mechanisms driving resistance and identifying effective therapeutic strategies. In this study, we employed temporal quantitative proteomics and phosphoproteomics, complemented by computational clustering, PTM-SEA analysis, and kinase activity prediction, to monitor the response of MFM223 triple negative breast cancer cells to FGFR2 inhibition. Strikingly, we observed a marked enrichment of ribosome biogenesis function modules immediately following treatment, a phenomenon not observed with other inhibitors. Additionally, we discovered that CX-5461, an RNA polymerase I inhibitor, synergistically enhanced the growth inhibition induced by PD173074, mechanistically attributed to its significant suppression of rDNA transcription stimulated by PD173074. Moreover, our phosphoproteomics dynamic profiling identified the clustering of kinases within MAPK and ErbB signalling pathways, indicative of their reactivation in response to FGFR2 inhibition. Experimentally validating this finding, we observed a notable rebound in phosphorylation levels of key kinases such as ERK1/2 and ErbB3, and demonstrated a substantial synergistic effect of PD173074 in combination with Trametinib, a MEK inhibitor, in suppressing cancer cell growth. Collectively, our findings provide critical insights into the network rewiring triggered by FGFR2 inhibition and offer a foundation for the rational design of combinatorial therapeutic strategies to overcome resistance mechanisms associated with FGFR2 inhibitors. Competing Interest Statement The authors have declared no competing interest. Footnotes 1. Updated the Corresponding author Dr. Lan Nguyen's email address: lan.nguyen{at}adelaide.edu.au on page 1. 2. Corrected typo for the first author's name: 'Tao Zang' to 'Tao Zhang' on page 1.