Transcriptomic comparison of a second-generation AKT degrader to the catalytic AKT inhibitor GDC0068 in breast cancer cells [PRO-seq]

We report the development of a second-generation AKT degrader INY-05-040, which outperformed catalytic AKT inhibition both with respect to biochemical and cellular suppression of AKT/mTORC1-driven phenotypes in diverse breast cancer cell lines. Using multi-omic profiling and causal network integration, we demonstrate that the enhanced efficacy of INY-05-040 relies in part on potent downstream activation of stress mitogen activated protein kinase (MAPK) signaling. Systematic measurements of growth inhibition across 288 cancer cell lines confirmed the substantial improvement in potency for INY-05-040 compared to the first-generation AKT degrader (INY-03-041) and catalytic AKT inhibition with GDC-0068. Subsequent integration of breast cancer cell line-specific data with publicly available transcriptomic, proteomic and reverse phase protein array (RPPA) measurements revealed that decreased sensitivity to INY-05-040 correlates with a high baseline activation of inflammatory/stress signaling pathways. Collectively, our data uncover a unique mechanism of breast cancer cell line sensitivity to AKT degradation, further suggesting that the efficacy of catalytic AKT inhibition may be enhanced by activation of stress MAPKs in breast cancer cells with low baseline activity of these components. We performed comparative precision nuclear run-on sequencing sequencing (PROseq) in ER+ T47D breast cancer cells, exposed to the catalytic AKT inhibitor GDC0068 or the second-generation AKT degrader INY-05-040 for 5 h. To limit the confounding effect of differential potency, we determined the doses of INY-05-040 (100 nM) and GDC-0068 (500 nM) that would result in comparable suppression of downstream signaling. Treatment with DMSO was used as control. The data are from two independent experiments, performed in growth factor-complete medium.