Multi-omic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation

Over 50% of human tumors display hyperactivation of the serine/threonine kinase AKT, but AKT inhibitors under clinical investigation lack therapeutic efficacy at tolerable doses and display significant on-target toxicities. Here 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-driven phenotypes in breast cancer cell lines. A systematic growth inhibition screen across 288 cancer cell lines confirmed a substantially higher potency for INY-05-040 (median GI50adj = 1.1 µM) compared to our first-generation AKT degrader (INY-03-041; median GI50adj = 3.1 µM), with both compounds outperforming catalytic AKT inhibition with GDC-0068 (median GI50adj > 10 µM). Using multi-omic profiling and causal network integration in breast cancer cells, we demonstrate that the enhanced efficacy of INY-05-040 is associated with sustained suppression of AKT signaling, followed by a potent induction of the stress mitogen activated protein kinase (MAPK) cJun N-terminal kinase (JNK). Further integration of growth inhibition assays with publicly available transcriptomic, proteomic, and reverse phase protein array (RPPA) measurements established low baseline JNK signaling as a biomarker for breast cancer sensitivity to AKT degradation. Collectively, our study presents a systematic framework for mapping the network-wide signaling effects of therapeutically relevant compounds, revealing that INY-05-040 is a potent pharmacological suppressor of AKT signaling.