JAK/STAT1-interferon-ISGylation networks in breast cancer resistance to inhibitors of FOXM1 and CDK4/6

The oncogenic transcription factor FOXM1 and the cyclin-dependent kinases 4 and 6 all promote cancer progression and aggressiveness that can be suppressed initially by targeted inhibitors, but resistance almost always develops. We show that ER-positive breast cancer cells that acquire resistance to FOXM1 inhibitors (FOXM1i) or CDK4/6 inhibitors (CDK4/6i) exhibit some key similarities including an increased JAK/STAT-interferon-ISGylation signaling network with elevated ISG15 and ISG15 protein conjugates, but with differences in magnitudes and patterns of ISGylated proteins. All the resistant cell lines also express higher levels of enzymes critical for ISGylation which predict poorer survival outcomes in ER-positive breast cancer patients. Reduction of these proteins pharmacologically or by siRNA knockdown greatly impairs the viability, colony formation, and proliferation of the FOXM1i-resistant cells, with lesser impact on CDK4/6i resistant cells. Notably, CDK4/6i resistant cells and 3D-Matrigel cultures can still be growth inhibited by FOXM1i, and conversely the FOXM1i resistance can be overcome by palbociclib or abemaciclib, indicating that while the resistance mechanisms of these two classes of drugs have some similar features, they are sufficiently distinct so that sequential treatment approaches could be effective in supporting new options such as FOXM1 inhibitor use after progression on CDK4/6 inhibitors.