LMTK2: A novel driver of endocrine resistance in ERalpha+ breast cancer

Breast cancer is the most common female malignancy in the U.S. and the leading cause of cancer-related deaths in women worldwide. Nearly 80% of breast tumors express estrogen receptor alpha (ERalpha) which drives tumor progression. While endocrine therapies and CDK4/6 inhibitors have increased overall survival, many patients experience recurrence of metastatic disease that is largely refractory to additional lines of endocrine therapy. Metastatic disease remains incurable, highlighting the need for alternative treatment approaches. Through a genome-wide CRISPR knockout screen, we identified Lemur Tail Kinase 2 (LMTK2) as the top hit exhibiting synthetic lethality in the presence of the endocrine therapy, endoxifen, in both endocrine-sensitive and -resistant cell line models. Using publicly available patient tumor databases we identified LMTK2 copy number gain/amplification in 67% of ERalpha+ human metastatic breast tumors, while only 1% of primary tumors harbored these genomic alterations. Elevated LMTK2 expression in early-stage primary breast tumors was associated with worse recurrence-free survival and overall survival. We discovered that LMTK2 mRNA and protein levels were substantially elevated in nearly all cell-line and patient-derived models of endocrine and CDK4/6i resistance. Utilizing siRNAs and dox-inducible shRNA expressing cell lines, we found that knockdown of LMTK2 enhanced the efficacy of multiple endocrine therapies in treatment naïve models and resensitized resistant models to their respective treatment. LMTK2 overexpression was found to be sufficient for conferring resistance to all standard of care therapies tested including endocrine agents, CDK4/6i, and PI3K inhibitors. RNAseq and global proteomics of LMTK2 overexpressing and knockout models revealed the PI3K/AKT pathway and estrogen signaling as highly regulated pathways by LMTK2. Confirmatory western blot studies demonstrated that LMTK2 overexpression results in dramatic increases in AKT and ERalpha phosphorylation and activity, while knockout of LMTK2 diminishes these effects. Attempts to completely ablate LMTK2 in endocrine/CDK4/6i-resistant models via CRISPR were not successful, and continuous siRNA or shRNA-mediated knockdown was lethal in resistant cell lines, confirming its essentiality in this setting. In summary we have uncovered LMTK2 as a novel mediator of endocrine/CDK4/6i resistance that is mechanistically linked to the PI3K/AKT pathway among others. Genetic manipulation of LMTK2 has validated it as an ideal therapeutic target for both advanced and newly diagnosed forms of ERalpha+ breast cancer.