Dissecting Response and Resistance to CDK4/6 inhibition in ER+ Breast Cancer

Abstract

Highly specific cyclin-dependent kinase 4 and 6 (CDK4 and CDK6) inhibitors comprise a novel and exciting class of targeted therapeutics in oncology. CDK4/6 inhibitors, such as palbociclib, abemaciclib and ribociclib prevent cell cycle progression from the first growth phase (G1) to the DNA synthesis (S) phase of the cell cycle. CDK4/6 inhibition in combination with endocrine therapy is the new standard of care for metastatic breast cancers that express the estrogen receptor (ER+). Many preclinical biomarkers of sensitivity to CDK4/6 inhibition, however, are not clinically relevant. Furthermore, some ER+ breast cancer patients present with intrinsic resistance to CDK4/6 inhibitors and others are progressing on therapy. Consequently, effective treatment of metastatic breast cancer patients necessitates an understanding of response and resistance to CDK4/6 inhibition. To this end, we conducted two projects to 1) determine whether breast cancer cells that are dependent on ER signaling require CDK4/6 and 2) identify the landscape of resistance to CDK4/6 inhibition. Recent sequencing studies have revealed that 20% of metastatic breast cancers harbor activating mutations in the gene encoding the ER (ESR1). Furthermore, ER+ breast cancer cells that are resistant to estrogen deprivation therapy exhibit a dependency on CDK4. We found that estrogen-independent growth of ESR1-mutant breast cancer cells require CDK4/6 and that sensitivity to CDK4/6 inhibition is dependent on an intact retinoblastoma protein (RB, the main downstream target of CDK4/6). Thus, ESR1-mutant breast cancer patients may benefit from CDK4/6 inhibition. To systematically identify genes whose upregulation confer resistance to CDK4/6 inhibition, we conducted five near genome-wide open reading frame (ORF) screens. While most in vitro characterizations of resistance have utilized estrogen-rich media, CDK4/6 inhibitors are only approved in combination with endocrine therapy. Thus, to recapitulate the clinical setting more closely, our expression screens utilized two different CDK4/6 inhibitors alone and in combination with estrogen deprivation. Several novel resistance drivers were nominated. In particular, RB phosphorylation emerged as a convergent node of resistance to CDK4/6 inhibition. Together with cultured to resistance cell models and clinical sequencing of patient tumors, our studies identify several strategies to combat resistance and help pinpoint patient populations for CDK4/6 inhibitor treatment.