Abstract P4-01-06: Genomic and transcriptomic analysis reveals known and novel resistance mechanisms to CDK4/6 inhibitors and sensitivity factors for the response to triplet therapy (palbociclib + everolimus + exemestane) in a phase I/IIb study in hormone-receptor positive (HR+)/HER2- metastatic breast cancer (MBC) after progression on a CDK4/6 inhibitor (CDK4/6i)
Authors: Zanudo Jorge Gomez Tejeda , Barroso-Sousa Romualdo , Jain Esha , Buendia-Buendia Jorge , Li Tianyu , Tayob Nabihah , Rees Rebecca , Pereslete Alyssa , Ferreira Arlindo R. , Abravanel Daniel L. , Helvie Karla , Partridge Ann H. , Overmoyer Beth , Winer Eric P. , Wagle Nikhil , Tolaney Sara M. 
Published: March 2022

Abstract
Background: Multiple studies in HR+/HER2- MBC have identified a variety of genomic resistance mechanisms to CDK4/6 inhibitors, but the complete landscape of resistance mechanisms is still being elucidated. A clinical trial evaluating the benefit of continued CDK4/6 blockade after disease progression on a prior CDK4/6i provides a unique setting to study the landscape of resistance to CDK4/6 inhibitors. Methods: We analyzed genomic data from a Phase I/II trial (NCT02871791) of triplet therapy: palbociclib (CDK4/6i) + everolimus (mTOR inhibitor) + exemestane (endocrine therapy) in patients (pts) with HR+/HER2− MBC who had progressed on prior CDK4/6i. For the phase IIa pts, a research tumor biopsy at baseline and serial research blood collection for circulating tumor DNA (ctDNA) analysis were mandatory. Additionally, when possible, we acquired tumor biopsies that preceded the patient's prior exposure to a CDK4/6i, which would allow us to identify acquired genomic resistance mechanisms to the prior CDK4/6i. The genomic data consisted of whole exome sequencing (WES) data from 23 tumor biopsies (19 pts) and 17 ctDNA samples (12 pts), and RNA sequencing (RNA-seq) from 27 tumors (22 pts). 4 pts had a biopsy or ctDNA sample at baseline and a biopsy that preceded their prior exposure to a CDK4/6i. WES data was used to identify mutations and copy number alterations, which was used to perform evolutionary analysis on the pts with multiple biopsies or ctDNA samples. RNA-seq data was used to make research-grade PAM50 calls and calculate gene expression signature scores. Results: For the baseline biopsy or ctDNA sample of most pts, we found genomic alterations in previously identified pathways and genes that could explain the tumor’s resistance to the prior CDK4/6i (16/19 pts) or to the prior endocrine therapies (17/19 pts). These pathways and genes include the PI3K/AKT/MTOR pathway (e.g. PTEN, AKT), the RAS/MAPK pathway (e.g. NF1), receptor tyrosine kinases (RTKs) (e.g. ERBB2, FGFR1), cell-cycle genes (e.g. RB1), and estrogen receptor signaling (e.g. ESR1, FOXA1). Two novel potential genomic resistance mechanisms in these pathways were identified: an activating MTOR T1977R mutation (PI3K/AKT/MTOR pathway) and an activating BRAF V600E mutation (RAS/MAPK pathway). Notably, the patient with the activating MTOR mutation responded to the triplet therapy (progression free survival of 8 months), consistent with prior work linking these mutations to sensitivity to everolimus. Evolutionary analysis revealed metastatic tumors with distinct lineages but derived from the same primary tumor (e.g. two lineages, one with activating ESR1 mutations and one with an activating MTOR mutation), some of which converged to activating the same pathway (e.g. two lineages with distinct activating ERBB2 mutations). Transcriptomic analysis found that activating mutations in ERBB2 and BRAF were correlated with the HER2-E PAM50 and that the expression signatures for MTOR and RTKs were correlated with clinical benefit to triplet therapy. Conclusions: Analysis of the genomic and transcriptomic data of baseline biopsies and ctDNA samples from NCT02871791 not only recapitulates genes and pathways previously implicated in resistance to endocrine therapy and CDK4/6i but also identified novel potential mechanisms of resistance including activating mutations in BRAF and MTOR. Evolutionary analysis demonstrates the complexity of resistance including both convergent and divergent paths to resistance. Integration of genomic and transcriptomic data may better identify pts likely to respond to CDK4/6i combinations.
Citation Format: Jorge Gomez Tejeda Zanudo, Romualdo Barroso-Sousa, Esha Jain, Jorge Buendia-Buendia, Tianyu Li, Nabihah Tayob, Rebecca Rees, Alyssa Pereslete, Arlindo R. Ferreira, Daniel L. Abravanel, Karla Helvie, Ann H. Partridge, Beth Overmoyer, Eric P. Winer, Nikhil Wagle, Sara M. Tolaney. Genomic and transcriptomic analysis reveals known and novel resistance mechanisms to CDK4/6 inhibitors and sensitivity factors for the response to triplet therapy (palbociclib + everolimus + exemestane) in a phase I/IIb study in hormone-receptor positive (HR+)/HER2- metastatic breast cancer (MBC) after progression on a CDK4/6 inhibitor (CDK4/6i) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-01-06.