Abstract 1789: Chromatin modifier alterations confer resistance to endocrine deprivation and CDK4/6 inhibitors in ER+ breast cancer and drive convergent evolution in patient autopsy lesions
Authors: Leshchiner Elizaveta , Leshchiner Ignaty , Martin Elizabeth E. , Chen Christopher T. , Zhang Thomas , Pinto Christopher , Rhrissorrakrai Kahn , Utro Filippo , Levovitz Chaya , Jacobs Raquel A. , Danysh Brian P. , Slowik Kara , Broudo Maida , Parida Laxmi , Juric Dejan , Getz Gad 
Published: June 2022

We studied resistance mechanisms to hormone therapy and CDK4/6 cell cycle inhibitors in ER+ breast cancer by analyzing whole-exome, whole-genome, single-cell, and bulk transcriptomes in 120 autopsy samples from 13 patients obtained by the Massachusetts General Hospital Rapid Autopsy program. For each patient, we inferred the clonal structure of the samples and tracked the metastatic spread of different clones throughout the body. For 7 patients, we also analyzed serial cfDNA samples to identify clones that were selected for during treatment. We identified significantly recurrent and convergent (arising independently in distinct clones) acquired mutations in ESR1, KRAS, and chromatin modifier genes, in particular, mutations in KMT2C, which may represent mechanisms of drug resistance in this clinical setting. To experimentally study the role of KMT2C mutations, we used CRISPR/Cas9 to knock out KMT2C in the ER+ CAMA1 breast cancer cell line that is sensitive to both ER and CDK4/6 inhibition. KMT2C knock-out cells demonstrated significantly increased viability under treatment with fulvestrant (ERi), palbociclib (CDK4/6i), or their combination compared to the control cell lines. We show that this increased drug resistance is driven by downregulation of the ESR1 pathway, suggesting a decreased dependency on ER signaling for cell cycle progression. In addition to the early survival benefit, KMT2C knock-out resulted in a dramatic outgrowth of cells under long-term fulvestrant treatment. The KMT2C KO fulvestrant-resistant outgrown cells were highly resistant to the CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib compared to control cells, as well as to novel ERalpha inhibitors and a range of targeted therapies currently in clinical trials. By testing a panel of compounds on KMT2C KO and control cell lines, we propose potential novel therapeutic strategies that may help overcome the development of resistance in KMT2C-mutant cells. These findings suggest that KMT2C mutations may be a mechanism of acquired resistance to CDK4/6 inhibitor combinations, and subsequent treatment with therapies directed towards ER or CDK4/6 pathways may be ineffective and other treatment avenues need to be developed.

Citation Format: Elizaveta Leshchiner, Ignaty Leshchiner, Elizabeth E. Martin, Christopher T. Chen, Thomas Zhang, Christopher Pinto, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Raquel A. Jacobs, Brian P. Danysh, Kara Slowik, Maida Broudo, Laxmi Parida, Dejan Juric, Gad Getz. Chromatin modifier alterations confer resistance to endocrine deprivation and CDK4/6 inhibitors in ER+ breast cancer and drive convergent evolution in patient autopsy lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1789.