Abstract PD9-06: Paired pre- and post-treatment DNA sequencing identifies genomic alterations mediating clinical resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer
Authors: Spring LM , Haddad S , Malvarosa G , Vidula N , Juric D , Iafrate AJ , Ellisen LW , Moy B , Isakoff SJ , Bardia A 
Published: May 2019

Abstract
Background: The combination of cyclin-dependent kinase 4 and 6 inhibitors (CDK 4/6 inh) and endocrine therapy have changed the treatment paradigm for hormone receptor-positive metastatic breast cancer (HR+ MBC). Three CDK 4/6 inhibitors (palbociclib, ribociclib, and abemaciclib) are now approved for HR+ MBC in combination with either an aromatase inhibitor (AI) or fulvestrant (a selective estrogen receptor degrader, SERD) after demonstrating significant improvement in progression-free survival compared to endocrine monotherapy. However, both primary and secondary resistance has been observed clinically, and the mechanisms of such resistance are not well understood. Here we describe emergence of molecular alterations following treatment with the combination of CDK 4/6 inhibitors and endocrine therapy.
Methods: We evaluated molecular alterations by next-generation sequencing (NGS) prior to and following treatment with CDK 4/6 + endocrine therapy pre and post CDK inh among patients with HR+ MBC. We performed circulating tumor (ct) DNA analysis via the Guardant360 assay, an NGS-based assay that identifies potential tumor-related (somatic) genomic alterations through sequencing of the critical exons within 73 cancer-related genes, and/or tissue-based genomic analysis utilizing our institutional NGS platform (SNaPshot), which targets hotspots and exons in 89 genes.
Results: A total of 33 HR+ MBC patients had paired pre/post CDK 4/6 tissue/liquid biopsies. 19 (57.6%) received palbociclib and 14 (42.4%) ribociclib, with 25 (75%) receiving an AI and 8 (24%) a SERD. Eight patients (24.2%) were first line. The median duration of response was 8 months (range 1-35 months). The most common acquired alterations at the time of progression that were not present in the pre-treatment specimens included mutations in ESR1 (30.3%), TP53 (30.3%), RB1 (12.1%) and PIK3CA (9.1%), and FGFR1 amplification (27.3%). We then evaluated these results in a subset of patients (N=17) who had paired pre/post liquid biopsies only and found similar results. We observed alterations in oncogenic pathways both upstream and downstream of CDK 4/6-cyclin-D complex (N=17), including upstream receptor tyrosine kinase alterations (29.4%), PI3K/AKT/mTOR alterations (5.9%), and MAPK alterations (17.6%), as well as downstream cell-cycle (35.3%) and DNA repair gene alterations (17.6%). Furthermore, 58.8% of patients had more than one acquired potential driver mutation, and 41.2% had both upstream and downstream alterations possibly reflecting emergence of different subclones and tumor heterogeneity under selective pressure from CDK 4/6 inhibitors.
Conclusion: Both upstream and downstream genomic alterations may mediate acquired clinical resistance to CDK 4/6 inhibitors, reflecting genomic evolution and diversification after exposure to CDK 4/6 inhibitors. Additional studies are needed to confirm these findings and develop potential therapeutic strategies to overcome clinical resistance to CDK 4/6 inhibitors for patients with MBC.
Citation Format: Spring LM, Haddad S, Malvarosa G, Vidula N, Juric D, Iafrate AJ, Ellisen LW, Moy B, Isakoff SJ, Bardia A. Paired pre- and post-treatment DNA sequencing identifies genomic alterations mediating clinical resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-06.