Genomic sequencing of metastatic hormone-receptor positive breast cancer implicates AKT1 in driving resistance to cyclin-dependent kinase 4/6 inhibitors

Introduction: The cyclin-dependent kinase 4/6 inhibitors (CDK4/6i), in combination with an antiestrogen, have emerged as standard-of-care options in both the first- and subsequent-line setting for patients with metastatic hormone-receptor positive (HR+)/HER2- breast cancer. Despite their widespread use, limited insight exists into the molecular pathways governing response and resistance to these agents. Methods and Results: We performed whole-exome sequencing on metastatic tumor specimens from 59 patients with HR+/HER2- breast cancer who had received CDK4/6i-based therapy. Tumor biopsies were characterized as demonstrating sensitivity, intrinsic resistance, or acquired resistance based upon the timing of resistance, radiographic response, and duration of therapy. In contrast to prior reports indicating PIK3CA enrichment in patients receiving CDK4/6i-based therapy, alterations in PI3K were approximately evenly distributed in this cohort between sensitive and resistant biopsies (8/20, 40% vs. 21/40, 52.5%, respectively, p = 0.808 via Fisher9s exact test). Activating alterations in AKT1, however, were identified in three resistant tumor specimens, including both point mutations and amplification. In two instances where matched pretreatment sensitive biopsies and post-treatment resistance biopsies were available, an AKT1 point mutation and an AKT1 amplification, respectively, were uniquely identified in the resistant biopsy. Immunohistochemical analysis of sensitive and resistance biopsy specimens in these patients confirmed upregulation of pAKT, pS6, and pRb, indicating upregulation of the AKT signaling axis. AKT1 was introduced into multiple HR+ breast cancer cell lines in vitro (T47D, MCF7, and CAMA1) via lentiviral overexpression. Overexpression of AKT1 in these cell lines provoked significant resistance to palbociclib, abemaciclib, fulvestrant, and estrogen deprivation (via charcoal-stripped serum, CSS). AKT1-expressing cells were also resistant to the various pairwise combinations of antiestrogen and CDK4/6i. Sensitivity to estrogen deprivation and CDK4/6i could be restored by treatment with the AKT inhibitor MK2206. Conclusions: In contrast to prior reports, PIK3CA mutations did not correlate with resistance to CDK4/6 inhibition in our cohort of tumor specimens from 59 patients with metastatic HR+ breast cancer. AKT1 has emerged as a key potential mediator of resistance to both antiestrogens and CDK4/6i in vitro and in vivo. AKT1 pathway activation may serve as a potential biomarker of resistance to CDK4/6i, while novel strategies to target AKT1 may restore sensitivity to CDK4/6i-based therapy in HR+ metastatic breast cancer. Citation Format: Seth A. Wander, Ofir Cohen, Gabriela N. Johnson, Jorge Buendia, Flora Luo, Joseph Geradts, Eric P. Winer, Nancy U. Lin, Levi A. Garraway, Nikhil Wagle. Genomic sequencing of metastatic hormone-receptor positive breast cancer implicates AKT1 in driving resistance to cyclin-dependent kinase 4/6 inhibitors [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B23.