Abstract P4-13-04: Upregulation of cell cycle pathway genes without loss of RB1 contributes to acquired resistance to single-agent treatment with palbociclib in breast cancer
Authors: DeMichele A , Shih NNC , Koehler M , Huang Bartlett C , Jiang Y , Harwick J , Huang D , Zheng X , Clark AS , Colameco C , Feldman MD , Gallagher M , Goodman N , O'Dwyer P , Rejto P 
Published: May 2016

Abstract
Background: The oral cdk4/6 inhibitor, Palbociclib (Palbo), has been shown to prolong progression-free survival when combined with anti-estrogen therapy and have single-agent activity in metastatic breast cancer (MBC). Progressive disease (PD) on therapy does occur, however, and little is known about resistance mechanisms. Preclinical data have suggested that cell cycle gene expression changes are a potential mechanism of resistance. We performed comprehensive genomic analyses on serial tumor samples from an exceptional responder to single-agent Palbo to determine whether such changes occur in vivo.
Methods: Serial biopsies were obtained from a 67 year old patient with MBC treated on a phase II trial of single-agent Palbo at the University of Pennsylvania. Tissue was obtained from the primary lesion (1999, Stage 3, ER-/PR+/Her2+) and first recurrence (2005, contralateral breast, bone, lung; ER+/PR-/Her2+, treated with Herceptin/letrozole). At PD (2010), pt received single-agent P, 50 mg daily for 21 days each 28-day cycle, with PR for 33 months. A sample from metastatic skin lesion at PD on P (2013) was obtained. Next generation targeted sequencing was performed at Foundation Medicine using the Heme Panel. RNA was profiled using a 784-gene custom Nanostring array including cell cycle genes and ER pathway genes. Determination of pathway enrichment was performed using GSEA and the statistical significance of network neighborhood over-representation was calculated using cumulative hypergeometric distribution.
Results: There was no genetic evidence suggesting loss of RB1, or alterations in p16, cyclin D1, cdk4, PIK3CA or ESR1, and the genomic profile did not change between the primary and recurrent tissue samples. As expected, amplification of ERRB2 was present in all samples. In contrast, expression of cell cycle-regulated genes (PLK1, TOP2A, CDK1, BUB1, CDC20, CCNA2, CCNE2, CCNB1 BIRC5) increased more than two-fold at PD on Palbo compared to pre-Palbo, along with evidence of activation of the FOXM1 network.
Conclusion: Gene expression changes associated with cell cycle activation and FOXM1 activation may lead to acquired resistance to Palbociclib, despite wild-type RB1. These data demonstrate the importance of pre-/post-treatment biopsies and the feasibility of high-level genomic assessment in archival tissues to elucidate resistance mechanisms of novel therapies.
Citation Format: DeMichele A, Shih NNC, Koehler M, Huang Bartlett C, Jiang Y, Harwick J, Huang D, Zheng X, Clark AS, Colameco C, Feldman MD, Gallagher M, Goodman N, O'Dwyer P, Rejto P. Upregulation of cell cycle pathway genes without loss of RB1 contributes to acquired resistance to single-agent treatment with palbociclib in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-13-04.