Research ArticleCancer

Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance

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Science Translational Medicine  09 Aug 2017:
Vol. 9, Issue 402, eaai7993
DOI: 10.1126/scitranslmed.aai7993

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A patient look at cancer resistance

A variety of drugs that inhibit estrogen signaling are in use for breast cancer, but patients often develop resistance to these treatments. To understand how this resistance develops, Giltnane et al. evaluated 143 patients who were receiving the aromatase inhibitor letrozole to block estrogen signaling before undergoing surgery for breast cancer. By performing genomic analysis on these patients’ tumors, the authors were able to identify not only changes in gene expression and estrogen receptor gene fusions that correlated with resistance to therapy but also potential leads for future treatments that could help overcome this resistance.

Abstract

Inhibition of proliferation in estrogen receptor–positive (ER+) breast cancers after short-term antiestrogen therapy correlates with long-term patient outcome. We profiled 155 ER+/human epidermal growth factor receptor 2–negative (HER2) early breast cancers from 143 patients treated with the aromatase inhibitor letrozole for 10 to 21 days before surgery. Twenty-one percent of tumors remained highly proliferative, suggesting that these tumors harbor alterations associated with intrinsic endocrine therapy resistance. Whole-exome sequencing revealed a correlation between 8p11-12 and 11q13 gene amplifications, including FGFR1 and CCND1, respectively, and high Ki67. We corroborated these findings in a separate cohort of serial pretreatment, postneoadjuvant chemotherapy, and recurrent ER+ tumors. Combined inhibition of FGFR1 and CDK4/6 reversed antiestrogen resistance in ER+ FGFR1/CCND1 coamplified CAMA1 breast cancer cells. RNA sequencing of letrozole-treated tumors revealed the existence of intrachromosomal ESR1 fusion transcripts and increased expression of gene signatures indicative of enhanced E2F-mediated transcription and cell cycle processes in cancers with high Ki67. These data suggest that short-term preoperative estrogen deprivation followed by genomic profiling can be used to identify druggable alterations that may cause intrinsic endocrine therapy resistance.

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