108O - Heterogeneity of endocrine resistance in estrogen-receptor-positive breast cancer

Background

ESR1 gene mutations are selected in advanced breast cancer patients treated with aromatase inhibitors (AI), leading to resistance. However, transcriptional heterogeneity of ESR1-mutant cancers and its impact on ER-signalling reactivation and endocrine therapy resistance remains poorly characterized.

Methods

We analysed bulk RNA sequencing (RNAseq) data from patients with endocrine resistant ER+/HER2- breast cancer (PALOMA-3 trial, n = 302) as well as single nucleus RNA sequencing (snRNAseq) data from AI-resistant patients who were previously sensitive to AI therapy (ESR1 mutants n = 3, ESR1 WT n = 3, ER- n = 3), augmented with recently published ER+, HER2+ and triple-negative breast cancer snRNAseq data (n = 47).

Results

Firstly, we undertook differential gene expression analysis of bulk RNAseq samples in groups by ESR1 mutation status. This analysis revealed ER target genes upregulation in ESR1-mutant metastatic tumours: PGR1 (p = 0.01); PDZK1 (p = 0.01), along with ER response gene sets scores (p = 0.009). In contrast to ESR1 mutation status, differences in ESR1 and ER target genes expression between groups by prior sensitivity to hormone therapy were not significant. Gene set enrichment analysis showed an upregulation of ERBB2/ERBB3 pathway in ESR1 WT group (p = 0.002). We next investigated transcriptional heterogeneity of AI-resistant tumours using snRNAseq data. Identifying malignant cells by aneuploidy presence, we demonstrated that ER-pathway- and ERBB2-driven clusters were identifiable within the same individual’s cancer for both ESR1 mutant and WT cancers, suggesting parallel evolution of diverse resistance mechanisms. AI-resistant tumours, whether ESR1 mutant, WT, or ER-, were transcriptionally more similar to each other than to untreated cancers, with major features including ESR1 upregulation and decreased compositional heterogeneity, dominated by a cluster enriched in MAPK/ERBB pathway genes.

Conclusions

Our data support the hypothesis that sub clones with diverse mechanisms of resistance to endocrine therapy arise contemporaneously in AI-treated breast cancer, with ERBB2 activation seen in ESR1 mutant and WT cancers. This could have implications for treatment combinations of endocrine and HER2-directed therapies.

Editorial acknowledgement

Clinical trial identification

NCT01942135.

Legal entity responsible for the study

The Institute of Cancer Research, London, UK.

Funding

Pfizer.

Disclosure

S. Deng:, Y. Liu: Financial Interests, Personal, Full or part-time Employment: Pfizer; Financial Interests, Personal, Stocks/Shares: Pfizer. N. Turner: Financial Interests, Personal, Advisory Board: AstraZeneca, Lilly, Pfizer, Roche/Genentech, Novartis, GSK, Repare Therapeutics, Relay Therapeutics, Zentalis, Gilead, Inivata, Guardant, Exact Sciences; Financial Interests, Personal, Funding: AstraZeneca, Pfizer, Roche/Genentech, Merck Sharpe & Dohme, Guardant Health, Invitae, Inivata, Personalis, Natera. B. O'Leary: Financial Interests, Personal, Speaker’s Bureau: Merck; Financial Interests, Personal, Advisory Role: Merck, Oliver Wyman; Financial Interests, Personal, Research Grant: Pfizer. All other authors have declared no conflicts of interest.