With current standard of care adjuvant therapy, approximately 25-30% of women with high risk early stage HR+/HER2- breast cancer experience relapse. The preoperative platform offers an opportunity to interrogate mechanisms of drug resistance that, in turn, could inform the choice of adjuvant therapy. We report herein a study where we performed targeted DNA sequencing and whole transcriptome analysis on whole tumor sections from a cohort of 68 operable ER+ breast cancers treated with the aromatase inhibitor letrozole for a median of 7.2 months before surgery, and a with a median follow up of 5 years. We found that resistant tumors were enriched in clinically actionable mutation and showed an enrichment in expression of genes involved in proliferation. Resistant tumors show a high degree of heterogeneity among them upregulating a variety of transcriptional programs. A common feature among resistant tumors was a co-expression of several genes dependent on the E2F4 transcription factor. We defined an E2F4 activation signature that define ER+ breast cancer with poor prognostic features and is sensitive to treatment with CDK4/6 inhibitors. This signature is of potential use for the identification of patients with ER+ breast cancer candidates for adjuvant therapy with CDK4/6 inhibitors in combination with antiestrogens. Our study also identifies a novel gene, PRR11 (Proline rich 11), as a putative driver of endocrine resistance in ER+ breast cancers and that merits further investigation to understand its mechanisms of action.

With current standard of care adjuvant therapy, approximately 25-30% of women with high risk early stage HR+/HER2- breast cancer experience relapse. The preoperative platform offers an opportunity to interrogate mechanisms of drug resistance that, in turn, could inform the choice of adjuvant therapy. We report herein a study where we performed targeted DNA sequencing and whole transcriptome analysis on whole tumor sections from a cohort of 68 operable ER+ breast cancers treated with the aromatase inhibitor letrozole for a median of 7.2 months before surgery, and a with a median follow up of 5 years. We found that resistant tumors were enriched in clinically actionable mutation and showed an enrichment in expression of genes involved in proliferation. Resistant tumors show a high degree of heterogeneity among them upregulating a variety of transcriptional programs. A common feature among resistant tumors was a co-expression of several genes dependent on the E2F4 transcription factor. We defined an E2F4 activation signature that define ER+ breast cancer with poor prognostic features and is sensitive to treatment with CDK4/6 inhibitors. This signature is of potential use for the identification of patients with ER+ breast cancer candidates for adjuvant therapy with CDK4/6 inhibitors in combination with antiestrogens. Our study also identifies a novel gene, PRR11 (Proline rich 11), as a putative driver of endocrine resistance in ER+ breast cancers and that merits further investigation to understand its mechanisms of action.