Abstract 4508: Genomic profiling of ER+ breast cancers treated with prolonged neoadjuvant letrozole reveal a high frequency of NOTCH2 mutations in clinically resistant tumors
Authors: Guerrero-Zotano Angel , Stricker Thomas , Hutchinson Katherine E. , Formisano Luigi , Giltnane Jennifer , Ruiz Amparo , Arteaga Carlos L. 
Published: July 2016

Abstract
Hypothesis: Approximately 20% of patients with early ER+ breast cancer (BC) treated with adjuvant antiestrogen therapy eventually relapse with endocrine-resistant metastatic disease. We hypothesized that profiling newly diagnosed ER+ breast tumors that persist following prolonged estradiol deprivation with letrozole would identify genomic alterations causally associated with endocrine resistance.
Methods: We treated 57 postmenopausal women (median 77 years; range 60-86) with ER+/HER2- early BC with neoadjuvant letrozole (median 7.5 months; range 3-36) followed by surgery and adjuvant endocrine therapy. Patients were followed with serial ultrasounds and defined as non-responders if they developed recurrent locally or metastatic disease, or had a preoperative endocrine response index (PEPI) ≥4 (composite score of post-treatment ER, Ki67, T and N status). DNA extracted from post-treatment specimens was profiled using targeted exome sequencing of 300 cancer-related genes. We screened for variants with a high probability of disrupting protein function and excluded variants likely to be germline by filtering out every alteration not present in the Catalogue of Somatic Mutations in Cancer (COSMIC), if the variant had an allele frequency &gt;0.2% as per the Exome Aggregation Consortium (ExAC) dataset.
Results: Ten (10) patients had a PEPI 0 score, 32 patients were PEPI 1-3, and 15 were PEPI ≥4. After a median follow-up of 50 months (range 12-100), 9 patients have recurred with metastatic disease (4 with PEPI1-3, 5 with PEPI≥4). We identified 535 variants with a median coverage &gt;200x (387 nonsynonymous, 23 stop-gain, 124 indels). The median number of mutations was similar in responder vs non responders (8.03 vs 8.6). Recurrently mutated genes (&gt;5%) included PIK3CA (38%), NOTCH2 (31%), KMT2C (22%), VEZF1 (21%), TP53 (12%), NF1 (9%), MTOR (9%), ESR1 (7%) and ERBB2 (5%). Recurrent amplifications were detected in CCND1 (15%), ERBB2 (12%), FGF19 (12%) and FGFR1 (8%). The only mutations enriched in the non-responders and that correlated with long-term outcome were those in NOTCH2. The relapse-free survival rate at 40 months for patients with NOTCH2 mutations was 89% vs 41% for patients with wild-type NOTCH2 (p = 0.001). NOTCH2 mutations clustered as a frameshift deletion (P6fs) in exon 1, with a 20% average allele frequency. This mutation has been reported in TCGA and COSMIC at a mutation rate of 6%, across all tumor types and is predicted to produce an N-terminally truncated NOTCH2 protein (39 amino acids shorter) lacking the signal peptide.
Conclusions: Genomic profiling of residual ER+ breast cancers treated with prolonged neoadjuvant letrozole revealed a high frequency of NOTCH2 mutations. These alterations in NOTCH2 may cause hormone independence in ER+ breast cancer and are worthy of further mechanistic and clinical investigation.
Citation Format: Angel Guerrero-Zotano, Thomas Stricker, Katherine E. Hutchinson, Luigi Formisano, Jennifer Giltnane, Amparo Ruiz, Carlos L. Arteaga. Genomic profiling of ER+ breast cancers treated with prolonged neoadjuvant letrozole reveal a high frequency of NOTCH2 mutations in clinically resistant tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4508.