Abstract P2-10-01: Genomic profiling of residual ER+ breast cancers treated with prolonged neoadjuvant letrozole reveals novel alterations in clinically resistant tumors
Authors: Guerrero AL , Stricker T , Hutchinson KE , Formisano L , Giltnane J , Fidalgo A , Schwarz LJ , Gavila J , Guillen V , Lluch A , Ruiz A , Arteaga CL 
Published: March 2017

Abstract
Background: 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+ BC that persist following prolonged estradiol deprivation with letrozole would identify genomic alterations associated with endocrine resistance.
Methods: We treated 57 postmenopausal women (median 77 years; range 60-86) with ER+/HER2– 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 prognostic index (PEPI) ≥4 (composite score of post-treatment ER, Ki67, T and N status). Post-treatment specimens were profiled by RNA-seq and targeted capture NGS of &gt;300 cancer-related genes. We screened for variants with a high probability of disrupting protein function (GERP score &gt;4) and excluded likely germline variants by filtering out every alteration not present in COSMIC, if the variant had an allele frequency &gt;0.1% as per the ExAC dataset.
Results: Ten patients (17.5%) had a PEPI 0 score, 31 (54%) were PEPI 1-3, and 16 (28%) were PEPI ≥4. After a median follow-up of 50 months (12-100), 9 patients (15.7%) had recurred with metastatic disease (4 with PEPI 1-3, 5 with PEPI ≥4). We identified 294 variants with a median coverage &gt;250x (206 nonsynonymous, 21 nonsense, 58 indels, 8 splice site). Recurrent mutations included PIK3CA (38%), KMT2C (28%), CDH1 (15%), NF1 (12 %), TP53 (10%), MAP3K1 (7%), ERBB2 (7%) and ESR1 (5%). Recurrent amplifications were identified in MCL1 (31%), GNAS (19%), CCND1 (16%), FYN (14%), AURKA (12%), and ERBB2 (10%), while recurrent deletions were found in DUSP4 (12%), NCOR1 (8%) and NF1 (6%). Compared to alterations reported in untreated ER+ breast cancers in TCGA, we observed a significant increase in KMT2C, NF1, MCL1 and FYN alterations (FDR&lt;0.05). MCL1, GNAS and FYN amplifications, DUSP4 deletions, MAP3K1 mutations, and ERBB2 and NF1 alterations were enriched in the non-responder group. Differential expression analysis of the RNA-seq data revealed an enrichment of E2F and MYC target genes, and genes involved in the G2/M checkpoint, TORC1 signaling, EMT and immunosuppression in non-responding tumors. PEPI 0 tumors were enriched with Luminal A subtype tumors, whereas PEPI 4 tumors were enriched with Luminal B, basal and HER2-enriched subtypes. Luminal A tumors exhibited improved disease free survival compared to other subtypes (HR 0.28, 95% CI 0.10-0.64). Gains in the proximal portion of chromosome 1q were associated with poor long-term outcomes as the relapse-free survival rate at 40 months for patients with 1q gains was 89% versus 41% for patients with no 1q gain (p=0.001).
Conclusions: Genomic profiling of residual ER+ breast cancers treated with prolonged neoadjuvant letrozole revealed a different mutational landscape than primary untreated ER+ BC. These alterations may be associated with poor response to estrogen deprivation in early breast cancer and deserve further study.
Citation Format: Guerrero AL, Stricker T, Hutchinson KE, Formisano L, Giltnane J, Fidalgo A, Schwarz LJ, Gavila J, Guillen V, Lluch A, Ruiz A, Arteaga CL. Genomic profiling of residual ER+ breast cancers treated with prolonged neoadjuvant letrozole reveals novel alterations in clinically resistant tumors [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-10-01.