Abstract S3-6: Profiling of triple-negative breast cancers after neoadjuvant chemotherapy identifies targetable molecular alterations in the treatment-refractory residual disease

Background: Neoadjuvant chemotherapy (NAC) is increasingly used in patients with triple-negative breast cancer (TNBC). NAC can induce a pathologic complete response (pCR) in ∼30% of patients which portends a favorable prognosis. In contrast, patients with residual disease (RD) in the breast at surgical resection exhibit worse outcomes.

Objective: We hypothesized that profiling residual TNBCs after NAC would identify molecularly targetable lesions in the chemotherapy-resistant component of the tumor and that the persistent tumor cells would mirror micro-metastases which ultimately recur in such patients.

Methods: We utilized targeted next generation sequencing (NGS) for 182 oncogenes and tumor suppressors in a CLIA certified lab (Foundation Medicine, Cambridge, MA) and gene expression profiling (NanoString) of the RD after NAC in 102 patients with TNBC. The RD was stained for Ki67, which has been reported to predict outcome after NAC in unselected breast cancers.

Results: Thirteen tumors were not evaluable due to low tumor cellularity. Of 89 evaluable post-NAC tumors, 57 (64%) were basal-like; 19% HER2-enriched; 6% luminal A; 6% luminal B and 5% normal-like. Mean depth of coverage was 635 (range: 135–1207). Of 81 tumors evaluated by NGS, 72/81 (89%) demonstrated mutations in TP53, 22 were MCL1-amplified (27%), and 17 were MYC-amplified (21%). Alterations in the PI3K/mTOR pathway (AKT1-3, PIK3CA, PIK3R1, RAPTOR, PTEN, and TSC1) were identified in 27 tumors (33%). Cell cycle genes were altered in 25 tumors (31%), including amplifications of CDK2, CDK4, and CDK6, CCND1-3, and CCNE1 as well as RB loss. Alterations in the DNA repair pathway (BRCA1/2, ATM; 16 tumors; 20%) and the Ras/MAPK pathway (KRAS, RAF1, NF1; 10 tumors; 12%) were also common. Sporadic growth factor receptor amplifications occurred in EGFR, KIT, PDGFRA, PDGFRB, MET, FGFR1, FGFR2, and IGF1R. NGS identified 7 patients with ERBB2 gene amplification in the RD which was confirmed by FISH in both the pre- and post-treatment tissue, suggesting NGS could assist in the identification of ERBB2-overexpressing tumors misclassified at the time of diagnosis. In general, the gene amplifications identified by NGS corresponded to enhanced gene expression levels. Amplifications of MYC were independently associated with poor recurrence-free survival (RFS) and overall survival (OS). An interaction effect on survival was observed between MEK activation (assayed by a gene expression signature) and MYC amplification, suggesting cooperation between these pathways. Alterations in DNA repair also identified a subgroup with poor RFS and OS. In contrast, high post-NAC Ki67 score did not predict poor RFS or OS in this predominantly TNBC cohort.

Conclusions: The diversity of lesions in residual TNBCs after NAC underscores the need for powerful and broad molecular approaches to identify actionable molecular alterations and, in turn, better inform personalized therapy of this aggressive disease. Incorporation of this platform into clinical studies and eventually standards of care should aid in the prioritization of patients with RD after NAC into rational adjuvant studies.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S3-6.

Prognostic significance of myeloid associated antigen expression in childhood acute lymphoblastic leukemia in Peru

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Background: The prognostic significance of coexpression of myeloid antigens in pediatric patients with acute lymphoblastic leukemia (ALL) has been reported by several authors, with a frequency that has ranged widely. All of these authors are from developed countries, the aim of this study is to evaluate the prognostic significance of these antigens in childhood ALL in a developing country. Methods: We retrospectively reviewed 729 newly diagnosed patients with ALL under 14 years of age, who had a bone marrow flow cytometry performed at our institution, between 1996–2002. Clinical data and treatment outcomes were reviewed and compared between patients with ALL who expressed myeloid antigens and those who did not using chi-square test. Results: 729 medical charts were studied, 81.6% of them were B-common, 8.2% were pro-B, 8.2% were T-cell and 2.1% were pre-B ALL patients. Overall frequency of myeloid antigen expression was 36.6%. The most frequent specific antigens found were: CD13, 15.5%; CD15, 6.0% and CD33, 4.5%. Evaluating the B-common ALL patients the presence of myeloid antigens rises to 43%. Patients who had coexpression of myeloid antigens had a relapse rate (any site) of 49.2% while 36.3% who had no coexpression had a relapse (p=0.001). There has also been statistical significance in bone marrow response on day 14 of induction with 64.9% having less than 5% blasts in the group without coexpression and 46.4% in the group with coexpression (p<0.0001). Conclusions: The present retrospective review shows the presence of associated myeloid antigens in our ALL patients in 36.6%. We have shown that it is an adverse prognostic factor for childhood ALL in a developing country, unlike reports from other centers in developed countries.

No significant financial relationships to disclose.