Abstract S3-06: Mutational analysis of CALGB 40601 (Alliance), a neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for HER2-positive breast cancer
Authors: Hoadley Katherine A , Barry William T , Pitcher Brandelyn N , Parker Joel S , Wilkerson Matthew D , Irvin William , Henry Norah Lynn , Tolaney Sara M , Dang Chau , Krop Ian E , Berry Donald A , Mardis Elaine R , Perou Charles M , Winer Eric P , Hudis Clifford A , Carey Lisa A 
Published: May 2015

Abstract
Background: In CALGB 40601, the HER2-Enriched (HER2-E) molecular subtype had significantly higher pathologic complete response (pCR) rates regardless of treatment arm (single HER2-targeting with T+L or T+H, dual targeting with T+H+L) (Carey et al, ASCO 2014). A TP53 mutation gene expression signature was significant in a multivariable analysis as were treatment, molecular subtype, proliferation, and an immune cell genomic signature. Mutational analysis is now available for this sample set.
Methods: 265 of 305 enrolled patients (pts) had RNA sequencing (RNAseq) of pre-treatment biospecimens; 181/265 had whole exome sequencing (WES) available from tumor and matched normal blood. Somatic mutations were detected by the program UNCeqR, which integrates WES and RNAseq. We examined the association of mutations with in-breast pCR, molecular subtypes, and gene expression signatures.
Results: In this subset, there were 57 HER2-E, 58 Luminal A, 51 Luminal B, 9 Basal-like, 4 Normal-like, and 2 Claudin-low. The pCR rate was 45% (51% THL, 47% TH and 34% TL), consistent with the entire study population. TP53 was the most frequently mutated gene (56%); frequency varied by molecular subtype (Fisher p&lt;0.0001) with the highest in the HER2-E (88%). Type of mutation also varied by molecular subtype: 34% of TP53 mutations in HER2-E pts were nonsense or frame shift mutations compared to 20% in Luminal B and 11% in Luminal A. The presence of a TP53 mutation was significantly associated with achieving pCR (59% compared to 28% in wildtype; odds ratio=3.7, p&lt;0.0001) which did not vary by treatment arm. TP53 mutation status by WES was strongly associated with a gene-expression based predictor (AUC=0.85, p&lt;0.001), suggesting the RNAseq-based signature could be used as a surrogate measure of genotype. PIK3CA mutations were present in 36 pts (20%); 33/36 (92%) were in exons 9 and 20. PIK3CA mutations varied moderately among subtypes and were most prevalent in Luminal B (31%) and HER2-E (25%). Rates of pCR did not vary by PIK3CA mutation status (39% vs 47% in wildtype, p=0.46). GATA3 mutations were identified in 7 pts (4 Luminal A, 3 Luminal B), but only 1 pt achieved pCR. ERBB2 mutations were found in 7 pts: 2 HER2-E, 2 Luminal A, 3 Luminal B. Two were previously identified (the lapatinib-sensitive activating mutation V777L and the lapatinib-resistant mutation L755S), both were trastuzumab resistant in experimental models (Bose et al, Cancer Discovery 2013). Consistent with these results, the V777L pt achieved pCR on the THL arm; the L755S pt did not achieve pCR on the TL arm.
Conclusions: TP53 mutation is a frequent, clinically important event in HER2-positive disease and predicts pCR to chemotherapy plus HER2-targeting. Frequency and type of mutation was dependent on molecular subtype within this clinically HER2-positive cohort. Ongoing analyses are comparing WES data between pre- and post-treatment samples as well as investigating copy number and clonality. This research is supported in part by funds from GlaxoSmithKline and grants from the Breast Cancer Research Foundation.
Citation Format: Katherine A Hoadley, William T Barry, Brandelyn N Pitcher, Joel S Parker, Matthew D Wilkerson, William Irvin Jr, Norah Lynn Henry, Sara M Tolaney, Chau Dang, Ian E Krop, Donald A Berry, Elaine R Mardis, Charles M Perou, Eric P Winer, Clifford A Hudis, Lisa A Carey. Mutational analysis of CALGB 40601 (Alliance), a neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for HER2-positive breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr S3-06.