Abstract 4064: Association of molecular signatures, mutations, and sTILs, with pCR in breast cancer patients in NRG Oncology/NSABP B-52
Authors: Pogue-Geile Katherine L. , Wang Ying , Feng Huichen , Lipchik Corey , Kim Rim S. , Cecchini Reena S. , Jacobs Samuel A. , Srinivasan Ashok , Costantino Joseph P. , Mamounas Eleftherios P. , Geyer Charles E. , Rastogi Priya , Lucas Peter C. , Paik Soonmyung , Osborne C. Kent , Wolmark Norman , Rimawi Mothaffar F. 
Published: August 2019

Abstract
Background: NRG Oncology/NSABP B-52 neoadjuvant clinical trial was conducted to test if the addition of estrogen deprivation (ED) would improve the pCR rate in HER2+/ER+ breast cancer pts treated with docetaxel, carboplatin, trastuzumab, and pertuzumab (TCHP). A numerical increase in the pCR rate was observed with ED (46.1% v 40.9%), but the difference was not statistically significant. The purpose of this study was to determine the utility of using stromal tumor infiltrating lymphocytes (sTILs), mutations, established, and novel signatures, to assess their value for predicting pCR, particularly in the TCHP + ED arm.
Methods: Whole transcriptome RNA-Seq and Ampli-Seq libraries were sequenced on the Ion Torrent platform. Mutations were assessed with a custom Ampli-Seq panel of 117 genes, including HER2-activated pathways and/or trastuzumab (T)-resistance markers. The 8-gene T-benefit signature was prospectively tested for association with pCR, and was previously validated in the adjuvant setting in B-31 and NCCTG N9831. Hot-spot mutations, sTILs, and signatures for immune cells, intrinsic subtypes, risk of recurrence proliferation (RORP), and MammaPrint, were also tested for associations with pCR. RNA-Seq data was also used to identify ED-predictive genes. Differential expression was assessed in normalized RNA-Seq data using DESeq2 and each sample was subtyped with the AIMS classifier. Wilcoxon two-sided test, chi-square, or Fisher's exact tests were used to assess associations with pCR.
Results: Subtypes were determined with RNA-Seq data from pretreatment biopsies (N=230). The 8-gene T-benefit signature was associated with pCR. The high-, medium-, and low- T-benefit groups had pCR rates of 55%, 44%, and 6.8%, respectively (p=1.3e-13). Intrinsic subtypes were associated with pCR by comparing HER2E to all other subtypes combined (69% v 28%, p=3.9e-08). Hot spot mutations in PIK3CA alone (p=0.014), or combined with hot spot mutations in ERBB2, ERBB3, AKT1, PTEN, and MAP3K1, were associated with no pCR (p=0.0007) and may be useful as resistance markers. sTILs, MammaPrint, RORP, and some immune cell signatures also showed statistically significant associations with pCR but did not identify a subset of pts with an increased pCR rate in the TCHP + ED arm. In contrast, expression of the SH3BP2 gene was associated with pCR only in the TCHP + ED arm (interaction p=0.03).
Conclusion: The previously validated 8-gene T-benefit signature identifies a subset of pts with very low pCR rate (6.8%) with TCHP. PIK3CA and other activating mutations were associated with no pCR. These findings may identify pts with resistant disease who may require a different treatment. Exploratory analyses suggest that SH3BP2 expression may identify pts who may benefit from TCHP + ED, but validation is required for clinically utility.
Support: BCRF, U10CA180868, -180822; UG1CA189867, Genentech, PUMA Biother
Citation Format: Katherine L. Pogue-Geile, Ying Wang, Huichen Feng, Corey Lipchik, Rim S. Kim, Reena S. Cecchini, Samuel A. Jacobs, Ashok Srinivasan, Joseph P. Costantino, Eleftherios P. Mamounas, Charles E. Geyer, Priya Rastogi, Peter C. Lucas, Soonmyung Paik, C. Kent Osborne, Norman Wolmark, Mothaffar F. Rimawi. Association of molecular signatures, mutations, and sTILs, with pCR in breast cancer patients in NRG Oncology/NSABP B-52 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4064.