Abstract P2-09-30: A gene expression signature that predicts for trastuzumab response in HER2+ breast cancer
Authors: Abukhdeir AM , Najor MS , Turturro SB , Armstrong AR , McDonald A , Fogg L , Cobleigh MA 
Published: February 2018

Abstract
Background: Approximately 15-20% of breast cancers overexpress HER2. These patients are eligible for trastuzumab in combination with chemotherapy. However, some patients are extreme responders to single agent trastuzumab and we wanted to identify differences in cancer gene expression that could predict response to single agent trastuzumab.
Methods: We performed paired-end RNAseq on an isogenic cellular model of trastuzumab sensitivity and resistance. We reasoned that the isogenic nature of the cellular clones used in this study would enrich for differentially-expressed genes (DEGs) that were associated with response to single-agent trastuzumab. DEGs where chosen based upon either i) large fold changes in resistant vs. sensitive clones, ii) high frequency in human HER2+ breast cancers, or iii) were found to be enriched with other DEGs in signaling pathways selected by Ingenuity Pathway Analysis (IPA). DEGs were further scrutinized based upon associations with overall survival (OS) in HER2+ human breast cancers. The resulting genes were validated using qPCR and in several independent sample sets containing gene expression profiles of human breast cancers.
Results: Discovery: RNAseq yielded 3,241 statistically-significant DEGs. We used two independent filtering pipelines to obtain 175 DEGs. Ingenuity Pathway Analysis found signaling pathways associated with eukaryotic initiation factor, lysine specific demethylase 5B, and estrogen receptor alpha to be enriched in DEGs associated with trastuzumab resistance. Of these DEGs, six genes correlated with a statistically significant change in OS in the training dataset, and were validated by qPCR in the cell lines used for the analysis. We further determined that the six-gene signature was a negative predictor of overall survival in HER2+ breast cancer patients whose cancers carried at least one DEG. Validation: Using independent cohorts from TCGA and the website KMplot.com, we validated the predictive power of the six-gene signature. Of the 47 HER2+ patients from TCGA, eight patients carried two more DEGs, while 39 carried ≤ 1 DEG. Although the numbers are small, of the 8 patients followed for four or more years, only one patient was alive as compared with 7 out of 39 patients without the signature. Similarly, Kaplan Meier analysis of gene expression data from KMplot.com revealed that only 1 out of 23 patients (4.3%) who carried high mean expression of the six-gene signature were free of distant metastases after 87 months, compared to 4 out of 43 patients (9.3%) from the cohort carrying low mean expression of the six-gene signature. In both validation cohorts, the six DEG signature was not predictive in HER2-negative breast cancers.
Discussion: Patients whose tumors lack this gene expression signature are more likely to experience a favorable response to trastuzumab therapy. This signature requires validation in a clinical cohort treated with trastuzumab monotherapy.
Citation Format: Abukhdeir AM, Najor MS, Turturro SB, Armstrong AR, McDonald A, Fogg L, Cobleigh MA. A gene expression signature that predicts for trastuzumab response in HER2+ breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-30.