Abstract P1-03-02: Histoepigenetic characterization of breast cancer patient derived xenografts (PDX) implicates epithelial-stromal interactions in differential chemotherapy resistance and PDX engraftment
Authors: Petrosyan Varduhi , Huang Chen , Srinivasan Ramakrishnan R , Dobrolecki Lacey E , Sallas Christina , Lewis Alaina N , Wang Tao , Zhang Bing , Milosavljevic Aleksandar , Lewis Michael T 
Published: March 2020

Abstract
Background: Epithelial-stromal interactions play a critical role in treatment resistance, and the state of the stroma can be an indicator for a tumor’s resistance profile. We have developed and characterized a large group of breast cancer PDX models (n=69) (Zhang et al.,2013) and have imported PDX from other sources for inclusion into preclinical drug testing trials. These PDX represent the three main subtypes defined clinically by IHC/FISH (i.e. Estrogen Receptor positive, HER2 positive, and “Triple-negative”). Because the epithelium and stroma in PDX are from two different species (human and mouse, respectively) mRNA (and protein) expression levels can be assigned in a species-specific manner and interrogated computationally to divine interactions that may be important for PDX behaviors including treatment response or engraftment behavior.
Methods: Fifty “triple negative” PDX were treated with four weekly cycles of either docetaxel (20mg/kg, IP) or carboplatin (50mg/kg, IP) vs. control, and evaluated quantitatively for the change in tumor volume from baseline (~200mm3) after four weeks. Using deep RNA-seq data (~200M reads/sample), we identified interactions between the epithelial and stromal in the PDX models using CASTIN (Komura et al.,2016) and variations in cancer specific pathways. We then employed a machine learning approach to identify ligand-receptor interactions whose differential expression correlated with treatment response to each agent. We also used epigenomic deconvolution (Onuchic et al., 2016) to devise a novel classification method based on the cancer-cell specific epigenomic profiles of TCGA samples, and then used it to classify the PDX with the intent to correlate with treatment response.
Results: PDX showed a full range of responses to each agent, from total resistance to complete response. However, several PDX showed differential responses to either docetaxel or carboplatin. We identified variation in the expression patterns of cancer-associated pathways in the epithelial cell fraction of the tumors, including Wnt signaling, as well as pathways involved in hepatic fibrosis. Informative interactions included bidirectional Eph receptor-ephrin signaling which has previously been found to be overexpressed in breast cancer (Vaught et al.,2008). In the epigenomic deconvolution analysis, our classification scheme divided the basal-like samples in TCGA into two groups: a “hot” immune profile-enriched group, and a “cold” or immune profile-deficient group. By applying this classification to the PDX models, unexpectedly, an overwhelming majority of the triple-negative PDX fell into the “cold” basal group. Thus, classification in this manner showed no association with treatment response in the PDX.
Conclusions: These results indicate that tumors may respond uniquely to a given chemotherapeutic, and suggest that differential expression of signaling pathways as well as specific ligand-receptor pairs may prove predictive of resistance and could allow for the development of novel therapies targeting these tissue interactions. While our epigenomic deconvolution results showed no association with treatment response, they unexpectedly suggested that success of PDX engraftment may depend on the stromal immune system composition of the primary tumor such that “hot” primary tumors have lower engraftment efficiency in the “cold” stromal environment of immunocompromised mice.
Citation Format: Varduhi Petrosyan, Chen Huang, Ramakrishnan R Srinivasan, Lacey E Dobrolecki, Christina Sallas, Alaina N Lewis, Tao Wang, Bing Zhang, Aleksandar Milosavljevic, Michael T Lewis. Histoepigenetic characterization of breast cancer patient derived xenografts (PDX) implicates epithelial-stromal interactions in differential chemotherapy resistance and PDX engraftment [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-03-02.