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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.

Background: Chemotherapy is essential for the management of patients with triple-negative breast cancer (TNBC). Identification of biomarkers that may indicate treatment efficacy will be critical to improve patient stratification prior to treatment. To elucidate molecular determinants underlying chemotherapy response, we conducted a proteogenomic study using TNBC patient-derived xenografts (PDXs) treated with chemotherapy. Approach: 50 TNBC PDXs were treated with either docetaxel or carboplatin. Changes in tumor volume after 4 weeks from baseline were evaluated. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatment to identify associations with chemotherapy response. Fisher's exact tests were used to test for significant enrichment of mutation and copy number events (p Results: At the DNA level, genomic aberrations in BRCA2 and BCL2 were enriched in carboplatin-responsive PDXs, while ARID1B aberrations were enriched in docetaxel-responsive PDXs. Gene-drug response correlations supported by both mRNA and protein-based measurements, but not mRNA or protein alone, for both carboplatin and docetaxel treatment in PDXs were associated with prognosis from basal and claudin-low human breast tumors in receipt of any chemotherapy from the METABRIC dataset. These data suggest that the combination of mRNA and protein data increased power to identify genes related to clinical outcome in TNBC. Some of the top genes overexpressed at both mRNA and protein levels in chemoresistant PDXs are targets of approved drugs, many of which have not been evaluated for their ability to augment response to taxane- or platinum-based chemotherapies. These genes are being investigated as therapeutic targets as well as markers of chemotherapy response. At the pathway level, both RNA and protein data associated models resistant to both agents with enhanced oxidative phosphorylation and translation regulation. Protein data further associated resistant models with elevated cytoplasmic ribosomal proteins. In contrast, both RNA and protein data associated tumors sensitive to both agents with genes involved in the E2F-Rb axis and cell cycle progression. Moreover, DNA mismatch repair and mRNA processing pathways were uniquely associated with carboplatin and docetaxel sensitivity, respectively, while amino acid metabolism and MAPK signaling pathways were uniquely associated with carboplatin and docetaxel resistance, respectively. Conclusion: Taken together, proteogenomic analysis of PDX tumors identifies diverse genes and pathways associated with chemotherapy response and further suggests potential therapeutic opportunities in TNBC. Citation Format: Jonathan T. Lei, Chen Huang, Ramakrishnan R. Srinivasan, Suhas Vasaikar, Lacey E. Dobrolecki, Alaina N. Lewis, Christina Sallas, Susan G. Hilsenbeck, C Kent Osborne, Mothaffar F. Rimawi, Matthew J. Ellis, Varduhi Petrosyan, Alexander B. Saltzman, Anna Malovannaya, Gerburg Wulf, Daniel C. Kraushaar, Tao Wang, Gloria V. Echeverria, Bing Zhang, Michael T. Lewis. Proteogenomic characterization of triple-negative breast cancer patient-derived xenografts reveals molecular correlates of differential chemotherapy response and potential therapeutic targets to overcome resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2992.