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BACKGROUND: Nearly 50% of patients with triple negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NACT) retain residual tumors resulting in high rates of metastatic relapse and poor overall survival. Residual tumors surviving NACT (Adriamycin plus cyclophosphamide; AC) were found to undergo a metabolic transition to heightened mitochondrial oxidative phosphorylation (oxphos; PMID: 30996079). Pharmacologic inhibition of mitochondrial electron transport chain (ETC) complex I with IACS-010759 (PMID: 29892070) had enhanced efficacy in residual, rather than treatment-naïve, tumors of orthotopic patient-derived xenograft (PDX) models. Our analyses of mitochondrial structure and function in human TNBC cell lines revealed differing adaptations in residual cells surviving treatment with conventional NACT agents. While DNA-damaging chemotherapies (e.g.Adriamycin, carboplatin) induced mitochondrial fusion and oxphos, taxanes (e.g.paclitaxel, docetaxel) induced mitochondrial fragmentation and reduced oxphos (Baek et al., Biorxiv Doi 10.1101/2022.02.25.481996). The mechanistic basis of these mitochondrial adaptations is not yet understood. The mitochondrial ETC consists of 92 proteins, 13 of which are encoded in the mitochondrial genome (mtDNA) and translated by the mitoribosome, while the remaining are encoded by the nuclear genome (nDNA), translated by the cytoribosome, and inserted into the inner mitochondrial membrane by accessory proteins, namely Oxidase (Cytochrome C) Assembly 1-Like (OXA1L). Disruption of OXA1L in mammalian cells has been shown to affect the levels and activity of ETC complexes I, III, IV, and V, and thus diminish oxphos. We aim to determine whether mitochondrial translation and OXA1L activity represent therapeutic vulnerabilities to overcome pro-survival metabolic adaptations in chemoresistant TNBC thereby augmenting treatment response. METHODS: Weare evaluating the effects of conventional TNBC chemotherapies singly, and in standard combinations, on mitochondrial translation and ETC formation in human TNBC cells and PDX models(PIM001-P, WHIM14, BCM15116) using metabolomic and proteomic profiling. To perturb these processes genetically, we knocked down (KD) OXA1Lwith siRNA. We are complementing these studies pharmacologically using conventional antibiotics, such as tigecycline, as previous studies showed they inhibit mitochondrial translation in breast and other cancers (PMID: 25625193). These studies will reveal whether OXA1L and mitochondrial translation are required for metabolic adaption and chemotherapy resistance of residual TNBC cells. PDX preclinical trials based on our published residual tumor testing schema (PMID: 30996079), will reveal whether the sequential combination of NACT followed by tigecycline can effectively perturb residual tumor relapse. RESULTS: Proteomic profiling of longitudinally harvested PDX tumors demonstrates substantial disruption of mitochondria-and nuclear-encoded ETC components in residual vs. treatment-naïve tumors. Interestingly, these patterns are distinct between different chemotherapy treatments, with an increase of ETC components in carboplatin-treated residual tumors compared to a decrease in docetaxel-treated residual tumors. Western blot analyses of human cell lines show OXA1LKD perturbs levels of both nuclear-and mitochondria-encoded ETC components. Preliminary findings suggest OXA1LKD increases sensitivity to chemotherapies in human TNBC cell lines. Finally, tigecycline effectively inhibits TNBC cell growth. We next will evaluate whether residual cells not killed by conventional chemotherapies have enhanced tigecycline susceptibility. CONCLUSION: These data suggest targeting mitochondrial translation may be a promising approach to overcome pro-survival metabolic adaptations in residual TNBC cells not killed by conventional chemotherapies. Citation Format: Mariah J. Berner, Lily Baek, Junegoo Lee, Philip L. Lorenzi, Mei Leng, Alexander B. Saltzman, Anna Malovannaya, Lacey E. Dobrolecki, Christina Sallas, Michael T. Lewis, Gloria V. Echeverria. Investigating the role of mitochondrial protein translation in the metabolic adaptation of chemoresistant triple negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-11-10.

Background.Targeting HER2 gene amplification is one of the great achievements in oncology resulting in the use of a wide array of anti-HER2 agents in the clinic. Unfortunately, 20% of patients still relapse with secondary organ metastasis and are currently incurable. While only 1.6% of primary non-HER2-amplified ER+ breast cancers harbor HER2 mutations, 6-10% of all metastatic breast cancers harbor HER2 mutations, suggesting their causal role in contributing to metastasis. The clinical value of HER2 activating mutations is being tested with the pan-HER tyrosine kinase inhibitor neratinib in phase II clinical trials (NCT01670877, NCT01953926, and NCT02465060). To date, neratinib has elicited only modest responses in ER+ breast cancer, often rapidly followed by progression. This study characterizes HER2-mutant induced resistance to endocrine therapy or neratinib induced resistance and resulting metastasis, in order to determine a more effective rational therapeutic approach for treating ER+ HER2-mutant breast cancer. Methods.HER2 mutation frequency and its impact on patient outcome was determined using METABRIC primary breast cancer (BC) and MSK IMPACT metastatic BC ER+ sequencing studies. Effects of estrogen (E2), fulvestrant, or neratinib on cell growth and HER2 signaling were examined on ER+/ILC cells (MM134) stably expressing HER2/WT, HER2/S310F, and HER2/L755S. Cell growth was measured using CellTiter-Glo and HER2 signaling was analyzed by western blot analysis. Additionally, the effect of these ER+/ILC and IDC HER2 mutations on tumor growth and endocrine or neratinib treatment resistance was determined using fat pad injections and MIND xenografts in NOD-scid gamma mice. Results.We searched ER+ sequencing datasets and identified HER2 mutations that are highly enriched in ER+ ILC as compared to ER+ IDC. These activating HER2 mutations in ER+ ILC are associated with early relapse and poor overall survival. Moreover, we are finding that ILC patients harboring the recurrent HER2/L755S mutation have worse overall survival compared to non-mutant HER2 ILC. MM134 cells expressing HER2/S310F and HER2/L755S show increased cell growth, strongly activated autophosphorylation of HER2, and increased downstream signaling (pMAPK and pAKT) as compared to cells expressing HER2/WT upon treatment with fulvestrant (1μM). Three clinically relevant in vivo models including ILC HER2/L755S Mammary INtraDuctal (MIND) xenografts, IDC HER2/L755S fat pad xenografts, and IDC HCI-003 (an ER+ patient-derived xenograft (PDX) naturally harboring the exon 20 activating HER2G778_P780 dup) exhibit fulvestrant and neratinib resistance and lung and ovary metastases. In addition, we find that HER2 mutations induced mTOR signaling. In contrast, however, the pan-HER drug poziotinib does potently inhibit tumor growth and organ-specific metastasis and perturbs mTOR activation in these models. Conclusion.We demonstrate that clinically associated HER2 mutations drive endocrine therapy or neratinib resistance and poor patient outcome in ER+ patients. Our data propose the use of the irreversible pan-HER TKI poziotinib for treating endocrine therapy or neratinib refractory ER+ HER2-mutant metastatic breast cancer. Citation Format: Shyam. M Kavuri, Rashi Kalra, Ching Hui Chen, Junkai Wang, Ahmad Bin Salam, Lacey Dobrolecki, Alaina Lewis, Christina Sallas, Clayton Yates, Carolina Gutierrez, Balasubramanyam Karanam, Meenakshi Anurag, Bora Lim, Matthew Ellis. Distinct HER2 allele specific therapeutic response and preclinical efficacy of poziotinib in metastatic ER+ HER2 mutant breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-13-24.

Supplementary Data from Poziotinib Inhibits HER2-Mutant–Driven Therapeutic Resistance and Multiorgan Metastasis in Breast Cancer

The pan-HER tyrosine kinase inhibitor (TKI) neratinib is therapeutically active against metastatic breast cancers harboring activating HER2 mutations, but responses are variable and often not durable. Here we demonstrate that recurrent HER2 mutations have differential effects on endocrine therapy responsiveness, metastasis, and pan-HER TKI therapeutic sensitivity. The prevalence and prognostic significance may also depend on whether the HER2 mutant has arisen in the context of lobular versus ductal histology. The most highly recurrent HER2 mutant, L755S, was particularly resistant to neratinib but sensitive to the pan-HER TKI poziotinib, alone or in combination with fulvestrant. Poziotinib reduced tumor growth, diminished multiorgan metastasis, and inhibited mTOR activation more effectively than neratinib. Similar therapeutic effects of poziotinib were observed in both an engineered HER2L755S MCF7 model and a patient-derived xenograft harboring a HER2G778_P780dup mutation. Overall, these findings support the need for clinical evaluation of poziotinib for the treatment of HER2-mutant metastatic breast cancer.Significance:Evaluation of the functional impact of HER2 mutations on therapy-induced resistance and metastasis identifies robust antitumor activity of poziotinib and supports the clinical evaluation of poziotinib in ER+ HER2 mutant breast cancer.

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. Methods: Orthotopic TNBC PDXs were treated with four weekly cycles of docetaxel, carboplatin, or the combination. Changes in tumor volume after 4 weeks of treatment were evaluated. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatments to identify associations with chemotherapy response (https://pdxportal.research.bcm.edu). Fisher’s exact test was used to identify significant associations between mutation and copy number events and dichotomized treatment response. For gene level analyses, Spearman’s correlation was calculated between mRNA or protein abundance and log2 fold change in tumor volumes after treatment. Signed -log10 p-values from Spearman’s correlation analysis were used as input for Gene Set Enrichment Analysis. Validation in external datasets was performed using METABRIC (PMID: 22522925) and BrighTNess clinical trial (PMID: 29501363) human datasets, an independent PDX dataset (PMID: 32546838), and shRNA screen data from DepMap (PMID: 30389920). Results: Combination carboplatin and docetaxel was largely ineffective at generating enhanced responses over the best single agent, suggesting de-escalation of chemotherapy may be possible. Genomic aberrations in BRCA2 and BCL9 were enriched in carboplatin-responsive PDXs while aberrations in RAF1 were enriched in docetaxel-resistant PDXs. Genes with gene-drug response correlations supported by both mRNA and protein measurements, but not mRNA or protein alone, for both carboplatin and docetaxel treatment in PDXs were associated with prognosis from basal human breast tumors receiving any chemotherapy from the METABRIC dataset. These data suggest that the combination of mRNA and protein data provided increased accuracy in identifying genes associated with clinical outcome in TNBC. Some of the top genes with genomic aberrations and/or overexpression at both mRNA and protein levels in chemoresistant PDXs, many of which have not been evaluated for their ability to augment response to taxane- or platinum-based chemotherapies, were validated in independent datasets with PDXs and TNBC patients receiving carboplatin and taxane combination. Further, some were found to be dependencies in TNBC cell lines from a publicly available genetic perturbation dataset. At the pathway level, both mRNA and protein data associated models resistant to both agents with enhanced oxidative phosphorylation and proteostatic pathways including proteosome degradation and the unfolded protein response (UPR) pathway related to endoplasmic reticulum stress. Pharmacological targeting the UPR pathway in combination with docetaxel showed activity in PDX models resistant to single-agent docetaxel. These results suggest targeting the UPR pathway as a novel therapeutic strategy to overcome chemotherapy resistance in TNBC. Conclusion: Proteogenomic analysis of PDX tumors identified diverse genes and pathways associated with chemotherapy resistance and 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, Xi Chen, Gloria V Echeverria, Meenakshi Anurag, Bing Zhang, Michael T Lewis. Proteogenomic analysis of differential chemotherapy responses in patient-derived xenografts of triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-07-01.

The pan-HER tyrosine kinase inhibitor (TKI) neratinib is therapeutically active against metastatic breast cancers harboring activating HER2 mutations, but responses are variable and often not durable. Here we demonstrate that recurrent HER2 mutations have differential effects on endocrine therapy responsiveness, metastasis, and pan-HER TKI therapeutic sensitivity. The prevalence and prognostic significance may also depend on whether the HER2 mutant has arisen in the context of lobular versus ductal histology. The most highly recurrent HER2 mutant, L755S, was particularly resistant to neratinib but sensitive to the pan-HER TKI poziotinib, alone or in combination with fulvestrant. Poziotinib reduced tumor growth, diminished multiorgan metastasis, and inhibited mTOR activation more effectively than neratinib. Similar therapeutic effects of poziotinib were observed in both an engineered HER2L755S MCF7 model and a patient-derived xenograft harboring a HER2G778_P780dup mutation. Overall, these findings support the need for clinical evaluation of poziotinib for the treatment of HER2-mutant metastatic breast cancer. Significance: Evaluation of the functional impact of HER2 mutations on therapy-induced resistance and metastasis identifies robust antitumor activity of poziotinib and supports the clinical evaluation of poziotinib in ER+ HER2 mutant breast cancer.

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.