Alicia Y. Zhou

Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer

Expression of the oncogenic transcription factor MYC is disproportionately elevated in triple-negative breast cancer (TNBC), as compared to estrogen receptor–, progesterone receptor– or human epidermal growth factor 2 receptor–positive (RP) breast cancer. We and others have shown that MYC alters metabolism during tumorigenesis. However, the role of MYC in TNBC metabolism remains mostly unexplored. We hypothesized that MYC-dependent metabolic dysregulation is essential for the growth of MYC-overexpressing TNBC cells and may identify new therapeutic targets for this clinically challenging subset of breast cancer. Using a targeted metabolomics approach, we identified fatty acid oxidation (FAO) intermediates as being dramatically upregulated in a MYC-driven model of TNBC. We also identified a lipid metabolism gene signature in patients with TNBC that were identified from The Cancer Genome Atlas database and from multiple other clinical data sets, implicating FAO as a dysregulated pathway that is critical for TNBC cell metabolism. We found that pharmacologic inhibition of FAO catastrophically decreased energy metabolism in MYC-overexpressing TNBC cells and blocked tumor growth in a MYC-driven transgenic TNBC model and in a MYC-overexpressing TNBC patient–derived xenograft. These findings demonstrate that MYC-overexpressing TNBC shows an increased bioenergetic reliance on FAO and identify the inhibition of FAO as a potential therapeutic strategy for this subset of breast cancer.

A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis

mir-17-92, a potent polycistronic oncomir, encodes six mature miRNAs with complex modes of interactions. In the Eμ-myc Burkitt’s lymphoma model, mir-17-92 exhibits potent oncogenic activity by repressing c-Myc-induced apoptosis, primarily through its miR-19 components. Surprisingly, mir-17-92 also encodes the miR-92 component that negatively regulates its oncogenic cooperation with c-Myc. This miR-92 effect is, at least in part, mediated by its direct repression of Fbw7, which promotes the proteosomal degradation of c-Myc. Thus, overexpressing miR-92 leads to aberrant c-Myc increase, imposing a strong coupling between excessive proliferation and p53-dependent apoptosis. Interestingly, miR-92 antagonizes the oncogenic miR-19 miRNAs; and such functional interaction coordinates proliferation and apoptosis during c-Myc-induced oncogenesis. This miR-19:miR-92 antagonism is disrupted in B-lymphoma cells that favor a greater increase of miR-19 over miR-92. Altogether, we suggest a new paradigm whereby the unique gene structure of a polycistronic oncomir confers an intricate balance between oncogene and tumor suppressor crosstalk. DOI: http://dx.doi.org/10.7554/eLife.00822.001

PIM1 kinase inhibition as a targeted therapy against triple-negative breast tumors with elevated MYC expression

Triple-negative breast cancer (TNBC), in which cells lack expression of the estrogen receptor (ER), the progesterone receptor (PR) and the ERBB2 (also known as HER2) receptor, is the breast cancer subtype with the poorest outcome. No targeted therapy is available against this subtype of cancer owing to a lack of validated molecular targets. We previously reported that signaling involving MYC—an essential, pleiotropic transcription factor that regulates the expression of hundreds of genes—is disproportionally higher in triple-negative (TN) tumors than in receptor-positive (RP) tumors. Direct inhibition of the oncogenic transcriptional activity of MYC has been challenging to achieve. Here, by conducting a shRNA screen targeting the kinome, we identified PIM1, a non-essential serine–threonine kinase, in a synthetic lethal interaction with MYC. PIM1 expression was higher in TN tumors than in RP tumors and was associated with poor prognosis in patients with hormone- and HER2-negative tumors. Small-molecule PIM kinase inhibitors halted the growth of human TN tumors with elevated MYC expression in patient-derived tumor xenograft (PDX) and MYC-driven transgenic mouse models of breast cancer by inhibiting the oncogenic transcriptional activity of MYC and restoring the function of the endogenous cell cycle inhibitor, p27. Our findings warrant clinical evaluation of PIM kinase inhibitors in patients with TN tumors that have elevated MYC expression.

Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map

UNLABELLED There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that charts the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model complex cellular contexts. Applying this dataset to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene, including resistance to AKT-PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic lethal manner, providing new drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of drug responses from patient data and can accelerate the development of new genotype-directed therapies. SIGNIFICANCE Determining how the plethora of genomic abnormalities that exist within a given tumor cell affects drug responses remains a major challenge in oncology. Here, we develop a new mapping approach to connect cancer genotypes to drug responses using engineered isogenic cell lines and demonstrate how the resulting dataset can guide clinical interrogation.

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors

Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon–exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk.

Cancer recurrence monitoring using hyperpolarized [1-13C]pyruvate metabolic imaging in murine breast cancer model

The purpose of this work was to study the anatomic and metabolic changes that occur with tumor progression, regression and recurrence in a switchable MYC-driven murine breast cancer model. Serial 1H MRI and hyperpolarized [1-13C]pyruvate metabolic imaging were used to investigate the changes in tumor volume and glycolytic metabolism over time during the multistage tumorigenesis. We show that acute de-induction of MYC expression in established tumors results in rapid tumor regression and significantly reduced glycolytic metabolism as measured by pyruvate-to-lactate conversion. Moreover, cancer recurrences occurring at the tumor sites independently of MYC expression were observed to accompany markedly increased lactate production.

Cancer cells exploit an orphan RNA to drive metastatic progression

Here we performed a systematic search to identify breast-cancer-specific small noncoding RNAs, which we have collectively termed orphan noncoding RNAs (oncRNAs). We subsequently discovered that one of these oncRNAs, which originates from the 3′ end of TERC, acts as a regulator of gene expression and is a robust promoter of breast cancer metastasis. This oncRNA, which we have named T3p, exerts its prometastatic effects by acting as an inhibitor of RISC complex activity and increasing the expression of the prometastatic genes NUPR1 and PANX2. Furthermore, we have shown that oncRNAs are present in cancer-cell-derived extracellular vesicles, raising the possibility that these circulating oncRNAs may also have a role in non–cell autonomous disease pathogenesis. Additionally, these circulating oncRNAs present a novel avenue for cancer fingerprinting using liquid biopsies.A novel orphan noncoding RNA species with tumor-specific expression across breast cancer subtypes promotes metastatic progression and holds potential for patient diagnosis.

Abstract B34: PIM kinase as a novel therapeutic target for triple-negative breast cancer

The greatest clinical challenge in treating breast cancer occurs in those patients whose tumors lack expression of the estrogen and progesterone receptors and that of the HER2 oncoprotein. No targeted therapeutic strategies currently exist against this aggressive type of “triple negative” breast cancer (TNBC) due to lack of validated targets. We previously found that MYC mRNA, protein, and its signaling were disproportionally elevated in TN compared to receptor positive (RP) breast cancer. We sought to take advantage of the unique molecular feature found in this tumor type to identify potent and effective treatment strategies. Since MYC is an oncogenic transcription factor, rationally designed small molecule inhibitors that can directly inhibit its activity are not available for clinical use. An alternative approach to selectively kill MYC-driven tumors is to inhibit those proteins that are indispensable for the viability of such tumors, but are not essential in non-tumorigenic cells. This form of “indirect” treatment strategy has become known as the “synthetic-lethal” approach. To identify novel targets that are readily druggable for treating MYC-driven TNBC, we conducted a kinome MYC synthetic lethal shRNA screen in non-immortalized human mammary epithelial cells expressing a 4-hydroxytamoxifen (TAM)-activatable MycER transgene (HMEC-MycER). Of 600 human kinases targeted by 2,000 individual shRNA clones, 9 kinases were identified as hits as they were essential specifically for the MYC-activated HMEC cells. Among these hits, we focused on PIM1, a non-essential kinase, the knock-down of which had the greatest efficacy in causing cell death in the MYC-activated cells and had minimum inhibitory effect on the growth of the control cells. We determined that PIM1 expression was elevated in TN tumors and was associated with poor prognosis specifically in patients with hormone receptor-negative tumors. Small molecule PIM kinase inhibitors halted the growth of human TN tumors with elevated MYC expression in a patient-derived tumor xenograft (PDX) mouse model by inhibiting oncogenic transcriptional activity of MYC while simultaneously restoring the function of the endogenous cell cycle inhibitor p27. Thus, our findings warrant clinical evaluation of small molecule PIM kinase inhibitors in patients with TN tumors that exhibit elevated MYC expression. Note: This abstract was not presented at the conference. Citation Format: Dai Horiuchi, Alicia Y. Zhou, Alexandra N. Corella, Christina Yau, Sanjeev Balakrishnan, Kai Kessenbrock, Devon A. Lawson, Roman Camarda, Brittany N. Anderton, Alexey V. Bazarov, Henok Eyob, Julia Rohrberg, Paul Yaswen, Michael T. McManus, Hope S. Rugo, Zena Werb, Andrei Goga. PIM kinase as a novel therapeutic target for triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B34.

Abstract 2673: Inhibition of fatty-acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer

Expression of the oncogenic transcription factor MYC is disproportionately elevated in triple-negative breast cancer (TNBC) compared to estrogen, progesterone and/or human epidermal growth factor 2 receptor-positive (RP) breast tumors. We and others have shown that MYC alters metabolism during tumorigenesis. However, the role of MYC in TNBC metabolism remains largely unexplored. We hypothesized that pharmacologic inhibition of MYC-driven metabolic pathways may serve as a therapeutic strategy for this clinically challenging subtype of breast cancer. Using a targeted metabolomics approach, we identified fatty-acid oxidation (FAO) intermediates as dramatically upregulated in a MYC-driven model of TNBC. A lipid metabolism gene signature was identified in patients with TNBC in the TCGA and multiple other clinical datasets, implicating FAO as a dysregulated pathway critical for TNBC metabolism. We find that MYC-overexpressing TNBC, including a transgenic model and patient-derived xenograft (PDX), display increased bioenergetic reliance upon FAO. Pharmacologic inhibition of FAO catastrophically decreases energy metabolism of MYC-overexpressing breast cancer, blocks growth of a MYC-driven transgenic TNBC model and MYC-overexpressing PDX. Our results demonstrate that inhibition of FAO is a novel therapeutic strategy against TNBCs that overexpress MYC. Citation Format: Roman Camarda, Alicia Y. Zhou, Rebecca A. Kohnz, Sanjeev Balakrishnan, Celine Mahieu, Brittany Anderton, Henok Eyob, Shingo Kajimura, Aaron Tward, Gregor Krings, Daniel K. Nomura, Andrei Goga. Inhibition of fatty-acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2673.

Abstract C88: Genomics, advocacy, and emerging therapeutics to address triple-negative breast cancer (TNBC) outcome disparities.

Background: Collaborative team science provides a starting point for comprehensive change, and advocates have a unique and important role developing and engaging in transdisciplinary collaboratives that focus on new questions and new possibilities to advance the science of ethnic and medically underserved health care disparities. Participating in four areas : 1) research and programmatic support, 2) education and outreach, 3) policy and strategy, and 4) representation and advisory, the UCSF Breast Science Advocacy Core (BSAC) Program, a volunteer affiliate of the Breast Oncology Program (BOP), one of ten multidisciplinary research programs under the umbrella of the UCSF Helen Diller Comprehensive Cancer Center promotes a transformative, transdisciplinary, integrated environment to study the biological basis of the diseases that comprise breast cancer; to define the risk of developing or progressing with specific types of breast cancer; to develop novel interventions that work locally and globally to reduce morbidity and mortality from breast cancer and its treatment; and to leverage new collaborative research, education, and mentoring/training opportunities that address cancer outcome disparities. Advocates involved in KOMEN, DOD, PCORI, AND CBCRP funded research and training grants apply four core principles that forge synergy with NCI Advocacy Research Working Group Recommendations: 1)strategic innovation, 2)collaborative execution, 3)evidence based decision-making, and 4) ethical codes of conduct. Embracing transdisciplinary professionalism, researchers and advocates build on their track record as shared value partners committed to furthering the collective impact of science advocacy exchange (SAE). Study Objectives: Genomic analyses of patient tumors have unearthed an overwhelming number of recurrent somatic alterations in genes that have dramatic effects on tumor biology, patient drug responses, and clinical outcomes. In one study, high grade triple negative breast cancer (TNBC) accounts for 34% of breast cancers in African American women versus 21% in white women. A growing body of evidence has shown that African American women have biologically more aggressive disease, independent of social determinants, and suffer the highest mortality rates. While biological breakthroughs of the last decade have greatly advanced our understanding of cancer, in advanced TNBC, a poor prognosis subtype, there is an urgent need to translate this evolving patient genomic data into new therapeutic paradigms. Our study focuses on the intersection of synthetic lethal approaches, MYC driven human cancers, and immunotherapy as an “innovation agenda”. A distinct MYC vision highlights how overexpression is associated with aggressive outcomes and poor patient outcomes, and synthetic lethal strategies to target MYC (CDK inhibitors, PIM2, as well as the PDI immune pathways) have potential for addressing outcome disparities In African American Women with Triple Negative Breast Cancer (TNBC). Key Findings: We have developed a screening technique that can be used to rapidly and accurately identify potential synthetic lethal interactions in TNBC. This platform utilizes an isogenic cell line system that we have developed to model oncogene activation in TNBC. A growing body of evidence has shown that: 1) Quantitative approach maps genotype-specific drug responses in isogenic cells 2) Systematic discovery of biomarkers for cancer drugs under clinical investigation 3) Clinically actionable synthetic lethal interaction between MYC and dasatinib is discovered 4) Mechanism of dasatinib action through inhibition of LYN kinase is described Key Take-Away Message: The inclusion of advocates in convergent science settings remind academic stakeholders that research is there to benefit the patient as they attempt to spark innovation, democratize science, and support smarter interventions that expedite the incredible potential of future investments in bioscience within disparities arenas. Citation Format: Susan Samson, Alicia Y. Zhou, Maria Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John Gordan, Rebecca Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul Clemens, Alykhan Shamji, Stuart Schreiber, Nevan Krogan, Kevan Shokat, Frank McCormick, Sourav Bandyopadhyay, Andrei Goga. Genomics, advocacy, and emerging therapeutics to address triple-negative breast cancer (TNBC) outcome disparities. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr C88.