Abstract P2-03-03: BRG1-SOX4 mediates a novel and essential signaling network that activates PI3K/Akt signaling in TNBC

Background:

Triple negative (TNBC) breast cancer, which is largely synonymous with the basal-like molecular subtype, is an aggressive malignancy that accounts for nearly 1 in 4 breast cancer related deaths and disproportionately affects younger women and women of African American decent. Given the lack of drug-able targets expressed by TNBC tumors, few therapeutic options exist beyond currently utilized cytotoxic therapies, and the overall prognosis for these patients remains poor. While TNBC tumors are characterized by high PI3K signaling, clinical trials targeting this pathway have had limited success. Therefore, identifying mechanisms driving key oncogenic pathways, including PI3K, is paramount to understanding the transformation process and enabling the development of rational, personalized therapeutic regimens.

Methods:

We utilized a PI3K gene expression signature as a conceptual framework to analyze genome-wide mRNA expression and DNA copy number data from human breast tumors to identify genetic drivers of PI3K/Akt signaling. Kinome profiling was used to identify changes in the drug-able kinome regulated by these genes and in vitro studies were used to delineate mechanisms by which identified genes mediate oncogenic PI3K signaling in TNBC.

Results:

Integrative proteogenomic analyses of orthogonal genome-wide data from ˜3,000 human tumors from the TCGA and METABRIC studies identified amplification and overexpression of the oncogenic transcription factor SOX4 as well as the SWI/SNF ATPase BRG1 in tumors with high PI3K activity. These alterations were predominantly expressed in TNBC or basal-like breast tumors. Chromatin immunoprecipitation followed by DNA sequencing (ChIPseq) as well as shRNA-based studies confirmed that BRG1 regulates SOX4 expression in TNBC cell lines. Analyses of data from a genome-wide RNA interference (RNAi) screen in 27 breast cancer cell lines further indicated that SOX4 is essential in cell lines with high PI3K activity and this was confirmed by colony formation and cell proliferation assays. Importantly, in vitro analyses confirmed that both BRG1 and SOX4 regulate Akt phosphorylation and down-stream signaling. Profiling of the drug-able kinome in SOX4 depleted cell lines compared to control cells using Multiplexed kinase Inhibitor Beads couple with quantitative Mass Spectrometry (MIB/MS) identified 21 drug-able kinases regulated by SOX4 activity including TGFBR2 which has been previously shown to regulate PI3K activity. RNA sequencing (RNAseq) and RT-PCR analyses confirmed that SOX4 mediates TGFBR2 mRNA levels and co-immunoprecipitation experiments in conjunction with ChIP assays demonstrated that BRG1 and SOX4 form a complex at the TGFBR2 promoter and enhancer region to regulate TGFBR2 expression.

Abstract P4-07-03: Immunomodulation of triple negative breast cancer by caffeic acid phenethyl ester (CAPE)

Background: CAPE is the major active component of propolis, a widely available, safe, honeybee natural product with anti-inflammatory, antioxidant, and antitumor properties. We have previously shown diverse effects of CAPE in breast cancer. We postulated that CAPE may be useful in primary or secondary prevention for triple-negative breast cancers (TNBC) and evaluated this in a Trp53 null mammary chimera model in which the tumor spectrum is shifted to TNBC when the host is irradiated (Nguyen, 2011). Bioinformatics species comparisons show that TNBC from this model exhibits a spectrum of tumors that is molecularly similar to that seen in human TNBC (Nguyen, 2013).

Methods: The model consists of Trp53 null mammary epithelium transplanted to cleared mammary glands of wildtype mice. Mice irradiated with 1 Gy received transplants 3 days later and were placed on a CAPE or a control diet at 1month post transplantation that was maintained throughout the experiment. Tumor development was monitored by palpation for up to 18 months. Tumors were immunostained for estrogen receptor (ER) status and ER negative tumors were selected from all the groups for RNA sequencing. TNBC molecular subtypes were determined for control (n=5) and CAPE treated (n=9) samples using methods described by Lehman, 2011. Gene expression signatures consisting of 270 genes was analyzed for functional enrichment to identify patterns of signaling, as well as additional tumor characteristics, in each cohort of tumors.

Results: Host irradiation significantly accelerated tumor growth rate compared to the control sham irradiated mice. CAPE treatment blocked this effect, but did not affect the control tumor growth rate. Resected tumors in CAPE treated mice recurred at significantly longer intervals (40 days in control group versus 90 days with CAPE) and much less frequently than tumors from mice on a control diet. Mean expression analysis showed that CAPE induces a distinct gene expression pattern in ER negative tumors from irradiated mice. As previously described (Illa-Bochaca, 2014), ER negative tumors from sham irradiated mice on a control diet were enriched in immune response genes. These genes were suppressed in tumors arising in irradiated host, but this effect of host irradiation was abrogated in mice on the CAPE diet. While untreated tumors were classified into the Basal-like 2 (BL2) or Mesenchymal TNBC molecular subtypes, we observed an increase in subtype diversity after CAPE treatment with tumors being classified as Immunomodulatory and Luminal Androgen Receptor (LAR) in addition to BL2 and Mesenchymal subtypes. Consistent with these data, functional enrichment analyses of RNA sequencing data identified increased immune signaling as well as upregulation of a number of signaling pathways including TGFβ, HGF, and EGFR in treated samples.

Conclusion: These findings support the potential use of CAPE to modify the aggressive behavior of TNBC, which may be due to effects on the immune system in which CAPE acts to re-establish anti-tumor immunity. The finding that CAPE treatment shifts the tumor spectrum to Immunomodulatory subtypes suggests that it may be useful both for women at high risk for TNBC and to prevent or delay TNBC breast cancer recurrence, perhaps in combination with immunotherapy.

Citation Format: Omene C, Patel M, Karagoz K, Gatza ML, Barcellos-Hoff MH. Immunomodulation of triple negative breast cancer by caffeic acid phenethyl ester (CAPE) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-07-03.

Anchorage-independent cell growth signature identifies tumors with metastatic potential

The oncogenic phenotype is complex, resulting from the accumulation of multiple somatic mutations that lead to the deregulation of growth regulatory and cell fate controlling activities and pathways. The ability to dissect this complexity, so as to reveal discrete aspects of the biology underlying the oncogenic phenotype, is critical to understanding the various mechanisms of disease as well as to reveal opportunities for novel therapeutic strategies. Previous work has characterized the process of anchorage-independent growth of cancer cells in vitro as a key aspect of the tumor phenotype, particularly with respect to metastatic potential. Nevertheless, it remains a major challenge to translate these cell biology findings into the context of human tumors. We previously used DNA microarray assays to develop expression signatures, which have the capacity to identify subtle distinctions in biological states and can be used to connect in vitro and in vivo states. Here we describe the development of a signature of anchorage-independent growth, show that the signature exhibits characteristics of deregulated mitochondrial function and then demonstrate that the signature identifies human tumors with the potential for metastasis.