Effective personalized therapy for breast cancer based on predictions of cell signaling pathway activation from gene expression analysis

Current therapeutic outcomes for breast cancer underscore the complexity of treating a heterogeneous disease. Indeed, studies have shown that differences in gene expression among patients with the same subtype of breast cancer are correlated with the response to treatment. This strongly suggests that there is an urgent need to treat breast cancer with a personalized approach. Here we employed cell signaling pathway signatures to predict pathway activity in subtypes of MMTV-Myc mammary tumors. We then split tumors into subsets and developed individualized combinatorial treatments for two subtypes with distinct pathway activation patterns. Elevation of the EGFR, RAS and TGFβ pathways was observed in one subtype whereas these pathways were not predicted to be active in the other subtype that had high predicted activity of the Myc, Stat3 and Akt pathways. In a proof-of-principle experiment, treatment of these two subtypes with targeted therapies inhibited tumor growth only in the subtype of tumor where the therapy was designed to be active. We then analyzed gene expression profiles of human breast cancer patients and patient-derived xenograft (PDX) samples to predict pathway activity, and validated our approach of developing individualized treatments in mice with PDX tumors. Importantly, our combinatorial therapy resulted in tumor regression, including regression in PDX samples from triple-negative breast cancer. Together our data is a proof-of-principle experiment that demonstrates that cell signaling pathway signature-guided treatment for breast cancer is viable.

HER2/Neu tumorigenesis and metastasis is regulated by E2F activator transcription factors

HER2 / Neu is amplified and overexpressed in a large proportion of human breast cancers, but the signaling pathways that contribute to tumor development and metastatic progression are not completely understood. Using gene expression data and pathway signatures we predicted a role for activator E2F transcription factors in Neu induced tumors. This was genetically tested by interbreeding Neu transgenics with knockouts of the three activator E2Fs. Loss of any E2F delayed Neu induced tumor onset. E2F1 loss accelerated tumor growth while E2F2 and E2F3 loss did not. Strikingly, it was observed that loss of E2F1 or E2F2 significantly reduced the metastatic capacity of the tumor and this was associated with a reduction in circulating tumor cells in the E2F2 knockout. Gene expression analysis between the tumors in the various E2F mutant backgrounds revealed that there was extensive compensation by other E2F family members in the individual knockouts, underscoring the importance of the E2Fs in HER2 / Neu induced tumors. Extension to HER2 positive human breast cancer revealed a number of HER2+ subtypes based on E2F activity with differences in relapse free survival times. Taken together these data demonstrate that the E2F transcription factors are integral to HER2+ tumor development and progression.

Heterogeneity in MYC-induced mammary tumors contributes to escape from oncogene dependence

A hallmark of human cancer is heterogeneity, reflecting the complex series of changes resulting in the activation of oncogenes coupled with inactivation of tumor suppressor genes. Breast cancer is no exception and indeed, many studies have revealed considerable complexity and heterogeneity in the population of primary breast tumors and substantial changes in a recurrent breast tumor that has acquired metastatic properties and drug resistance. We have made use of a Myc-inducible transgenic mouse model of breast cancer in which elimination of Myc activity following tumor development initially leads to a regression of a subset of tumors generally followed by de novo Myc-independent growth. We have observed that tumors that grow independent of Myc expression have gene profiles that are distinct from the primary tumors with characteristics indicative of an epithelial-mesenchymal transition (EMT) phenotype. Phenotypic analyses of Myc-independent tumors confirm the acquisition of an EMT phenotype suggested to be associated with invasive and migratory properties in human cancer cells. Further genomic analyses reveal mouse mammary tumors growing independent of myc have a higher probability of exhibiting a gene signature similar to that observed for human 'tumor-initiating' cells. Collectively, the data reveal genetic alterations that underlie tumor progression and an escape from Myc-dependent growth in a transgenic mouse model that can provide insights to what occurs in human cancers as they acquire drug resistance and metastatic properties.

Abstract P1-03-04: Genomic Prediction and Genetic Validation of a Role for the E2F Transcription Factors in Breast Cancer

Background: A key and dominant feature of human breast cancer is the morpholiogical, molecular and genomic heterogeneity evident in the disease. This presents a problem in both understanding the mechanisms of progression and in developing therapeutic options. Although mouse models of cancer have traditionally been used to simplify the study of human disease, we suggest that there are opportunities to also model the complexity and heterogeneity of human cancer. Recently we have used signatures of cell signaling pathways to investigate the pattern of gene expression in a Myc initiated mouse model of breast cancer. This revealed the presence of a number of distinct subgroups that correlated with the histological variation. An examination of the predicted activation of E2F transcription factors revealed that individual E2Fs were differentially regulated in the various subtypes of Myc driven breast cancers. Materials and Methods: To directly test the computational prediction that E2Fs had divergent roles in breast cancer, we interbred MMTV-Myc transgenic mice with E2F knockout mice. Mammary gland morphology, tumor latency, growth rate and histology were then examined. The resulting tumors were also examined through microarrays (Affymetrix 430A 2.0) for gene expression and activation of gene expression signatures using our previously characterized methods.

Results: The ablation of E2F1 resulted in a decrease in Myc initiated tumor latency and an increase in growth rate of the resulting tumors. Conversely, E2F2 and E2F3 mutant backgrounds resulted in a delay of tumor formation and a marked decrease in incidence. The E2F3 mutant background also result in tumors that grew significantly more slowly compared to the wild type controls. Investigating the mechanism behind these effects revealed that E2F1 loss was associated with a decrease in apoptosis in the normally highly apoptotic Myc tumors. E2F2 and E2F3 effects were a result of reducing the Myc mediated effects to the mammary gland, reducing the pool of susceptible cells. In addition to examining the mechanism that resulted in latency alterations we examined the tumors from the various backgrounds to determine whether loss of the individual E2Fs had effects on the genomic heterogeneity through gene expression analysis. This revealed that the E2F2 null tumors had a reduction of the EMT tumor type, a finding we validated through a histological examination. Finally, to determine whether the role of the E2Fs in the mouse model would translate to human breast cancer we examined a panel of human tumors and noted that a low probability of E2F2 activation was associated with extended relapse free survival times.

Discussion: Previous studies have illustrated that breast cancer is a heterogeneous disease. Here we have predicted and then genetically tested a variable role for the E2F transcription factors in a heterogeneous mouse model of breast cancer. This genetic test has illustrated the power of the genomic signatures in predicting involvement of signaling pathways in breast cancer. In addition, we demonstrated a key role for the E2Fs in both a mouse model of mammary tumorigenesis and in human breast cancer.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P1-03-04.

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.

Amplification of the neu/erbB-2 oncogene in a mouse model of mammary tumorigenesis

The neu (c-erbB-2, Her-2) protooncogene is amplified and overexpressed in 20-30% of human breast cancers. Although transgenic mouse models have illustrated the role of Neu in the induction of mammary tumors, Neu expression in these models is driven by a strong viral promoter of questionable relevance to the human disease. To ascertain whether expression of activated Neu under the control of the endogenous promoter in the mammary gland could induce mammary tumors we have generated mice that conditionally express activated Neu under the transcriptional control of the intact endogenous Neu promoter. Expression of oncogenic neu in the mammary gland resulted in accelerated lobulo-alveolar development and formation of focal mammary tumors after a long latency period. However, expression of activated Neu under the normal transcriptional control of the endogenous promoter was not sufficient for the initiation of mammary carcinogenesis. Strikingly, all mammary tumors bear amplified copies (2-22 copies) of the activated neu allele relative to the wild-type allele and express highly elevated levels of neu transcript and protein. Thus, like human erbB-2-positive breast tumors, mammary tumorigenesis in this mouse model requires the amplification and commensurate elevated expression of the neu gene.

Tyrosine kinase signalling in breast cancer: tyrosine kinase-mediated signal transduction in transgenic mouse models of human breast cancer

The ability of growth factors and their cognate receptors to induce mammary epithelial proliferation and differentiation is dependent on their ability to activate a number of specific signal transduction pathways. Aberrant expression of specific receptor tyrosine kinases (RTKs) has been implicated in the genesis of a significant proportion of sporadic human breast cancers. Indeed, mammary epithelial expression of activated RTKs such as ErbB2/neu in transgenic mice has resulted in the efficient induction of metastatic mammary tumours. Although it is clear from these studies that activation these growth factor receptor signalling cascades are directly involved in mammary tumour progression, the precise interaction of each of these signalling pathways in mammary tumourigenesis and metastasis remains to be elucidated. The present review focuses on the role of several specific signalling pathways that have been implicated as important components in RTK-mediated signal transduction. In particular, it focuses on two well characterized transgenic breast cancer models that carry the polyomavirus middle T(PyV mT) and neu oncogenes.

Accelerated mammary tumor development in mutant polyomavirus middle T transgenic mice expressing elevated levels of either the Shc or Grb2 adapter protein

The Grb2 and Shc adapter proteins play critical roles in coupling activated growth factor receptors to several cellular signaling pathways. To assess the role of these molecules in mammary epithelial development and tumorigenesis, we have generated transgenic mice which individually express the Grb2 and Shc proteins in the mammary epithelium. Although mammary epithelial cell-specific expression of Grb2 or Shc accelerated ductal morphogenesis, mammary tumors were rarely observed in these strains. To explore the potential role of these adapter proteins in mammary tumorigenesis, mice coexpressing either Shc or Grb2 and a mutant form of polyomavirus middle T (PyV mT) antigen in the mammary epithelium were generated. Coexpression of either Shc or Grb2 with the mutant PyV mT antigen resulted in a dramatic acceleration of mammary tumorigenesis compared to parental mutant PyV mT strain. The increased rate of tumor formation observed in these mice was correlated with activation of the epidermal growth factor receptor family and mitogen-activated protein kinase pathway. These observations suggest that elevated levels of the Grb2 or Shc adapter protein can accelerate mammary tumor progression by sensitizing the mammary epithelial cell to growth factor receptor signaling.