CCE Breast

Background: Metastatic breast cancer (mBC) present an interpatient heterogeneity in terms of outcome, with some patients dying very early, while other living >10 years. There is no driver alteration, except ER/Her2 expression, that predicts poor outcome in mBC. Breast cancers also present an intratumor heterogeneity both at the genetic and phenotypic levels. Presence of minor subclonal alterations or cell subpopulations, together with clonal evolution could explain cancer progression and resistance to therapy. Two groups from our consortium have pioneered the development of blood-based tools to assess intratumor heterogeneity, including sequencing of circulating tumoral DNA and detection of metastases-initiating cells (MICs). The project will use these tools to explore clinical impact of intratumor heterogeneity and to decipher molecular mechanisms involved in the progression of metastases.
Hypothesis: The hypothesis of the present project is that detection of minor subclonal genomic alterations and metastases-initiating cells in the blood could be associated with poor outcome and resistance to therapy.
Aims & methods: In the specific aim 1, we will evaluate whether detecting minor subclonal alterations and genetic intratumor heterogeneity using circulating tumoral DNA could identify a population of ER+ mBC with poor outcome. A training set of 150 samples will be used to derive a predictor of very poor outcome. Subclonal alterations will be identified using exome sequencing. The predictor will subsequently be validated in 100 patients. In the specific aim 2, we will explore whether a fraction of circulating tumor cells, named MICs, generate metastases and cancer progression in mBC. These genomic and functional analyses will be done on 12 patients. The goal is to provide evidence that metastases are arising from MICs, thereby generating the rationale to test prognostic value of MICs and to identify new targets in this subcellular fraction. In the specific aim 3, we will evaluate whether minor subclonal PTEN alterations detected in plasma are associated with resistance to alpha-selective PI3K inhibitors. In order to achieve this goal, we will use ctDNA to sequence PTEN before and after resistance to PI3K inhibitors in 50 patients with PIK3CA mutated BC included in a randomized trial testing GDC-0032. Finally, in the specific aim 4, we will assess the presence of ERBB2 mutations in patients who became resistant to trastuzumab.
Expected impacts: The project will have three potential impacts. First, it will identify a predictor for early death in mBC. This predictor could define a subset of patients for which drug approval based on phase II data is acceptable, given the very poor outcome. Second, the project will validate mechanism of resistance to PI3K or Her2 inhibitors, and therefore allow to develop some early strategies to overcome such resistance. Third, the project will identify new targets located in subcellular fractions.