A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds

Abstract

SummaryThe inter- and intra-tumor heterogeneity of breast cancer needs to be adequately captured in pre-clinical models. We have created a large collection of breast cancer patient-derived tumor xenografts (PDTXs), in which the morphological and molecular characteristics of the originating tumor are preserved through passaging in the mouse. An integrated platform combining in vivo maintenance of these PDTXs along with short-term cultures of PDTX-derived tumor cells (PDTCs) was optimized. Remarkably, the intra-tumor genomic clonal architecture present in the originating breast cancers was mostly preserved upon serial passaging in xenografts and in short-term cultured PDTCs. We assessed drug responses in PDTCs on a high-throughput platform and validated several ex vivo responses in vivo. The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies (http://caldaslab.cruk.cam.ac.uk/bcape), including identification of biomarkers of response or resistance.

Modeling Breast Cancer Intertumor and Intratumor Heterogeneity Using Xenografts

“…Significantly, we have observed the proportion of mouse stromal cells in the PDTXs remains stable through serial passages. These data were confirmed by orthogonal methods such as fluorescence in situ hybridization (FISH) and immunohistochemistry (Bruna et al 2016).…”

“…It is hence more likely that patient-and tumor-specific determinants, in combination with growing in a new environment in the immunodeficient mouse host, affects the observed drifts. Significantly, all the molecular traits examined remained remarkably stable through serial passages in the mouse, even after more than 10 passages (Bruna et al 2016).…”

“…The copynumber profiles of PDTXs classified into each IntClust are similar to those reported in primary tumors, contrasting to what we observed in cell lines (Curtis et al 2012;Ali et al 2014). The subtype distribution of engrafted PDTX samples in the biobank is biased toward ER 2 and ER þ tumors with worse prognosis (Curtis et al 2012;Bruna et al 2016), reflecting the favored engraftment of more aggressive breast cancer subtypes. Hence, the ER -PDTX samples in the biobank have a distribution of most frequently mutated genes similar to that found in ER 2 breast cancers from the The Cancer Genome Atlas (TCGA) cohort (Cancer Genome Atlas 2012).…”

“…We further investigated the intratumoral composition and architecture of PDTX samples and observed xenografts are communities of clones with varying degrees of complexity similar to those observed in the breast cancer clinical population, and these communities share most of the clones found in the matched originating cancer sample (Bruna et al 2016;Pereira et al 2016). Because cancer genomes constantly evolve under selective pressure, we investigated the extent of the human-to-mouse and mouse-to-mouse clonal dynamics using PyClone (Roth et al 2014;Eirew et al 2015), a method for estimating the proportion of cells in a tumor carrying each mutation and clustering them into subclones (groups of cells with the same genotype).…”

“…These short-term cultures from PDTXs (PDTX-derived tumor cells or PDTCs) retain similar molecular features, including the intratumor heterogeneity, as in the originating PDTX sample ( Fig. 3; Bruna et al 2016). We then did a proof of concept screen, using the Welcome Trust Sanger Institute setup for high-throughput drug testing in cell lines (Garnett et al 2012), in 22 PDTX models at different passages.…”