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A 13-gene signature predicting rapid development of brain metastases in breast cancer

ABSTRACT: Brain metastases from breast and other cancers constitute an important part of therapeutic failures and are associated with severe morbidity and mortality. Here, we have examined histopathological data and generated gene expression data in two independent cohorts of primary tumors from HER2-positive advanced breast cancer patients. We report that the combination of estrogen receptor (ER) negativity and expression of a novel 13-gene signature identify a subset of patients with rapid (median, 31 and 41 months in discovery and validation cohorts, respectively) versus slower (median, 66 months and 77 months in discovery and validation cohorts, respectively) development of brain metastases (P<0.0001). The 13-gene signature also predicted rapid brain metastasis formation within the ER-negative subset of patients (P=0.014). Interestingly, three of the genes in the signature (RAD51, BARD1, FANCG) function in DNA double strand break repair. Overexpression of RAD51 in immortal MCF-10A breast epithelial cells altered their three-dimensional acinar morphology to increase the percentage of invasive structures by 6.5 fold, in the presence or absence of HER2 overexpression. In summary, ER negativity and a novel 13-gene signature may have the potential to identify subpopulations at highest immediate risk for the development of brain metastases in HER2-positive advanced breast cancer. Our results also suggest that RAD51, found in the 13-gene signature, may promote aggressiveness in breast epithelial cells. These data may be useful in the design of brain metastasis preventive trials and may prompt new treatment strategies Median normalized data provided

ORGANISM(S): Homo sapiens

PROVIDER: GSE38057 | GEO | 2012/07/01

SECONDARY ACCESSION(S): PRJNA167135

REPOSITORIES: GEO

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Project description:Brain metastases are an increasing burden among breast cancer patients, particularly for those with HER2+ and triple negative (TN) subtypes. Mechanistic insight into the pathophysiology of brain metastases and preclinical validation of therapies has relied almost exclusively on intracardiac injection of brain-homing cells derived from highly aggressive TN MDA-MB-231 and HER2+ BT474 breast cancer cell lines. Yet, these well characterized models are far from representing the tumor heterogeneity observed clinically and, due to their fast progression in vivo, their suitability to validate therapies for established brain metastasis remains limited. The goal of this study was to develop and characterize novel human brain metastasis breast cancer patient-derived xenografts (BM-PDXs) to study the biology of brain metastasis and to serve as tools for testing novel therapeutic approaches. We obtained freshly resected brain metastases from consenting donors with breast cancer. Tissue was immediately implanted in the mammary fat pad of female immunocompromised mice and expanded as BM-PDXs. Brain metastases from 3/4 (75%) TN, 1/1 (100%) estrogen receptor positive (ER+), and 5/9 (55.5%) HER2+ clinical subtypes were established as transplantable BM-PDXs. To facilitate tracking of metastatic dissemination using BM-PDXs, we labeled PDX-dissociated cells with EGFP-luciferase followed by re-implantation in mice, and generated a BM-derived cell line (F2-7). Immunohistologic analyses demonstrated that parental and labeled BM-PDXs retained expression of critical clinical markers such as ER, progesterone receptor (PR), epidermal growth factor receptor (EGFR), HER2 and the basal cell marker cytokeratin 5 (CK5). Similarly, RNA sequencing analysis showed clustering of parental, labeled BM-PDXs and their corresponding cell line derivative. Intracardiac injection of dissociated cells from BM-E22-1, resulted in MRI-detectable macrometastases in 4/8 (50%) and micrometastases (8/8) (100%) mice, suggesting that BM-PDXs remain capable of colonizing the brain at high frequencies. Brain metastases developed 8 to 12 weeks after ic injection, located to the brain parenchyma, grew around blood vessels and elicited astroglia activation characteristic of breast cancer brain metastasis. These novel BM-PDXs represent heterogeneous and clinically relevant models to study mechanisms of brain metastatic colonization, with the added benefit of a slower progression rate that makes them suitable for preclinical testing of drugs in therapeutic settings.

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A 13-gene signature predicting rapid development of brain metastases in breast cancer

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