Identifying New Drug Targets to Treat Breast Cancer Brain Metastasis

Breast cancer brain metastasis (BrM) is indicative of poor prognosis, with a short median survival time and limited disease management strategies. Current treatment options are restricted to surgical resection, radiation therapy and limited targeted therapies. Therefore, there is an urgent need to uncover alterations responsible for BrM and to define novel effective therapeutic targets. RNA-sequencing (RNA-Seq) was performed to analyse gene expression differences between patient-matched breast tumours and their associated resected BrM. Importantly, common transcriptional differences in breast cancer specific genes were observed, particularly BrM–acquired aberrant enrichment in multiple receptor tyrosine kinase (RTK) driven signalling pathways. The most notable recurrent alterations were expression gains in RET and HER2. Hence, given the observed enriched kinase landscape these alterations were investigated as clinically actionable therapeutic targets in BrM. To evaluate the effect of RET and HER2 inhibition in a preclinical setting, the efficacy of two FDA-approved agents were examined; a RET inhibitor, cabozantinib, and a pan-HER inhibitor, afatinib. Being small molecule tyrosine kinase inhibitors (TKIs), both drugs have the potential of crossing the blood brain barrier (BBB). In vitro, both agents demonstrated a significant effect on the cellular viability and migratory capacity of brain-metastasising cell lines and primary cells derived from a patient brain metastasis tumour. Significant anti-tumour activity was also shown for anti-HER2 and anti-RET therapies in unique patient derived ex vivo and patient-derived xenograft (PDX) models developed from patients undergoing BrM resection. This study demonstrates profound and recurrent transcriptional remodelling events in BrM, which is critical to understanding the pathobiology of BrM. Furthermore, this work supports comprehensive profiling of metastasis as a compelling and underutilised tool to inform clinical care and reveal novel targeted treatment paradigms. Given the remarkably high recurrence rates of specific targetable alterations, further clinical investigations of recurrent aberrations are in demand, especially considering some are readily druggable. </p

Dynamic epi-transcriptomic landscape mapping with disease progression in estrogen receptor-positive breast cancer

The molecular determinants that drive breast cancer progression to metastasis are complex and partly controlled by nucleic acid epi-modifications. Although DNA-methyl modifications in breast cancer metastasis have been well described, there is limited understanding of the role of RNA methylation in advanced disease. This study aimed to provide an understanding on the role of the epi-transcriptome in estrogen receptor-positive (ER+) breast cancer progression to metastasis.</p

Transcriptome characterization of matched primary breast and brain metastatic tumors to detect novel actionable targets.

Background: Breast cancer brain metastases (BrMs) are defined by complex adaptations to both adjuvant treatment regimens and the brain microenvironment. Consequences of these alterations remain poorly understood, as does their potential for clinical targeting. We utilized genome-wide molecular profiling to identify therapeutic targets acquired in metastatic disease.Methods: Gene expression profiling of 21 patient-matched primary breast tumors and their associated brain metastases was performed by TrueSeq RNA-sequencing to determine clinically actionable BrM target genes. Identified targets were functionally validated using small molecule inhibitors in a cohort of resected BrM ex vivo explants (n = 4) and in a patient-derived xenograft (PDX) model of BrM. All statistical tests were two-sided.Results: Considerable shifts in breast cancer cell-specific gene expression profiles were observed (1314 genes upregulated in BrM; 1702 genes downregulated in BrM; DESeq; fold change > 1.5, Padj Conclusions: RNA-seq profiling of longitudinally collected specimens uncovered recurrent gene expression acquisitions in metastatic tumors, distinct from matched primary tumors. Critically, we identify aberrations in key oncogenic pathways and provide functional evidence for their suitability as therapeutic targets. Altogether, this study establishes recurrent, acquired vulnerabilities in BrM that warrant immediate clinical investigation and suggests paired specimen expression profiling as a compelling and underutilized strategy to identify targetable dependencies in advanced cancers.</p