Related Experiment Video
Updated: Feb 8, 2026
An Ex Vivo Brain Slice Model to Study and Target Breast Cancer Brain Metastatic Tumor Growth
Published on: September 22, 2021
Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable
Damir Varešlija1, Nolan Priedigkeit2,3, Ailís Fagan1
1Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland.
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 < .05). Subsequent bioinformatic analysis for readily druggable targets revealed recurrent gains in RET expression and human epidermal growth factor receptor 2 (HER2) signaling. Small molecule inhibition of RET and HER2 in ex vivo patient BrM models (n = 4) resulted in statistically significantly reduced proliferation (P < .001 in four of four models). Furthermore, RET and HER2 inhibition in a PDX model of BrM led to a statistically significant antitumor response vs control (n = 4, % tumor growth inhibition [mean difference; SD], anti-RET = 86.3% [1176; 258.3], P < .001; anti-HER2 = 91.2% [1114; 257.9], P < .01).
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.
Insights
This study identified new therapeutic targets for breast cancer brain metastases (BrMs) by analyzing gene expression. Targeting RET and HER2 significantly reduced BrM growth in preclinical models, offering new treatment avenues.
Area of Science:
- Oncology
- Genomics
- Translational Medicine
Background:
- Breast cancer brain metastases (BrMs) present unique challenges due to adaptations to treatment and the brain microenvironment.
- Understanding BrM adaptations and identifying therapeutic targets are crucial for improving patient outcomes.
- Current knowledge of BrM-specific alterations and their clinical targeting potential remains limited.
Purpose of the Study:
- To identify clinically actionable therapeutic targets in breast cancer brain metastases through genome-wide molecular profiling.
- To functionally validate identified targets in preclinical models of BrM.
- To establish acquired vulnerabilities in BrM for potential clinical investigation.
Main Methods:
- Genome-wide gene expression profiling using TrueSeq RNA-sequencing on patient-matched primary breast tumors and brain metastases (n=21).
- Bioinformatic analysis to identify druggable targets with recurrent expression gains in BrM.
- Functional validation of identified targets (RET and HER2) using small molecule inhibitors in ex vivo BrM explants (n=4) and a patient-derived xenograft (PDX) model.
Main Results:
- Significant shifts in gene expression were observed, with 1314 genes upregulated and 1702 downregulated in BrM compared to primary tumors.
- Recurrent gains in RET and HER2 signaling were identified as druggable targets.
- Inhibition of RET and HER2 significantly reduced BrM proliferation in ex vivo models and demonstrated significant antitumor responses in a PDX model.
Conclusions:
- Recurrent gene expression changes and acquired vulnerabilities distinct from primary tumors were uncovered in BrM.
- Aberrations in key oncogenic pathways, specifically RET and HER2, were validated as suitable therapeutic targets.
- Paired specimen expression profiling is a valuable strategy for identifying targetable dependencies in advanced cancers like BrM.
More Related Videos
07:13Initiation of Metastatic Breast Carcinoma by Targeting of the Ductal Epithelium with Adenovirus-Cre: A Novel Transgenic Mouse Model of Breast Cancer
Published on: March 26, 2014
06:52Monitoring Breast Cancer Growth and Metastatic Colony Formation in Mice using Bioluminescence
Published on: November 5, 2021
Related Concept Videos
01:26Targets for Drug Action: Overview
Receptors are either membrane-spanning or intracellular proteins, which upon binding a ligand, get activated and transmit the signal downstream to elicit a response. Drugs bind receptors, either mimicking the action of endogenous ligands or blocking the receptor activity to bring about a modified response. Nearly 35% of approved drugs target the G...
01:17Sign Test for Matched Pairs
To conduct the sign test, we first calculate the differences in...
01:06Fixed Action Patterns
01:09Wilcoxon Signed-Ranks Test for Matched Pairs
01:41Action Potentials
01:31Action Potential
Membrane potential in neurons
Neurons typically have a resting membrane potential of about -70 millivolts (mV). When they receive...