BioProject

The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed clinicians to estimate the overall metastatic burden in breast cancer patients. More...

The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed clinicians to estimate the overall metastatic burden in breast cancer patients. However, a thorough understanding of CTCs associated with breast cancer brain metastasis (BCBM) is necessary for early identification and evaluation of treatment response to BCBM. In this study, we report that BCBM CTCs are enriched in a distinct sub-population of cells identifiable by their biomarker expression and mutational content. Here we report the discovery of a unique “CTC gene signature” that is distinct from primary breast cancer tissues. Further dissection of the CTC signature identified signaling pathways associated with BCBM CTCs that may play roles in potentiating BCBM. Overall design: Blood samples were collected from 10 advanced-stage breast cancer patients at MD Anderson Cancer Center according to an IRB-approved protocol. While all 10 patients had metastatic breast cancer with multi-organ involvement; only 5 patients had clinically detectable brain metastasis (BCBM), while the other 5 did not have brain metastasis (No BCBM). After red blood cell lysis, the remaining buffy coat layer was subjected to flow cytometry for isolation of circulating tumor cells (CTC) following a workflow made of three sequential steps – (i) doublet discrimination and dead cell elimination (DAPI-), (ii) depletion of cells normally present in the peripheral blood using lineage-specific (CD45-/CD34-/CD105-/CD90-/CD73-) antibodies, and (iii) positive selection of PanCK+ (epithelial) or CD44+/CD24- (stem-like) CTCs. Sorted cells were collected directly into a pre-chilled tube maintained at 4oC containing RNA lysis buffer and total RNA was collected followed by RNA and cDNA amplifications, quality controls and gene expression arrays using the Affymetrix HTA 2.0 array. CTC gene expression was compared to whole gene expression data from 31 breast cancer patient samples representing each of the most common molecular subtypes were obtained from three publicly available GEO datasets (GSE65505 – ER+/PR+/HER2-, GSE67982 – ER+/PR+/HER2+, GSE76250 – triple negative breast cancer. As a control experiment, whole gene expression of CD4+ and CD8+ T-cells were also compared using data from GSE73079 and GSE73081, respectively. Comparison between CTC and primary breast cancer transcriptomes provided the transcriptomic landscape of breast cancer CTCs in general while further dissection into the BCBM and No BCBM subtypes yielded a 126-gene signature of BCBM associated CTCs. breast cancer without brain metastasis (No BCBM): BrPt1CTC, BrPt2CTC, BrPt3CTC, BrPt4CTC, BrPt5CTC breast cancer with brain metastasis (BCBM): BrPt6CTC, BrPt7CTC, BrPt8CTC, BrPt9CTC, BrPt10CTC biological replicate: BrPt1CTC, BrPt2CTC, BrPt3CTC, BrPt4CTC, BrPt5CTC biological replicate: BrPt6CTC, BrPt7CTC, BrPt8CTC, BrPt9CTC, BrPt10CTC Less...