Understanding Tumor Cell Heterogeneity
It is widely accepted that cancer is a highly heterogeneous disease and that subpopulations of cells within a single tumor can exhibit distinct genomic profiles. Exposure to therapeutic agents can cause changes to cancer cells that may alter their response to treatment (i.e. acquired somatic resistance). Within the cancer research community much effort is being put into identifying genomic biomarkers and determining their clinical relevance in the hopes of moving towards more personalized patient care through monitoring disease progression, relapse and tailoring treatments.
Important genetic variations, which may be present in only a small number of cells, can be masked when the molecular analysis is performed on a larger mixed population of normal and variant tumor cells – effectively drowning out the voices of the tumor cells that are driving tumor progression. Primary tissue biopsies, such as FFPE samples, typically will have tumor cells intermixed with stromal cells and may have tumor cells present in quantities too low for many downstream molecular methods. Even with the best genomic sequencing technologies reliably determining the underlying biology of the tumor is compromised by contaminating normal cells. Similarly, CTCs are very rare, with patients often exhibiting only 10’s of CTCs amongst the billions of cells in a peripheral blood sample. Trying to identify tumor cell variants amongst all the contaminating normal cells, like white blood cells, is challenging.
The DEPArray™ system is the only automated platform that can identify and recover target tumor cells with the resolution and purity required for sensitive downstream genomic and expression analyses.
Recovering tumor cells with the DEPArray™ system
DEPArray™ technology allows purification of multiple different types of cells to be collected from a single sample. Target cells are identified by combinations of intracellular and extracellular markers, as well as with the use of morphological features such as circularity or size. Image-based selection ensures recovery of intact cells of interest, free of non-specific and false-positive cells or contaminants.
Applications of DEPArray™ technology in oncology research include:
Characterization of tumor biopsies and CTCs
Analysis of markers of epithelial-mesenchymal transition (EMT)
Understanding intracellular heterogeneity and clonal evolution in tumors
Recovery of clonal variants for xenograft and genetically engineered mouse (GEM) models
Flexibility of Sample type
Fixed cells – Most cell fixatives are compatible with the DEPArray™ system and Ampli1™ WGA kits. Fixatives allow cellular integrity to be maintained and improving cell recovery by reducing sample processing time. FFPE samples or whole blood collected in CellSave or other blood collection tubes that use a fixative agent can be used with the DEPArray™system.
Live cells – DEPArray™ technology is gentle on cells and exerts no shear forces, so cells can be recovered for DNA analysis, RNA expression studies, or captured in culture media for proliferation. Culture media can be used as the buffer solution for the DEPArray system helping to preserve cell viability during sorting.
Tissue biopsies – DEPArray™ cartridge buffers work with cell suspensions made from fresh, frozen, and even FFPE tissue biopsies.
Whole blood – Rare cells, such as CTCs, can be recovered from whole blood following standard enrichment procedures such as density gradient, FACS, filtration devices, or immunomagnetic separation/depletion.
Small cell loads - Cell suspensions from fine needle aspirates, pleural fluid, and urine require little sample preparation and yield sufficient cells for recovery with DEPArray™ technology.
Flexibility in Downstream Analysis
Cells recovered using DEPArray™ technology can be used for the most challenging downstream applications:
Whole genome amplification*
Whole genome sequencing
Mutation and CNV analysis
*For whole genome amplification optimized for single cells, Silicon Biosystems offers the Ampli1™ WGA kit.
To review publications and resource references, please visit our Publications page.