A Novel Method for the Isolation of Highly Pure Carcinoma Cell Populations from FFPE Tissue Improves Sensitivity for Detecting Somatic Mutations

DATE:  August 20, 2020

TIME:   10:00am PT, 1:00pm ET

Millions of formalin-fixed paraffin-embedded (FFPE) tissue specimens are archived annually. The enormous number of FFPE specimens available provides an invaluable resource for research. Historically used for immunohistochemistry to examine the morphology of tissues and protein biomarkers, FFPE tissue is now increasingly devoted to genetic analysis.

There are many challenges associated with genetic analysis of FFPE tissue, such as the difficulty of isolating different cell populations from highly heterogenous tissues like tumors. It’s difficult to detect cancer-associated somatic sequence variants when the allele frequency is lowered by the contamination of normal cells around and within the tumor. We will present a novel method for isolating highly pure populations of carcinoma cells from FFPE tissue for analysis by next generation sequencing.

The FFPE Tissue Dissociation Kit, in conjunction with the gentleMACS™ Octo Dissociator with Heaters, is optimized for fast, gentle, and effective generation of single-cell suspensions. This method preserves the important epitopes of cytokeratin and vimentin cells, which can be used for the isolation of carcinoma and stromal cells, respectively. Dissociated cells can be separated with high purity by magnetic microbead-based technology or flow sorting. We show that this method can increase the frequency of somatic mutations by severalfold. Moreover, when a matched normal tissue sample is not available, it’s possible to use the separated stromal cells to analyze the germline sequence. Thus, somatic mutations can be clearly distinguished from germline mutations.

Learning Objectives:

• FFPE tumor tissue is a plentiful and valuable resource for studying the genetics of cancer and advancing precision medicine.

• Separating carcinoma cells from stromal cells is an effective method to increase sensitivity for detecting somatic mutations, and enables analysis of the germline DNA — when matched normal tissue is not available.

• The FFPE Tissue Dissociation Kit, in conjunction with the gentleMACS Octo Dissociator with Heaters, quickly and effectively generates single-cell suspensions from FFPE tissue while preserving important epitopes for cell separation.

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