Circulating Tumor Cells in Soft Tissue Sarcomas Patients

Rapid and highly sensitive approach for multiplexed somatic fusion detection

Somatic gene translocations are key to making an accurate diagnosis in many cancers including many pediatric sarcomas. Currently available molecular diagnostic approaches to identifying somatic pathognomonic translocations have limitations such as minimal multiplexing, high cost, complex computational requirements, or slow turnaround times. We sought to develop a new fusion-detection assay optimized to mitigate these challenges. To accomplish this goal, we developed a highly sensitive multiplexed digital PCR-based approach that can identify the gene partners of multiple somatic fusion transcripts. This assay was validated for specificity with cell lines and synthetized DNA fragments. Assay sensitivity was optimized using a tiered amplification approach for fusion detection from low input and/or degraded RNA. The assay was then tested for the potential application of fusion detection from FFPE tissue and liquid biopsy samples. We found that this multiplexed PCR approach was able to accurately identify the presence of seven different targeted fusion transcripts with a turnaround time of 1 to 2 days. The addition of a tiered amplification step allowed the detection of targeted fusions from as little as 1 pg of RNA input. We also identified fusions from as little as two unstained slides of FFPE tumor biopsy tissue, from circulating tumor cells collected from tumor-bearing mice, and from liquid biopsy samples from patients with known fusion-positive cancers. We also demonstrated that the assay could be easily adapted for additional fusion targets. In summary, this novel assay detects multiple somatic fusion partners in biologic samples with low tumor content and low-quality RNA in less than two days. The assay is inexpensive and could be applied to surgical and liquid biopsies, particularly in places with inadequate resources for more expensive and expertise-dependent assays such as next-generation sequencing.

Epithelial cell adhesion molecule is expressed in a subset of sarcomas and correlates to the degree of cytological atypia in leiomyosarcomas

Epithelial cell adhesion molecule (EpCAM) is a protein involved in cell-to-cell attachment and is considered to be strictly expressed in epithelial tissues and epithelial-derived tumors. Furthermore, EpCAM has been shown to be a negative prognostic marker for several carcinomas. In this study, we performed a genomic meta-analysis of gene expression profiles housed in the Cancer Cell Line Encyclopedia to demonstrate that EpCAM mRNA is expressed at low to moderate levels in certain sarcoma cell lines. We utilized immunohistochemical staining to confirm that the EpCAM protein is expressed in a subset of angiosarcomas and leiomyosarcomas and in all the investigated osteosarcomas. Finally, we conducted a statistical analysis of clinical data to demonstrate that EpCAM protein expression is significantly and directly correlated with the degree of cytological atypia in leiomyosarcomas. In conclusion, this data suggests that, contrary to conventional beliefs, EpCAM is expressed in a subset of sarcomas and is a negative prognostic marker for leiomyosarcomas.