Device Captures Individual Cancer Cells For Genome Analysis

Cancer cells can change significantly as a patient’s disease progresses. The first cells that turn malignant, seeding the growth of a tumor, may have very different genetic makeups from the dangerous metastatic cells that later circulate in the bloodstream. Now, researchers have developed an approach that could capture circulating tumor cells in a microfluidic device, allowing them to strip off each cell’s outer membrane and isolate its nuclear DNA for sequencing (Anal. Chem. 2014,DOI: 10.1021/ac503453v). Identifying mutations from individual circulating tumor cells may help doctors detect disease recurrence early or select a targeted treatment.

Analyzing the genetics of a particular cancer in a patient isn’t new. Researchers can analyze the DNA from cells extracted from a tumor to learn about disease progression or to inform treatment decisions. But this analysis has a significant caveat. “A long-standing frustration of cancer researchers and clinicians is that, although the characteristics of a tumor removed from a patient sometimes help identify the correct therapy, late-stage cancer often behaves in a way that does not correlate with the behavior of the original tumor that was removed,” says Brian J. Kirby of Cornell University. By contrast, he says, circulating tumor cells reflect the current state of a cancer.

Capturing and analyzing the DNA of circulating tumor cells is possible, but current methods pool DNA from multiple cells. That’s a problem, Kirby says, because circulating tumor cells can be heterogeneous, so pooled analyses will leave out small genetic subpopulations, missing the complete picture of the cancer. Kirby’s goal was to develop a simple and rapid method for analyzing DNA from individual circulating tumor cells.

In a previous study, Kirby had developed a microfluidic device for grabbing these cells. The interior walls of the channels were coated with an antibody that binds to a surface protein on prostate cancer cells. Tests showed that about 60% of the cells captured by the device were prostate cancer cells (Lab Chip 2010, DOI: 10.1039/b917959c). The researchers used the device to capture circulating tumor cells from patients’ blood samples. In the new study, the researchers took the approach a step further and showed that they could analyze the genome of each captured cell.

The researchers studied two cell lines derived from tumors that grew after an original prostate tumor metastasized. The researchers ran each cell line separately through their device, captured the cells, and then added a lysis buffer that dissolved the cell membranes over three hours. The team then eluted the exposed nuclei from the device into a tube and performed serial dilutions to isolate each nucleus. Using an established sequencing technique, the researchers analyzed the nuclei’s copy-number variations. Normally, each cell contains two copies of a gene, but cancer cells can have more or fewer than two. The scientists could distinguish between the two cell lines based on their differences in copy number. They also identified mutations in each cancer cell line that could guide chemotherapy choices.

A major plus for the technique is its simplicity, says Edward J. Fox of the University of Washington. “I think that the ease and speed would be clinically meaningful.” However, one potential obstacle, he says, is cost: The sequencing technique remains expensive and may be out of reach for many clinics.