Genetic Profiling

A new way to cleanly separate out cancer cells from a blood sample; but enables comprehensive genetic profiling of the cancer cells; which could help doctors target tumors and monitor treatments more effectively. It is a dramatic improvement over current approaches; because it also encompasses the variation among cancer cells within a single patient. “This could be a whole different ball game,” said Max Wicha; the Madeline and Sidney Forbes Professor of Oncology at the University of Michigan; and senior physician on the study in Nature Communications.

Earlier techniques meant a trade-off between a comprehensive genetic profile of a limited subset of cancer cells; or capturing most of the cancer cells and only being able to look for a few genes. As a result, the genetic profiles often neglected important populations of cancer cells; including cells believed to spread cancer in the body.

“Our chip allows us to capture pure circulating tumor cells; and then extract genetic information without any contamination; from red and white blood cells,” said Euisik Yoon, U-M professor of electrical engineering; and computer science and senior author on the study. Many modern cancer drugs work by going after cells with certain genes in play—genes that flag their identities as cancer cells. But these genes aren’t uniformly active in a patient’s cancer cell population and can change over the course of treatment.

Capturing cancer cells

Repeated biopsies to monitor the tumor are painful and potentially dangerous for the patient. Capturing cancer cells from blood samples offers a noninvasive way to observe whether the cancer is disappearing or whether it is becoming resistant to the treatment. “It allows you not only to select targeted therapies, but to monitor the effects of these therapies in patients by doing this blood test,” Wicha said. Using this method, the team collected and analyzed 666 cancer cells from the blood of 21 breast cancer patients.

The genetic analysis confirmed that even within a single patient, the cancer cells often behave very differently. Wicha’s group has previously shown that cancer metastasis is mediated by cancer cells that have the properties of stem cells. Although cancer stem cells make up only a few percent of a tumor’s cells, they make up a higher proportion of the cancer cells in the bloodstream. In this study, about 30-50% of the cancer cells captured from the blood samples displayed stem-like properties.

This population is particularly easy to miss with techniques that capture clean-but-incomplete samples of cancer cells from patient blood by grabbing onto proteins on the cells’ surfaces. Stem-like cells are on a spectrum between two more-typical cell types, which means that they don’t display consistent protein markers.

Cancer cell in a billion blood cells

To get a clean and unbiased set of cancer cells from a vial of blood, the team started with a technique that removes blood cells by sorting the blood sample according to cell size. Starting with about one cancer cell in a billion blood cells, this step left only about 95 or so blood cells for every cancer cell. But that’s still far too contaminated for a detailed genetic analysis.

The new method, which the researchers call Hydro-Seq, gets rid of those last blood cells and then analyzes each cell. The key technology is a chip with a system of channels and chambers. It traps cancer cells one at a time by drawing fluid through a drain in each chamber, which gets plugged when a cancer cell arrives. Once the chamber is plugged, cells in the channel pass it by and get sucked into the next chamber. Then, to “wash” the blood cells off the chip, they ran clean fluid backward through the chip and drew it out again, taking nearly all the rest of the contaminating cells along.