Microfluidic Platforms Help Isolate Rare Cells in Leukemias

Microfluidic technology is available in the clinical setting for isolation of rare cells, including circulating leukemia cells. This form of liquid biopsy can be used at a very low cost, which experts consider to be an exciting advancement in the treatment landscape.

One challenge, however, in this type of technology is the limitations caused by strict requirements. More material is required than what is necessary for next-generation sequencing (NGS) assays, for example.

“Many processing strategies on the molecular level require stringent requirements in terms of the mass input,” said Steve A. Soper, PhD. “That is the challenge with liquid biopsies, that you are typically mass-limited, and accommodating the downstream molecular process can be somewhat problematic.”

In an interview with Targeted Oncology, Soper, foundation distinguished professor, University of Kansas, discussed microfluidic platforms for use in isolating circulating leukemia cells and plasma cells in patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML).

TARGETED ONCOLOGY: Could you discuss what this technology is and its purpose?

Soper: About 10 years ago, we developed a microfluidic technology for isolating rare cells. This technology is based upon the use of a plastic, plexiglass, that can be machined efficiently into very small structures, small meaning 25 microns to 100 microns or so. What we can do with this plastic is use this in a very high production mode at very low cost, then decorate the surfaces of these microfluidic antibodies that are targeted against a certain type of rare cell; the protein or antigen that it is targeting is found in the membrane of these rare cells.

We are now looking at new application areas for this technology. For many years, we have worked on the use of this technology for isolating bacterial cells from water samples and circulating tumor cells from cancer patients. The recent work we have done is to use this same technology to isolate leukemia cells out of peripheral blood in patients with either AML or ALL. All of those different applications are easily accommodated by the same technology by simply changing the antibody within that microfluidic device. For the circulating leukemia cells, I spoke about at the AMP meeting was using antibodies directed against CD19, which is used for ALL and CD33, CD34, and CD117 for AML. Basically, what we are doing there is we can actually take blood samples securely from the patient, run it through the chip, and pull out the leukemia cells from that blood sample.

TARGETED ONCOLOGY: Why is this technology important in the clinic?

Soper: There are a lot of technologies in the market and published in research labs that will isolate rare cells. However, they are fraught with some challenges. The biggest challenge is the purity. They don’t only isolate the cells for which they are targeting but they isolate a lot of, for example, white blood cells. That presents a challenge because after the isolation, a lot of people like to take those cells to do some type of molecular profiling on those cells. When the purity is below 1% of the target cell, then it becomes intractable in some cases to do the downstream molecular analysis.

Our technology does a good job of recovering those rare cells because of the architecture, which is employed in the microfluidic. It also does a really good job at the purity because of the fact that we are using unique architecture that allows us to remove the interfering cells so the purity goes up.

What is the purity in the recovery? Recovery in many cases is well above 90%, and the purity of the target cell is well above 80%m, irrespective of the number of cells we are going after. For example, in 1 mL of blood, we may have 1 to 10 target cells we are looking at. At 1 mL of blood, we are only pulling out 3 to 6 white blood cells, so very minimal amounts of interfering white blood cells even though there are many orders of magnitude more abundant than the target cells we are going after.

TARGETED ONCOLOGY: Is this technology widely available yet?

Soper: There is a company that is marketing this technology, and they are participating in several clinical studies disseminating this to various collaborators. At the University of Kansas, specifically Kansas University Medical Center, we have a liquid biopsy laboratory that we have set up. That laboratory will analyze and isolate any type of liquid biopsy marker. For example, this technology is focused exclusively on isolating rare cells, like leukemia cells, plasma cells associated with multiple myeloma, and tumor cells associated with many solid tumors. We also have chips that run up the same instrument that will isolate cell-free DNA from plasma or extracellular vesicles from plasma as well. They all run on the same instrument, but the only difference is the chip configuration is a little different for the cell-free DNA and the extracellular vesicles as opposed to the circulating rare cells.

TARGETED ONCOLOGY: What are the challenges in using this type of technology?

Soper: The challenge with liquid biopsies is there are some great technologies out there that will do an efficient job of isolating any type of circulating marker encompassing the liquid biopsy area, whether it is cell-free DNA, exosomes, extracellular vesicles, or circulating leukemia or tumor cells. The challenge is connecting them to the downstream processing, which is the molecular analysis, becomes challenging. The reason for this is when you do a solid tissue biopsy, for example, you are getting millions of cells, which makes it very easy to accommodate any type of molecular processing strategy, for example NGS. However, in the case of liquid biopsies, the amount of material is much lower. There are also challenges in translating that conventional molecular processing strategy.

Many processing strategies on the molecular level require stringent requirements in terms of the mass input. That is the challenge with liquid biopsies, that you are typically mass-limited, and accommodating the downstream molecular process can be somewhat problematic.

TARGETED ONCOLOGY: What are your key takeaways from all of this?

Soper: That does not mean that liquid biopsies can’t be used. It means the community needs to devote a little more time in terms of developing molecular process strategies that will either work on smaller amounts of material or build up sufficient quantities of these biopsy markers to accommodate that down streaming processing. That is 1 of the big things we are working on right now, developing new processing strategies to accommodate the mass limits associated with liquid biopsy markers.

Efforts need to be invested in developing assay strategies that accommodate the mass-limits associated with liquid biopsy samples. People also talk about doing single-cell analysis, which, from a discovery and basic science perspective, is great, but in the clinic, it becomes much more problematic. In the clinic, it isn’t necessary to do single-cell analysis. There is some controversy on that, and I won’t answer either way. However, the point is doing single-molecule or single-cell sequencing becomes extremely difficult because of the high cost and the high failure rate of trying to do single-cell processing for NGS. Again, a new molecular assay strategy to accommodate the mass-limits will be very important to bring into play.