Nanofluidic biopsy detects subtle changes in cancer cells

By taking two standard laboratory techniques - capillary electrophoresis and antibody-based protein detection - and shrinking them to the nanoscale, researchers at the Stanford University School of Medicine have created a new method for detecting miniscule changes in the levels of proteins associated with cancer.

In a study published in the journal Nature Medicine, the investigators used their new device to analyze whether individual cancer-associated proteins were present in the tiny samples and even whether modifications of the proteins varied in response to cancer treatments. Although the study focuses on blood cancers, the hope is that the technique also might provide a faster, less invasive way to track solid tumors.

"Currently, we don't know what's going on in a patient's tumor cells when a treatment is given," said Alice C. Fan, M.D., who along with Dean W. Felsher, M.D., headed the team that developed this nanofluidic proteomic immunoassay (NIA) system. "The standard way we measure whether a treatment is working is to wait several weeks to see if the tumor mass shrinks. It would be a leap forward if we could detect what is happening at a cellular level."

Dr. Felsher, who is a member of the Center for Cancer Nanotechnology Excellence Focused on Therapy Response based at Stanford University, added, "This technology allows us to analyze cancer-associated proteins on a very small scale. "Not only can we detect picogram levels - one-trillionth of a gram - of protein, but we also can see very subtle changes in the ways the protein is modified."

Variations in the way a protein is modified, or phosphorylated, can affect how it functions in tumor progression. Cancer cells often evade common therapies by altering levels of protein expression and degrees of phosphorylation. Analyzing repeated small samples from a tumor undergoing treatment may let doctors head off rogue cells before they proliferate into a more resistant tumor as well as identify patients likely to fail standard approaches to treatment.

Drs. Fan and Felsher collaborated with researchers from Cell Biosciences, Inc., to create the NIA system that separates cancer-associated proteins in narrow capillary tubes based on their charge, which varies according to modifications on the surfaces of the proteins. Two versions of the same protein - one phosphorylated and one not - can be easily distinguished because they travel different distances in the tube. The researchers then use antibodies to identify the relative amounts and positions of the various proteins.

Not only was the technique able to identify oncogene activation in cultured tumor cells, but also it worked in lymphoma samples drawn from mice. Furthermore, it was able to detect varying levels of expression of two common oncogenes in 44 of 49 lymphoma samples from human patients compared with normal controls and even was able to distinguish some types of lymphomas from others. The assay system also detected subtle differences in phosphorylation in several other cancer-associated proteins. "Some of these proteins can exist as five or six phosphorylated variants," said Dr. Felsher. "With this technology, we can see changes that occur in as little as 10 percent of the total protein pool. Now we have a tool that will help us look at what's happening in cells over time."

"Surgical biopsies usually require general anesthesia and large amounts of tissue," agreed Dr. Fan. "If we can figure out how to go in with a needle and remove just a few cells for analysis, we could repeatedly assess how the tumor is responding to treatment."

For example, the researchers were able to confirm through serial biopsies of a human lymphoma patient that, as suggested by previous research in the Felsher lab, the lipid-lowering drug atorvastatin reduces phosphorylation of yet another cancer-associated protein. "This is the first time we've been able to see that this compound affects the biology of cancer cells in patients," said Dr. Felsher.

Dr. Fan is now expanding her investigations to include head and neck tumors, which tend to be accessible for cell sampling. Drs. Fan and Felsher caution that more research is needed before the technology would be widely available clinically.

This work, which is detailed in the paper "Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens," was supported by the NCI Alliance for Nanotechnology in Cancer, a comprehensive initiative designed to accelerate the application of nanotechnology to the prevention, diagnosis, and treatment of cancer. An investigator from the Hospital Saint-Louis in Paris, France, also participated in this study. An abstract of this paper is available at the journal's Web site. View bstract