By Deborah Borfitz
November 6, 2019 | Exosomes are promising targets for liquid biopsy diagnostics, but they’ve proven difficult to quickly capture and analyze. Oregon Health & Science University (OHSU) scientists are helping to overcome this hurdle with an alternating current electrokinetic (ACE) microarray chip that integrates the isolation and analysis of exosomes and cell-free DNA (cfDNA) biomarkers from a drop of blood.
Michael J. Heller, distinguished scientist at OHSU Knight Cancer Institute’s Cancer Early Detection Advanced Research (CEDAR) center, presented on the topic at the 2019 Next Generation Dx Summit. It’s a surprisingly simple approach to multi-omic analysis that uses on-chip immunofluorescence analysis to identify and quantify biomarkers in as little as 15 to 20 minutes, he says.
In addition to being a renowned expert in nanotechnology, Heller is emeritus professor of bioengineering and nanoengineering at the University of California San Diego (UCSD). The lab-on-a-chip platform under discussion is known commercially as Verita, ACE technology manufactured by Biological Dynamics that is target-agnostic. Heller mentored its CEO, Raj Krishnan, while at UCSD and receives royalties for much of his work with the company.
The technology has been used to extract cfDNA as well as circulating tumor DNA from blood, says Heller, and digital polymerase chain reaction and Sanger sequencing have provided a “reality check” of its performance relative to traditional methods of differentiating lethal from nonlethal conditions.
Low levels of exosomes and cfDNA in samples is the central problem, says Heller. But “a lot of other things are floating around in there” that potentially harbor mutations and shouldn’t be overlooked, including high molecular weight DNA abundant in cancer screening samples. “There’s not a lot of DNA in there, period, so we don’t want to throw any of it away.”
The ACE microarray chip features 400 tiny electrodes that cause everything of potential interest to congregate in high electric field regions, Heller explains. Immunofluorescence staining is then used to immediately label the findings—for example, a cancer immunotherapy target such as programmed death-ligand 1 (PD-LI).
A few years back, researchers demonstrated that the device could be used to quickly isolate cfDNA in the blood of patients with chronic lymphocytic leukemia. In a subsequent study (DOI: 10.1021/acsnano.7b08199) published last year in ACS Nano, the chip was used to rapidly detect pancreatic cancer by staining the target biomarkers glypican-1 and CD63. In a smaller group of colon cancer patient samples, elevated glypican-1 was also observed but only for those with metastatic disease.
The “big lesson” from the study came from the one-third of samples (about a dozen) that doctors had determined were either benign or pancreatitis, says Heller. Two of the outliers ended up with pancreatic cancer, as the ACE microarray chip had predicted, and one later turned out to be liver cancer.
Most recently, Heller and his colleagues showed how the device could be used as a glioblastoma biomarker platform by isolating and characterizing extracellular vesicles derived from plasma specimens of patients with brain tumors—specifically, glial fibrillary acidic protein (GFAP) and Tau.
In a forthcoming publication, Heller says, its utility in evaluating patients with traumatic brain injury will be described. In the 40-patient study, results produced by the chip in searching for brain biomarkers in three-day-old blood correlated well with findings on CT scans. The chip is also showing promise in the diagnosis of prostate cancer using a biomarker specific to bone metastasis, and the findings can be generated in about one hour.