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New Platform to Analyse exRNA for Cancer Diagnostics

New Platform to Analyse exRNA for Cancer Diagnostics content piece image
Melanoma cells surrounded by shed extracellular vesicles. Credit: University of Notre Dame / Alanna Sedgwick, D'Souza-Schorey Laboratory
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University of Notre Dame researchers have recently been awarded $2.9 million from the National Institutes of Health to design a diagnostic platform capable of efficiently analysing extracellular RNA (exRNA).

We interviewed Professor Hsueh-Chia Chang, the Bayer Professor of Chemical and Biomolecular Engineering and project lead, to learn more about the proposed diagnostic platform and some of the advantages it could offer over current methods of analysing exRNA.

Anna MacDonald (AM): Can you tell us a little about exRNA and the role it could play in diagnostics?

Professor Hsueh-Chia Chang (HC):
 Extracellular RNA (exRNA) are molecules released by certain cells in the body to communicate with other cells that take in these exRNA. They are encapsulated in nano-sized particles called exosomes, which protect the exRNA during their journey from the host cell to the recipient cell. The exosomes are hence always present in the blood. Cancer cells are known to release excessive numbers of exosomes with particular exRNAs to convert healthy cells into tumor cells during metastasis. Hence, isolating the exosomes and detecting an abundance of these specific exRNA in blood samples would indicate that the tumor cells are present. This is the basis of liquid biopsy, which is non-invasive and hence can be done more frequently for general population screening.

AM: What current technologies are available for analysing exRNA? What are their limitations?

Current technologies use ultra-centrifugation and a precipitation technique to isolate exosomes from blood. They are extremely low yield--they capture only a small fraction of the exosomes and, in fact, may destroy some of the exosomes. After the isolation of exosomes, the analysis of their exRNA cargo also involve multiple steps that lose many of the exRNAs. One of them involves the Polymerase Chain Reaction (PCR) to amplify the number of specific exRNA. PCR amplification rate is also highly variable, adding further to the exRNA quantification inaccuracy. Since quantification is absolutely important for cancer screening based on exRNA, these technologies would not provide accurate diagnosis.

AM: Can you give us an overview of how your proposed diagnostic platform will work?

We use a patented nanopore membrane to allow high-yield isolation of the exosome. Each nanopore has a conic geometry to minimize exosome damage and loss. We are able to demonstrate much higher isolation efficiency than the current method. We also use new analysis methods, invented in our lab, to achieve PCR-free quantification of the exRNA in the exosomes. One method relies on a solid-state nanopore technology to count each exRNA molecule individually.

AM: What are the benefits of using nano/microfluidic technologies? What challenges do they present?

The benefit is that it lowers the loss of the exRNA and the nanoscale exosomes, which is extremely important in a quantitative assay like exRNA liquid biopsy. The main challenge is that the physics of fluid and exosomes at micro/nanoscale is very different and one needs to design the micro/nanofluidic chips very differently from larger fluidic devices in the current blood test labs. You need new pump, filter and particle/molecule manipulation technologies at such small scales. We use electrokinetic technologies driven by microelectrodes for our technologies.

Hsueh-Chia Chang, Professor of Engineering. Ccredit: University of Notre Dame photography

Professor Hsueh-Chia Chang was speaking to Anna MacDonald, Science Writer for Technology Networks.