A simple paper test can offer an early cancer diagnosis
(Nanowerk News) MIT engineers have designed a new nanoparticle sensor that allows early diagnosis of cancer with a simple urine test. The sensors, which can detect many different cancer proteins, can also be used to differentiate the type of tumor or how it is responding to treatment.
The nanoparticles are designed so that when they encounter a tumor, they release short DNA sequences which are excreted in the urine. Analyzing these DNA “barcodes” can reveal features that distinguish a particular patient’s tumor. The researchers designed their test so that it could be administered using a piece of paper, similar to an at-home Covid test, which they hoped would make it affordable and accessible to as many patients as possible.
“We are trying to innovate in the context of making technology available to low and medium resource settings. Putting these diagnostics on paper is part of our goal to democratize diagnostics and create low-cost technology that can give you quick answers at the point of care,” said Sangeeta Bhatia, John and Dorothy Wilson Professor of Health Sciences and Health Technology and Electrical Engineering and Computer Science at MIT and member of the Koch Institute for Integrative Cancer Research and the MIT Institute of Engineering and Medical Sciences.
In testing on mice, the researchers demonstrated that they could use the sensor to detect the activity of five different enzymes expressed in tumors. They also demonstrated that their approach could be scaled up to distinguish at least 46 different DNA barcodes in a single sample, using a microfluidic device to analyze the sample.
Bhatia is the senior author of the paper, which appears in Natural Nanotechnology (“CRISPR-Cas amplified urine biomarker for multiplex and portable cancer diagnostics”). Liangliang Hao, a former MIT research scientist who is now an assistant professor of biomedical engineering at Boston University, is the study’s lead author.
Over the years, Bhatia’s lab has been developing “synthetic biomarkers” that can be used to diagnose cancer. This work is based on the concept of detecting cancer biomarkers, such as circulating tumor proteins or cells, in patient blood samples. These natural biomarkers are so rare that they are nearly impossible to find, especially in the early stages, but synthetic biomarkers can be used to amplify the small-scale changes that occur within small tumors.
In his previous work, Bhatia created nanoparticles that can detect the activity of enzymes called proteases, which help cancer cells move out of their original location, or settle in a new location, by cutting proteins from the extracellular matrix. The nanoparticles are coated with peptides that are cleaved by different proteases, and once these peptides are released into the bloodstream, they can then be concentrated and more easily detected in urine samples.
The original peptide biomarkers were designed to be detected based on small engineered variations in their mass, using a mass spectrometer. Such equipment may not be available in low-resource environments, so researchers are beginning to develop sensors that can be analyzed more easily and affordably, using DNA barcodes that can be read using CRISPR technology.
For this approach to work, researchers must use chemical modifications called phosphorothioates to protect circulating DNA reporter barcodes from breaking down in the blood. This modification has been used to increase the stability of modern RNA vaccines, allowing them to last longer in the body.
Similar to a peptide reporter, each DNA barcode is attached to a nanoparticle by a link that can be cleaved by a specific protease. If the protease is present, the DNA molecule is released and free to circulate, eventually ending up in the urine. For this study, the researchers used two types of nanoparticles: one, a particle made of a polymer that has been FDA-approved for use in humans, and the other, a “nanobody” — an antibody fragment that can be designed to accumulate at certain levels. tumor site.
Once the sensor is secreted in the urine, the sample can be analyzed using a paper strip that recognizes a reporter activated by a CRISPR enzyme called Cas12a. When certain DNA barcodes are present in the sample, Cas12a amplifies the signal so that it can be seen as a dark strip on the test paper.
The particle can be designed to carry many different DNA barcodes, each of which detects a different type of protease activity, allowing “multiplex” sensing. Using more sensors provides an increase in both sensitivity and specificity, allowing the test to more easily differentiate between tumor types.
In testing in mice, the researchers demonstrated that a panel of five DNA barcodes could accurately distinguish tumors that first appeared in the lung from tumors formed by colorectal cancer cells that had metastasized to the lungs.
“Our goal here is to establish disease signatures and to see if we can use these barcoding panels not only to read disease but also to classify disease or differentiate between different types of cancer,” said Hao.
For use in humans, the researchers hope that they may need to use more than five barcodes because there is so much variation between patient tumors. To help achieve that goal, they worked with researchers at the Broad Institute of MIT and Harvard, led by Harvard University Professor Pardis Sabeti, to create a microfluidic chip that could be used to read up to 46 different DNA barcodes from a single sample.
Such a test can be used not only to detect cancer, but also to measure how well a patient’s tumor responds to treatment and whether it recurs after treatment. Researchers are now working to develop the particles further with the aim of testing them in humans. Glympse Bio, a company co-founded by Bhatia, has conducted phase 1 clinical trials of earlier versions of urine diagnostic particles and found them to be safe in patients.