MIT engineers have designed a new nanoparticle sensor that could allow early diagnosis of cancer with a simple urine test. The sensors, which can detect many different cancer proteins, could also be used to distinguish the type of tumor or how it responds to treatment.
The nanoparticles are designed so that when they encounter a tumor, they shed short sequences of DNA that are excreted in the urine. Analysis of these DNA “barcodes” can reveal distinctive features of a particular patient’s tumor. The researchers designed their test so that it can be done with a paper strip, similar to a home covid test, which they hope will be affordable and accessible to as many patients as possible.
“We’re trying to innovate in a context of making technology available to low- and medium-resource settings. Putting this diagnosis on paper is part of our goal to democratize diagnostics and create inexpensive technologies that can give you rapid response to the point of care,” says Sangeeta Bhatia, John and Dorothy Wilson Professor of Health Sciences and Technology and of Electrical Engineering and Computer Science at MIT and a member of the Koch Institute for Integrative Cancer Research and the Institute for Engineering and Sciences. MIT Physicians.
In tests on mice, the researchers showed that they could use the sensors to detect the activity of five different enzymes that are expressed in tumors. They also showed that their approach could be extended to distinguish at least 46 different DNA barcodes in a single sample, using a microfluidic device to analyze the samples.
Bhatia is the lead author of the article, which appears today in nature nanotechnology. Liangliang Hao, a former MIT research scientist who is now an assistant professor of biomedical engineering at Boston University, is the lead author of the study.
dna barcodes
For several years, Bhatia’s lab has been developing “synthetic biomarkers” that could be used to diagnose cancer. This work is based on the concept of detecting cancer biomarkers, such as proteins or circulating tumor cells, in a patient’s blood sample. These natural biomarkers are so rare that they are nearly impossible to find, especially at an early stage, but synthetic biomarkers can be used to amplify the smaller-scale changes that occur within small tumors.
In earlier work, Bhatia created nanoparticles that can detect the activity of enzymes called proteases, which help cancer cells escape from their original locations or take up residence in new ones by cleaving extracellular matrix proteins. The nanoparticles are coated with peptides that are cleaved by different proteases, and once these peptides are released into the bloodstream, they can be more easily concentrated and detected in a urine sample.
The original peptide biomarkers were designed to be detected based on small engineered variations in their mass, using a mass spectrometer. This type of equipment may not be available in low-resource settings, so the researchers set out to develop sensors that could be analyzed more easily and cheaply, using DNA barcodes that can be read with CRISPR technology.
For this approach to work, the researchers had to use a chemical modification called phosphorothioate to protect the circulating DNA reporter barcodes from breaking down in the blood. This modification has already been used to improve the stability of modern RNA vaccines, allowing them to survive longer in the body.
Similar to peptide reporters, each DNA barcode is attached to a nanoparticle by a linker that can be cleaved by a specific protease. If that protease is present, the DNA molecule is released and circulates freely, eventually ending up in the urine. For this study, the researchers used two different types of nanoparticles: one, a particle made of polymers approved by the FDA for use in humans, and the other, a “nanobody,” an antibody fragment that can be engineered to accumulate in a tumor site.
Once the sensors are secreted into the urine, the sample can be tested using a paper strip that recognizes a tracer that is activated by a CRISPR enzyme called Cas12a. When a particular DNA barcode is present in the sample, Cas12a amplifies the signal so that it can be seen as a dark strip on a paper test.
Particles can be engineered to carry many different DNA barcodes, each detecting a different type of protease activity, allowing for “multiplexed” detection. Using a larger number of sensors provides a boost in both sensitivity and specificity, allowing the test to more easily distinguish between tumor types.
disease signatures
In tests on mice, the researchers showed that a panel of five DNA barcodes could accurately distinguish tumors that first arose in the lungs from tumors formed by colorectal cancer cells that had metastasized to the lungs.
“Our goal here is to build disease signatures and see if we can use these barcoded panels not only to read a disease but also to classify a disease or distinguish different types of cancer,” Hao says.
For use in humans, the researchers expect they will need to use more than five barcodes because there is so much variety among patients’ 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 can be used to read up to 46 different DNA barcodes. of a sample.
This type of test could be used not only to detect cancer, but also to measure how well a patient’s tumor responds to treatment and whether it has come back after treatment. The researchers are now working on further developing the particles with the goal of testing them in humans. Glympse Bio, a company co-founded by Bhatia, conducted phase 1 clinical trials of an earlier version of the urinary diagnostic particles and found that they are safe in patients.
In addition to Bhatia, Hao, and Sabeti, study co-authors include Renee T. Zhao, Nicole L. Welch, Edward Kah Wei Tan, Qian Zhong, Nour Saida Harzallah, Chayanon Ngambenjawong, Henry Ko, and Heather E. Fleming.
The research was funded by the National Cancer Institute Koch Institute Support Grant (Core), a National Institute of Environmental Health Sciences Core Center grant, the Marble Center for Cancer Nanomedicine at the Koch Institute, the Frontier Research Program from the Koch Institute, the Virginia and DK Ludwig Fund for Cancer Research, and a Road to Independence Award from the National Cancer Institute.
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