Breath-based Biomarker Detection Using Nanoparticle Sensor System

Significance 

Breath tests are practical diagnostic tools due to the ease and non-invasive nature of breath sampling, the scientists noted. There are a number of commercial sampling tools that could be used to streamline breath detection, and sensitive, miniaturized gas analysis tools are also available that could be used to bring breath analysis to point-of-care use. And while the rate-limiting step in the translation of breath volatiles to clinical diagnostics is the identification of disease-specific breath biomarkers.

MIT engineers have developed a nanoparticle sensor system that can detect and monitor lung diseases by measuring compounds exhaled in the breath. Initial studies in mice demonstrated use of the technology to detect pneumonia and the genetic disorder alpha-1 antitrypsin deficiency, but the team said the same approach could one day also be used for other diseases, including lung infections such as coronavirus. The technology would allow the patient to inhale a sensor and then breathe out a volatile gas in about 10 minutes that reports on the status of the lungs. The research is lead by Professor Sangeeta Bhatia, PhD, the John and Dorothy Wilson professor of health sciences and technology and electrical engineering and computer science at MIT. Bhatia, who is also a member of MIT’s Koch Institute for Integrative Cancer Research and the Institute for Medical Engineering and Science, is the senior author of the team’s published paper in Nature Nanotechnology.

Breath contains many different volatile compounds, but exploiting these compounds for clinical diagnostic applications has been a challenging and slow process. Breath is a practical and potentially informative clinical analyte because it can be sampled non-invasively and contains hundreds of trace volatile organic compounds (VOCs) that are produced in the body as metabolites or from environmental exposure,” the authors wrote. However, few breath tests are currently used in the clinic to monitor disease due to bottlenecks in biomarker identification.

One potential approach to overcome current challenges is to administer a form of nanosensor that will be metabolized by disease-specific molecular processes into detectable volatile products. This strategy is used, for example, in the 13C-urea breath test for Helicobacter pylori detection, and the 13C methacetin breath test for liver fibrosis. To carry out these tests patients ingest isotope-labeled small molecules, which are metabolized by relevant enzymes into 13CO2. These clinical tests and others in development leverage known enzyme biology to produce breath read-outs, and in the case of 13C breath tests, produce a volatile that is not naturally found in the body, thereby reducing signal-to-noise ratio (SNR).

For several years, The MIT research team has been working on nanoparticle sensors that can be used as synthetic biomarkers. These markers are peptides that are not naturally produced by the body but are released from nanoparticles when they encounter proteins called proteases. The peptides coating the nanoparticles can be customized so that they are cleaved by different proteases that are linked to a variety of diseases. When a peptide is cleaved from the nanoparticle by a protease it is then later excreted in the urine, where it can be detected with a strip of paper similar to a pregnancy test. Previously they developed this type of urine test for pneumonia, ovarian cancer, lung cancer, and other diseases.

More recently, the research team turned her attention to developing biomarkers that could be detected in the breath rather than in the urine. This would allow test results to be obtained more rapidly, and it also avoids the potential difficulty of having to acquire a urine sample from patients who might be dehydrated. The investigators realized that by chemically modifying the peptides attached to the synthetic nanoparticles, they could enable the particles to release gases called hydrofluoroamines (HFAs) that would be exhaled in the breath. The researchers attached volatile molecules to the end of the peptides in such a way that when the disease-associated protease cleaves the peptides, the volatiles are released into the air as a gas, and breathed out.

The authors devised a method for detecting the gas from the breath using mass spectrometry. They then tested their nanosensors, which they called volatile-releasing activity-based nanosensors (vABNs), in mouse models of two diseases, bacterial pneumonia caused by Pseudomonas aeruginosa, and the genetic disorder alpha-1 antitrypsin deficiency. Both diseases trigger inflammatory responses that are linked with the production of protease called neutrophil elastase by immune cells. It is this neutrophil elastase enzyme that cleaves the volatile compounds from the nanosensors administered to the mice, which are then detected in the breath using mass spectrometry.

The nanosensors shed volatile reporters upon cleavage by neutrophil elastase, an inflammation-associated protease with elevated activity in lung diseases such as bacterial infection and alpha-1 antitrypsin deficiency. After intrapulmonary delivery into mouse models with acute lung inflammation, the volatile reporters are released and expelled in breath at levels detectable by mass spectrometry.

For both pneumonia and alpha-1 antitrypsin deficiency, the researchers showed that they could detect neutrophil elastase activity within about 10 minutes. Additional studies also demonstrated that the sensors could be used to monitor the effectiveness of drug treatment for both the disorders. Using these nanosensors, we performed serial breath tests to monitor dynamic changes in neutrophil elastase activity during lung infection and to assess the efficacy of a protease inhibitor therapy targeting neutrophil elastase for the treatment of alpha-1 antitrypsin deficiency.

The researchers used nanoparticles that were injected intratracheally in their initial experimentation, but they are working on a more clinically relevant version that could be inhaled using a device similar to the inhalers used to treat asthma. The researchers is also designing new devices for detecting the exhaled sensors that would be easier to use, potentially even allowing patients to use them at home. The findings can be of help in developing sensors that could detect more than one type of protease at a time. These nanosensors could be designed to reveal the presence of proteases associated with specific pathogens, potentially including SARS-CoV-2.

Breath-based biomarker detection using nanoparticle sensor system - Medicine Innovates

About the author

Sangeeta N. Bhatia, MD, PhD

John J. and Dorothy Wilson Professor of Health Sciences and Technology and of Electrical Engineering and Computer Science
Director, Marble Center for Cancer Nanomedicine
Member, Ludwig Center for Molecular Oncology
Investigator, Howard Hughes Medical Institute

Sangeeta is a biomedical researcher, MIT professor, and biotech entrepreneur who works to adapt technologies developed in the computer industry for medical innovation. Trained as both a physician and engineer at Harvard, MIT, and Brown University, Bhatia leverages ‘tiny technologies’ of miniaturization to yield inventions such as human microlivers that model human drug metabolism and liver disease, as well as responsive nanoparticles and nanoporous materials that can be engineered to diagnose, study, and treat a variety of diseases, including cancer. She and her trainees have launched multiple biotechnology companies to improve human health. As a prolific inventor and passionate advocate for diversity in science and engineering, Bhatia has received many honors including the Lemelson-MIT Prize, known as the ‘Oscar for inventors,’ and the Heinz Medal for groundbreaking inventions and advocacy for women in STEM fields. She is a Howard Hughes Medical Institute Investigator, the Director of the Marble Center for Cancer Nanomedicine at the Koch Institute for Integrative Cancer Research at MIT, and an elected member of the National Academy of Sciences, the National Academy of Engineering, the National Academy of Medicine, the American Academy of Arts and Science, the National Academy of Inventors, and Brown University’s Board of Fellows.

Dr. Bhatia is a Board member of Brown University, Vertex Pharmaceuticals, the International Cancer Early Detection Alliance — Cancer Research UK, and the Association for Women in Science. She has an advisory role with Chan Zuckerberg Biohub, Allen Institute for Cell Science, Global Oncology Inc., Glympse BIO, Maverick Therapeutics, Synlogic, and Cristal Therapeutics.

Reference

Leslie W. Chan, Melodi N. Anahtar, Ta-Hsuan Ong, Kelsey E. Hern, Roderick R. Kunz & Sangeeta N. Bhatia. Engineering synthetic breath biomarkers for respiratory disease. Nature Nanotechnology volume 15, pages792–800(2020)

Go To Nature Nanotechnology

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