Researchers reveal CRISPR-powered diagnostic system

A team of scientists, hailing from the Broad Institute of MIT and Harvard, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering and Science at MIT, and the Wyss Institute for Biologically Inspired Engineering at Harvard University have adapted a CRISPR protein to serve as a highly sensitive diagnostic tool. This protein targets RNA, rather than DNA, and has the potential to revolutionize research and global public health.

Their findings, published today in the scientific journal Science, describe the harnessing of the RNA-targeting CRISPR enzyme as a highly sensitive detector. This enzyme can indicate the presence of as little as a single molecule of a target RNA or DNA. The scientists dubbed the new tool SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing). It could someday be used to respond to viral and bacterial outbreaks, monitor antibiotic resistance, and detect cancer.

Co-first authors Omar Abudayyeh and Jonathan Gootenberg, graduate students at MIT and Harvard, respectively, lead the study, demonstrating the method's versatility on a range of applications. These include detecting the presence of Zika virus in patient blood or urine samples within hours, distinguishing between the genetic sequences of African and American strains of Zika virus, discriminating specific types of bacteria, such as E. coli, detecting antibiotic resistance genes, identifying cancerous mutations in simulated cell-free DNA fragments, and rapidly reading human genetic information from a saliva sample.

Because the tool can be designed for use as a paper-based test that does not require refrigeration, the researchers believe it is well-suited for fast deployment and widespread use, such as in field hospitals during an outbreak or rural clinics with limited access to advanced equipment.

Feng Zhang, core institute member of the Broad Institute, an investigator at the McGovern Institute, and the James and Patricia Poitras '63 Professor in Neuroscience and associate professor in the departments of Brain and Cognitive Sciences and Biological Engineering at MIT, notes the exciting potential of the Cas13a enzyme. This enzyme, originally identified in a collaboration with Eugene Koonin to study bacterial immunity, has been adapted to achieve extraordinary sensitivity, which will be powerful for both science and clinical medicine.

In June 2016, Zhang and his colleagues first characterized the RNA-targeting CRISPR enzyme, now called Cas13a (previously known as C2c2). The team was able to use a different amplification process, relying on body heat to boost the levels of DNA or RNA in their test samples, and then apply a second amplification step to convert the DNA to RNA, increasing the sensitivity of the RNA-targeting CRISPR by a millionfold.

Jim Collins, the Termeer Professor of Medical Engineering and Science at MIT and core faculty member at the Wyss Institute, emphasizes the significance of the tool's sensitivity, which could detect an extremely small amount of cancer DNA in a patient's blood sample, enabling researchers to better understand how cancer mutates over time. For public health, it could help researchers monitor the frequency of antibiotic-resistant bacteria in a population, opening up a world of potential research and better preparedness for outbreaks.

As the global race to develop rapid and accurate diagnostic tools for infectious diseases continues, SHERLOCK represents an exciting step forward. With further development, it could fundamentally change the diagnosis of common and emerging infectious diseases.

The RNA-targeting CRISPR enzyme, named Cas13a, was initially studied by Feng Zhang, a scientist hailing from the Broad Institute, the McGovern Institute, MIT's departments of Brain and Cognitive Sciences, and Biological Engineering.
SHERLOCK, a highly sensitive diagnostic tool, was developed by a team of students, Omar Abudayyeh and Jonathan Gootenberg, from MIT and Harvard respectively, along with faculty from various departments.
SHERLOCK's potential applications extend beyond viral and bacterial outbreaks, encompassing health and wellness, such as detecting cancer, monitoring antibiotic resistance, and even identifying mental health-related genetic sequences.
The versatility of SHERLOCK was demonstrated through its ability to detect various targets, including Zika virus in patient samples, differentiating between strains, discriminating specific bacteria, identifying cancerous mutations, and reading human genetic information from a saliva sample.
The tool's paper-based design and lack of refrigeration requirements make it suitable for rapid deployment in field hospitals during outbreaks or rural clinics with limited equipment.
Jim Collins, a faculty member at MIT and the Wyss Institute, points out the tool's significant potential in detecting extremely small amounts of cancer DNA in a patient's blood sample, contributing to a better understanding of cancer mutations.
In addition, SHERLOCK could aid public health researchers in monitoring the frequency of antibiotic-resistant bacteria in a population, enhancing research and preparedness for outbreaks.
The tool's sensitivity could revolutionize science and medicine, particularly in the realms of neuroscience, medicine, and biotechnology, offering advancements in research and diagnostics.
In June 2016, the RNA-targeting CRISPR enzyme was first characterized by Zhang and his colleagues, laying the groundwork for the development of SHERLOCK.
As the global race for rapid and accurate diagnostic tools continues, SHERLOCK represents a significant stride forward, with potential to fundamentally change the diagnosis of common and emerging infectious diseases, and contribute to the field of medical-conditions and technology.