CRISPR technology has the potential to transform diagnostic capabilities by providing the sensitivity and flexibility of PCR tests but with increased speed and lower cost.

By Michael Heltzen

Over the last 40 years, researchers have discovered new ways to leverage the polymerase chain reaction (PCR) for various purposes, including as a molecular diagnostic testing technique for diseases ranging from cancer to COVID-19. PCR is a sensitive technique that makes billions of copies of a specific DNA fragment or gene, which allows for their detection and characterization. Now, a new technology might cause us to reassess how we approach molecular diagnostics. That technology is CRISPR-Cas9 (CRISPR). 

A simple yet powerful tool for editing genomes, CRISPR allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases, and modifying crops to make them healthier and less vulnerable to climate change. In fact, CRISPR is opening the door to find new ways to revolutionize medicine—from the way we fight genetic illness to the way we treat cancer1. Researchers, academics, and organizations have begun to advance this technology even further— pushing the limits of what is possible in genomics.

CRISPR: A Short History

CRISPR, an acronym for clustered regularly interspaced short palindromic repeats, describes unique DNA sequences in bacterial genomes that are derived from viral DNA, especially bacteriophages. When a bacteriophage attacks a bacterial cell, CRISPR recognizes the viral DNA and recruits enzymes—called cas proteins—to cut it up and inactivate the virus. This process forms the bacteria’s immune system.

Scientists realized that they could exploit CRISPR’s ability to recognize specific DNA sequences and cut them as a method to detect and edit specific genes in other cells from animals, including mice and humans. Scientists are continuously working to improve it even further—constantly modifying CRISPR components to make them more targeted and sensitive. CRISPR could potentially treat a range of medical conditions that have a genetic component, including cancer, hepatitis B or even high cholesterol2.

The Limits of PCR Testing

The COVID-19 pandemic has shown the value of PCR in diagnostics, as mass PCR testing has formed the basis of testing for and tracking the SARS-CoV-2 virus. PCR is the gold standard for genetic research and molecular diagnostics for many reasons: it is vastly flexible, as it can amplify and detect virtually any nucleic acid sequence. Also, most molecular biologists are familiar with the technique and know-how to leverage it for a multitude of research and diagnostics applications. This familiarity is what enabled the biopharmaceutical industry to develop PCR-based COVID-19 tests within months of the pandemic’s beginning. 

Despite its widespread use, however, PCR does have its limitations. PCR is, by definition, an amplification step, which is time-consuming to run. Moreover, the reagents needed to perform PCR are expensive, and PCR platforms are not portable—instead, samples must be sent to a lab for analysis. The future of molecular diagnostics is one that will include fast, convenient, and accurate testing.

Ultimately, individuals should be able to perform these tests on-site using portable devices, just as someone with diabetes tests their blood glucose using a handheld monitor or someone with heart disease identifies potential atrial fibrillation with their watch. These types of convenient, handheld devices can provide a long-term assessment of these measures inexpensively and noninvasively3.

Leveraging CRISPR Technology 

Researchers have developed new ways to leverage CRISPR technology for diagnostic purposes. CRISPR helps tackle some of the challenges associated with molecular testing platforms like PCR. For example, researchers have developed methods to detect when CRISPR binds to specific nucleic acid sequences without having to amplify the sample.

Sherlock Biosciences, for example, has developed a diagnostics platform based on this concept. Their technology, SHERLOCK, leverages CRISPR to detect and quantify specific genetic sequences. The technology indicates that a sequence has been found within a solution by cleaving a reporter molecule, which is then detected using a lateral flow strip. The technique can achieve single-molecule detection of nucleic acid targets; however, the detection method—visualizing bands on a strip—requires significant technical skill to execute and interpret correctly.

Cardea Bio, in contrast, developed a CRISPR-based tool that reports the detection of DNA via a digital signal. Its system uses a one-atom-thick graphene conductor to detect the subtle electrical current discharged during a CRISPR binding event. That current gets transformed into a digital signal that can be viewed on a benchtop platform or handheld device. This chip is capable of quickly detecting single nucleotide polymorphisms associated with heritable disease variants associated with sickle cell disease and ALS as well as infectious diseases like COVID-19. The potential for applications is vast. 

There are many challenges associated with molecular diagnostics and, in many cases, it comes down to a search for something rare: either rare variants or residual disease. Scientists are constantly seeking to develop more sensitive diagnostics that give physicians a clearer picture of a patients’ tumor load both before treatment and after. A CRISPR-based method, which can detect single nucleotide polymorphisms with single-molecule resolution, provides the sensitivity physicians need to feel confident in their diagnoses and refine their treatment regimens to bring their patients better outcomes. 

Accelerating Genomics 

The discovery of CRISPR and its application as a powerful gene-editing tool has transformed the world of science and healthcare. And the quick, flexible and highly efficient nature of this technology has enabled scientists to accelerate progress in the field of genomics, making it easier and faster than ever. 

CRISPR’s ability to detect specific genetic sequences will enable a new generation of molecular diagnostics that match the speed and convenience of other handheld or wearable diagnostics used today. 

With CRISPR technology, the opportunities are endless—from detecting genetic mutations to facilitating more effective treatments. Scientists and researchers have just scratched the surface of what this technology can do for the healthcare industry. While there are many unknowns, continued exploration of this technology will continue to unlock new, life-changing discoveries. 

About the Author

As CEO of Cardea Bio, Michael Heltzen spearheads Digital Biology leadership and strategy. Michael has an extensive background in tech business development in Bioinformatics, Next-Gen Sequencing, Genomics, and Intercellular communication. He has held leadership positions at CLC bio, BGI, EXO Incubator, Nanosens and BlueSEQ before heading up the leadership team at Cardea Bio Inc.

References

  1. “How CRISPR Is Changing Cancer Research and Treatment.” NCI Staff. National Cancer Institute. July 27, 2020. www.cancer.gov/news-events/cancer-currents-blog/2020/crispr-cancer-research-treatment
  2. “What is CRISPR-Cas9?” Yourgenome.org. July 21, 2021. www.yourgenome.org/facts/what-is-crispr-cas9
  3. Wasserlauf J, You C, Patel R, Valys A, Albert D, Passman R. Smartwatch Performance for the Detection and Quantification of Atrial Fibrillation. Circ Arrhythm Electrophysiol. 2019 Jun;12(6):e006834. doi: 10.1161/CIRCEP.118.006834. PMID: 31113234.