10 Promising CRISPR Applications Beyond Gene Editing
CRISPR technology swept the biotech community like a wildfire starting in early 2013 when CRISPR gene editing was first introduced. Since then it has become the workhorse of biotechnology research, spanning applications like therapeutics, drug discovery, protein and antibody engineering, development of crops, animal models, and microbes for production of valuable chemicals.
The word “CRISPR” has entered mainstream vocabulary thanks to controversial headlines about engineered babies and a Netflix series Unnatural Selection. Most people use the acronym to refer to CRISPR/Cas editing, a technique that uses a DNA cutting enzyme called Cas. In a process analogous to word processing, the cut site can be repaired by “pasting” another DNA sequence encoding the desired change.
CRISPR/Cas gene editing is much more precise and efficient than the previous generation tools used to genetically engineer organisms. Because of this, CRISPR technology has dramatically sped up the efforts to edit the genomes of different organisms, from CRISPR gene drives in mosquitos, to improving crops, to hornless cows. But this is not the only application that scientists studying CRISPR are exploring. The unique ability to target any genetic region makes CRISPR-based tools amenable to a range of interesting uses beyond gene editing. Here are some of those:
1. CRISPR interference: CRISPR interference (CRISPRi) refers to a technique where the expression of a given gene is temporarily reduced or blocked. The gene itself (that is, the DNA sequence that encodes it) is not affected but the expression of the gene is hindered by placing a modified inactive Cas protein (dCas) in front of the gene and blocking its transcription. This is a really useful tool that allows scientists to get an idea of what would happen if the gene was deleted without actually deleting it. It can be used as a quick way to screen for potential drug targets or genes involved in producing a certain molecule. It can also be used to study the dynamics of gene interactions by switching them on and off.
2. CRISPR activation: Similar to how CRISPR interference can be used to block transcription, CRISPR activation (CRISPRa) can be used to enhance transcription of a given gene. Here the guide RNA molecule used to find the gene to be upregulated is targeted upstream of that gene. Together with it, another protein is tethered to inactive dCas that functions
as a transcriptional activator. This can increase production of
a protein encoded by the gene by multiple times. Additionally,
you can add a light-inducible switch to precisely control the
timing of gene activation.
Photo of bacterial cultures in test tubes in which the genes responsible for production of pigment have been turned down using CRISPRi. The result is an array of different colors
3. Cell imaging: While we are on the topic of light, another cool feature of the CRISPR toolkit is fluorescent imaging. By attaching dCas to a green fluorescent protein, scientists could detect localization of nucleic acids in cells and study telomere dynamics. A new technique called Fluorescence in situ hybridization (FISH) allows to monitor the changes in transcription and gene editing events in real time. That’s a CRISPR movie I would watch!
Image of fluorescent bacterial colonies in a petri dish
4. Epigenetic modification: Not quite the same as genetic engineering, epigenetic modification allows to make semi-permanent changes to the way DNA is packaged inside the nucleus, making some regions more or less accessible to transcription. Regarded as primary driver that influences how our genes respond to environmental factors, it is an important area of study in cancer biology, aging, etc. Now, thanks to CRISPR, we have the ability to effectively target and modify the epigenetic markets using a dCas coupled with chromatin modifying enzymes.
5. CRISPR recorder: A little known function of CRISPR systems is the ability to incorporate pieces of foreign DNA as a form of “genetic memory”. By providing different types of information encoded in DNA, scientists have managed to write an entire short film into bacterial DNA. Another approach allows to use the CRISPR/Cas system to record events in the life of a cell, such as exposure to drugs, viruses, nutrients or light. By reading the fraction of swapped DNA, one can even determine the duration of event.
Image of fluorescent cells in a test tube
6. CRISPR diagnostics: a group of scientists from the Broad Institute and MIT has developed a took called SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) that can detect nucleic acids from a virus or tumor, presence of pathogens and even be used for genotyping. The method detects tiny amounts of DNA or RNA. The scientists further enhanced the tool by adapting it into a test-strip format that can rapidly detect nucleic acids in the field.
7. CRISPR sensor/chip: this team of scientists went even further and integrated CRISPR signaling with an actual graphene chip. This method allows digital detection of nucleic acids without amplification within intact genomic material and is compatible with automation methods, making it a promising future technology.
9. Synthetic gene circuits: the ability to selectively up- and down-regulate gene expression using CRISPR can be used to build logic circuits inside living cells. These gene circuits allow living cells to change their behavior in response to external stimuli, such as light, or internal processes, like accumulation of a metabolite. The use of genetic circuits is especially promising in microbial biotechnology: it allows to create controlled processes where cells to not have to be monitored constantly, but instead regulate their own metabolism and physiology.
10. Programmed DNA degradation: With all the crazy gene editing applications happening all around us, one cannot help but wonder “How safe is it?” Scientists have long been concerned with accidental release of synthetic DNA into the environment (such as the spread of antibiotic resistance) and now they are also worried about leaking of precious intellectual property. This is where programmed DNA degradation comes into play: when a new environment is detected (such as if the organism escapes from the lab) the DNA is degraded by an encoded CRISPR-based device. With the self-destruction mechanism encoded within in these engineered cells, we can all sleep better knowing they are confined to the perimeter of a research lab.
8. Smart materials: Since DNA is a polymer, it can, like other polymer such as collagen, be made into a matrix that holds water, known as a hydrogel (think of it as DNA Jell-O). MIT scientists decided to see if they can modify the material properties of the gel with CRISPR. In this application an environmental trigger, such as a change in pH or presence of a specific molecule, triggers the expression of the Cas protein, which makes cuts the DNA hydrogel and degrades the matrix. This process can be used, for example, as a slow-release drug delivery mechanism.
DNA fragments visualized under UV light