The Wonderful Applications of CRISPR

From Agriculture, Biofuels to Healthcare

The ultimate long-standing goal of biomedical research is the ability to make precise, targeted changes to the genome of all living cells. This is an enormous challenge when it comes to altering the genes of humans, plants and animals. We’re all made up of eukaryotic cells that are far more advanced than prokaryotes, which are predominantly bacteria.

At the heart of all living cells lies the genetic material. Eukaryotic cells have long genetic sequences that comprise billions of DNA bases. Furthermore, these sequences are double-stranded. Imagine if you will, two long strings that could only ‘zip’ together when the components match. Therefore, if a genetic edit were not done properly it would result in either a gene knockout or mutation.

To date, there are a couple of well-known options to perform gene editing:

1. Zinc-finger nuclease (ZFN) – Known as the first gene-editing tool. ZFNs are artificial restriction enzymes (functional proteins) made by fusing a ‘zinc finger’ DNA-binding domain to a DNA-cleavage domain. ZFNs can be engineered to target specific desired DNA sequences within complex genomes.
2. Transcription activator-like effector nuclease (TALEN) – Restriction enzymes that are made by fusing a TAL effector (proteins) and DNA-binding domain to a DNA cleavage domain (a nuclease which cuts DNA strands). Transcription activator-like effectors (TALEs) can be engineered to bind to practically any desired DNA sequence, so when combined with a nuclease, DNA can be cut at specific locations.

These gene-editing tools, however, are expensive and require time to produce. ZFNs are generally complex to build and assemble, while TALENs require a lengthy process of up to several months to perform.

CRISPR: A Novel Way to Edit Genes

For the past several years, scientists have been exploiting a quirk in the immune systems of bacteria to edit genes in eukaryotes. With CRISPR, they can now make these edits quickly, precisely and cheaply in a matter of days instead of weeks or months.

With this discovery of CRISPR-Cas9 as a genome-editing tool, it has ushered in a new era in molecular biology. Here’s why:

1. Precise targeting – CRISPR uses ribonucleotide formations (RNA) to target DNA sequences, unlike their ZFN and TALEN counterparts that use complex proteins. This makes the targeting design simple yet effective. Guide RNAs can be readily designed at a cheap price, making CRISPR-Cas9 easy to use.
2. Efficient – The targeting efficiency of Cas9 is higher than that of its predecessors, about 4 times more efficient than TALEN (on average). For example, ZFNs and TALENs could only achieve efficiencies ranging from 1% – 50% while Cas9 has efficiencies of more than 70% in zebrafish and plants, ranging from 2–5% in induced pluripotent stem cells.
3. Fast –ZFNs and TALENs require a substantial amount of time to construct, as they are using proteins as guides. Target cells need to be exposed for sufficient periods for the gene edits to take effect. In addition, the host organism would need to multiply or bred further to evaluate the desired expression. This could take anywhere from several weeks to several months. A CRISPR edit on the other hand, can be performed in a matter of days.
4. Cheap – CRISPR tools are far cheaper and more cost effective. As of 2013, ZFNs typically cost from USD 3,000 to 7,000 dollars apiece depending on their complexity. TALENs can cost from to USD 3,360 to 5,000 dollars. A mail order CRISPR kit can cost as low as USD 75 to 130 dollars.

A simple, yet precise, efficient, fast and cheap tool makes the CRISPR-Cas9 highly scalable. Such a tool can be applied in various industry sectors such as healthcare, pharmaceuticals, food & agriculture, biofuels and even animal models.

Applications of CRISPR

Here are some of the ways we can put CRISPR to good use:

1. Fighting cancer – The most significant potential of CRISPR is in the detection and treatment of cancer. Scientists are using CRISPR to study and pick apart cancer cells to determine which genes are critical to the disease’s survival. Scientists can also enhance immune cells that would eventually silence cancerous genes.
2. A cure for HIV/AIDS – CRISPR was reported to be successful in removing HIV from human immune cells. At Temple University, a research team managed to destroy HIV-1 DNA from T cell genomes in human lab cultures. And when these cells were exposed to the same virus later, they were not re-infected. This is a major advancement in the potential to treat patients with AIDS.
3. Hacking diseases to self-destruct – Scientists are developing antibiotics that force pathogens to ‘commit suicide’. First, they introduce CRISPR to destroy the genes of invading bacterium. Then, they insert modified bacteriophages (which only infects bacteria), that are retrofitted with CRISPR, into the pathogen, ‘programming’ it to destroy itself. The method effectively kills off the targeted disease.
4. Eliminate malaria for good – Research teams are actively working on eliminating malaria genes in mosquitos. With CRISPR, scientists can ‘cut’ out genes that are critical in the spread of malaria within the mosquito population. Coupled with a ‘gene drive’ (enabled via CRISPR as well), can ensure that genetically modified mosquitos pass on such resistance to their offspring.
5. Food technology & agriculture – There are 2 ways CRISPR can help improve the sustainability of food production. One way is to equip plants with resistance genes. Crops would be resistant to drought, viruses, fungi and insects. It would also reduce the reliance on pesticides and herbicides which are potentially toxic to human health. CRISPR can also lead to the creation of seedless fruits for sustainable food production. They can be grown in laboratories or closed environments, avoiding setbacks such as landslides, extreme weather, lack of sunlight, little rain, etc.
6. Production of biofuels – J. Craig Venter (who mapped the human genome) and Exxon Mobil are using CRISPR to improve the yield of bio-fuel production from algae. After more than 8 years of research, they have successfully doubled the amount of oil produced by the aquatic organism via CRISPR gene editing.

But Wait, There’s More

These are new and fascinating developments which are already at the scene of genetic engineering:

1. Gene surgery – A new era of ‘gene therapy’. CRISPR-Cas9 can be used to precisely target genetic defects in our genome. Such therapies can be customised to benefit individuals or families with rare genetic defects or hereditary diseases.
2. Revive extinct animals – This may sound crazy, but researchers from Harvard University has revealed plans to bring back the woolly mammoth with CRISPR. The idea is to combine elephant genes with mammoth genes recovered from fossils, and create hybrid embryos which could then be grown in an artificial womb.
3. Gene Scaring or ‘Barcoding’ – Scientists can ‘barcode’ each cell in order to simultaneously trace the lineage and profile thousands of single cells.
4. Fluorescent gene tagging – Like something out of a sci-fi movie, researchers will soon be able to perform live-cell imaging to be incorporated into endogenous genes. This new method is easier, faster and cheaper than traditional fluorescent protein tagging.
5. Live-cell chromatin imaging – The entire construct of chromatin in 3-dimensional space plays a critical role in regulating gene expression. With CRISPR, scientists can see which regions are transcriptionally active throughout the cell cycle, by having multi-colored tracking of chromatin loci.
6. Gene drives – Simply put, a gene drive allows the edited gene to be passed on to more than 50% of its offspring, as in conventional reproduction. For example; with mosquitos, researchers were able to push a gene that inhibits the transmission of malaria to more than 95% of the progeny.

What we know for sure is that CRISPR has already disrupted the genome-editing scene. It is far cheaper, more precise, highly efficient and much faster to perform due to its simplicity. Used responsibly, the possibilities are endless. CRISPR can be used for cancer treatment, to potentially cure HIV/AIDS, rewire diseases to kill themselves and even destroy harmful genes.

Outside of healthcare, the technique has a huge potential to enhance food production, ecology, conservation efforts and sustainable energy. Considering the advances that have already been made, CRISPR’s future potential is limitless.

We hope you find this article useful, feel free to view our SlideShare to know more on the subject.

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Sources:

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343198/
• https://www.livescience.com/58790-crispr-explained.html
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• https://www.scientificamerican.com/article/mail-order-crispr-kits-allow-absolutely-anyone-to-hack-dna/
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• https://www.vox.com/2018/7/23/17594864/crispr-cas9-gene-editing
• https://disruptionhub.com/9-amazing-applications-crispr/
• https://medium.com/@32ATPs/top-10-crispiest-crispr-applications-33db9cc3ef5b