Genome Editing 101: Future of Genome Editing

Foreword

For the first time in human history, we not only understand the language of life, but we can also manipulate it. In the past two decades, a lot of advancements have been made to contribute to the realm of genome editing. Genome editing is the combination of techniques that allow us to manipulate the DNA of bacteria, fungi, and even humans. Manipulating genetic codes have an enormous influence and can be used to increase crop yields, produce medicines in bacteria, and even cure genetic diseases.

The Genome Editing 101 series offers to explain the relevant biology of gene editing, the mechanisms by which such techniques work, and the ethical and political problems that arise from this new field of biology. It will be mainly divided into the following chapters:

1. Genome Editing 101: Central Dogma of the Cell

2. Genome Editing 101: Gene Editing Techniques

3. Genome Editing 101: Applications of Genome Editing

4. Genome Editing 101: Politics on Genome Editing

5. Genome Editing 101: Ethical Problems in Genome Editing

6. Genome Editing 101: Future of Genome Editing

Genome Editing 101: Future of Genome Editing

As explained in past articles of this 101 series, a lot of research is currently being done on CRISPR/Cas9 and its possible applications in agriculture, medicine, and other fields. Although the ethical issues have not been fully tackled yet, it is worth having a look at a world in which genome editing is more developed and widely applied. The focus of this article shifts away from the techniques that are currently in experimental phases, which was the focus of the third article of this series. Instead, this article lists ground-breaking discoveries and ways of implementation through which CRISPR/Cas9 and other techniques may change the world for the better.

Unsurprisingly, the first thing that research should focus on is the errors induced by CRISPR/Cas9. Like many other forms of technology, the more time and money invested into its research, the more accurate and reliable it becomes. Since the first description of CRISPR/Cas9 back in 2012, numerous different biological versions of CRISPR-Cas types have been identified, the most recent one being type VI (Nakagawa et al., 2022). The major difference between various CRISPR-Cas types is that the enzyme is built up of different parts of proteins. CRISPR/Cas9, however, remains the most effective one in the general eye of researchers, because Cas9 has the versatility to achieve the same function as multiple enzymes in other types. These different techniques and their variants are continuously under rigorous research, which further shows how the science on this topic is rapidly evolving.

Figure 1: An overview of the different types of CRISPR/Cas9 that have been identified (Scholarly Community Encyclopedia, 2022).

CRISPR/Cas9 as the Future of Medicine

As mentioned in the first article of this series, the DNA in the human body determines many features. Therefore, rearranging or replacing faulty disease-causing DNA with a normal sequence seems to be a straightforward implementation of CRISPR/Cas9 to restore health in many patients suffering from genetic disorders. Many existing diseases, including sickle-cell disease, are caused by a single mutation in the DNA. Changing these single nucleotides, in theory, is very doable, though it has not been performed in humans on a large scale (Rees et al., 2018).

While changing the genetic makeup of patients is likely the most common and clinically significant use of CRISPR/Cas9 in medicine, the technique has many other applications. For instance, it could start a revolution in the way researchers deal with antimicrobial resistance, or how companies find new therapeutical drugs. Because CRISPR/Cas9 offers an easy and reliable way of turning genes on and off, it may prove very useful in the laboratory. On a large scale, bacteria that are known to cause disease may be grown in a laboratory, with genes knocked in or knocked out. If this is done in a systematic way, it will be very easy to observe whether bacteria grow in the presence of different possible drugs. Say bacterial population 1 and population 2 are grown in presence of drug X. Population 1 has a certain gene knocked out, whereas population 2 does not. If results show that population 1 does not survive well, while population 2 does, then the researchers would have located the specific gene involved in the resistance to drug X, which would in turn contribute to identifying a possible target for new drugs. This way of research has been conducted extensively and is referred to as reverse genetics (Gurumurthy et al., 2016). CRISPR/Cas9 would increase the speed of this research immensely because of the ease by which genes can be knocked in or out (Gurumurthy et al., 2016).

Figure 2: The difference between forward and reverse genetics (Ben-Amar et al., 2016).

Antibiotic resistance is a growing problem around the world. Because of misuse of antibiotics, microbes are exposed to different antibiotics to which they grow resistant as a direct consequence of natural selection. As it has proven difficult to identify new antimicrobials, the future of combatting bacterial infections is not great. Unless new techniques are deployed on a massive scale soon, it is estimated that 10 million people will die every year as a consequence of antimicrobial resistance from 2050 onwards, with bacteria becoming more resistant to therapeutic agents (Murray et al., 2022). One therapeutic technique that is receiving an increasing amount of attention is the use of bacteriophages, i.e., naturally occurring viruses that are only able to infect and replicate in bacteria, thereby creating no danger to humans or other animals. Often, bacteriophages are very specific in their targets. In other words, they are ideal weapons against specific resistant bacteria. These can be easily engineered using CRISPR/Cas9, which is more than capable of creating different variants of the same bacteriophage depending on the target (Chen et al., 2019).

Gene-Editing in the Context of Evolution and Ecology

Another method that sounds very farfetched, but could very much become a reality thanks to CRISPR/Cas9, is the so-called gene drive. Natural selection, the foundation of evolution, dictates that only genes with a beneficial influence on the organism, or an increased “fitness”, will be selected for and kept over generations. Genes that introduce a decrease in fitness will be selected against, and will therefore never appear widespread in a population. Moreover, genes that offer a neutral influence will likely not be selected for either, although natural selection does not work towards its extinction in the population (Alphey, 2016). This process can be explained by the following example:

Figure 3: An example of natural selection (Khan Academy, n.d.).

In this fictional population of mice, there is a genetic variation that results in some mice having a light colour of fur, while others have a darker one. Because the darker mice are less likely to be noticed by preying birds, they will live longer and have more time to reproduce. The lighter mice, however, are more likely to be spotted and eaten. This difference in survival outcomes leads to a shift in gene frequencies because the darker mice are more likely to reproduce. As a result, future generations of mice will have higher frequencies of darker fur compared to the earlier generations.

Gene drives seem to defy this inherent trait of natural selection. Gene drives are synthetic genetic elements that spread through a population although they do not confer an increase in fitness (Alphey, 2016). On the contrary, they may actually cause a decrease in fitness. In order to understand how this mechanism works, it is important to note that the CRISPR/Cas9 complex itself is encoded by genes, just like any other set of proteins. The already-characterised CRISPR genes in bacteria encode for different parts of the Cas9 enzymes and of the CRISPR-array, as explained in the second article of this 101 series. If these genes are knocked into an organism, the organism becomes capable of synthesising the Cas9 enzyme and the RNA molecules associated with it. To create a true gene drive, however, the genes should be manipulated in such a way that they recognise a specific sequence to cut while possessing another gene for insertion, which is referred to as a cargo. Through sexual reproduction, the progeny of living organisms receives one set of chromosomes from each parent. The cellular process of meiosis ensures that each progeny will receive exactly two copies of each chromosome, on which there is variation per parent. Using mosquitoes as an example, if a mosquito has the gene drive present in both copies of a certain chromosome, it is guaranteed that its progeny will receive a chromosome with the gene drive from this parent. This way, these manipulated genes are passed onto all the progeny. Subsequently, upon translation of the genes into proteins, Cas9 will recognise a site to cut into the other copy of this chromosome and insert the cargo sequence, leading to an enormously increased abundance of a gene with respect to general natural selection (Alphey, 2016).

Figure 4: An illustration of how gene drives create a dominant population of modified mosquitoes (in blue) over generations (Oye et al., 2014).

Experiments in this field of biology using fruit flies have proven to be successful. This has made researchers think about a possible implementation of gene drives to combat mosquitoes that spread diseases such as malaria. One of the ways to achieve this is by inserting an infertility gene. This gene would render mosquitoes that have the gene present on both copies of a certain chromosome infertile. Mathematical modelling has shown that this method could reduce mosquito populations by about 90% in only two years, significantly decreasing the burden of malaria on humans (Alphey, 2016).

Ecology is the study of biological relationships in nature. Within a certain area, predators can only sustain themselves well enough if there is enough prey. Though this relationship is very well understood and can even be modelled accurately through Lotka-Volterra equations, looking into a certain environment and understanding all the relationships within can be incredibly complex. As a consequence, scientists are very bad at predicting what would happen if a complete population of mosquitoes was eradicated. Therefore, an alternative to the infertility gene method was proposed: a gene that renders the mosquito resistant to the malaria parasite. It would work in exactly the same manner, by spreading the gene rapidly across populations and making a large portion of the global mosquito population resistant to malaria, thereby lowering the transmission of malaria to humans (Alphey, 2016). In sum, mosquito-borne diseases represent an immense global health burden. The current way of controlling or preventing these diseases is by using insecticides and anti-mosquito nets. These insecticides, however, have been shown to cause resistance in the target insects. The breakthrough in genetic manipulation may offer an alternative solution to this problem, but the long-term effects of using gene drives are simply not well understood yet. Additionally, changing the genetic makeup of a complete species may have detrimental, unknown consequences in itself. As more research is currently being done on this technique, the answers to these questions will become clearer over time (Wang et al., 2021).

Figure 5: An example of a system modelled by Lotka-Volterra equations (Strimas-Mackey, 2020).

Gene-Editing in Agriculture and Food Production

Apart from the medical field, the agricultural industry is an area in which CRISPR/Cas9 is researched the most. Recent studies have shown that food can be engineered to be more nutritious or more resistant to environmental factors. Optimising crops this way may cause an absolute revolution in agriculture, as crops can be produced in a more efficient manner and in larger amounts. This in turn may prove to be a favourable factor in fighting global hunger, or simply enhancing the efficiency and productivity of the food-production industry. In addition, with advancing technology and research, there are increasingly more opportunities for genetic-engineered crops. One such example is editing plants to not cause any allergy. In one study performed in 2008, even before the start of the CRISPR era, researchers successfully made hypoallergenic nuts by silencing the aha h gene, which is responsible for the overwhelming majority of nut allergies (Dodo et al., 2008).

CRISPR/Cas9 to Regulate Global Biological Balance

Manipulating the biological balance of different species on Earth may sound like science fiction, but it is a real possibility nonetheless. Scientists know surprisingly much about the DNA of extinct animals, from the dodo to the mammoth. In theory, these species could be resurrected using gene-editing techniques like CRISPR/Cas9. This can be done by knocking their genomes into proper cells, developing the edited embryos of these animals, and eventually growing them into full organisms. While scientists do not yet know enough about how to synthesise these proper cells, ongoing research is being done on this very topic (Callaway, 2023).

Figure 6: Gene-editing could potentially resurrect extinct species like the dodo (Callaway, 2023).

Perhaps farther into the future, CRISPR/Cas9 will allow experts to synthesise animals to create more stable ecosystems. In the course of Earth's history, many events have occurred and caused massive death among biological entities that once roamed the planet. One of the more recent and devastating ones was the asteroid that killed the dinosaurs, and 76% of all the life on Earth with it (Klein et al., 2021). Now, experts believe that the biosphere finds itself in the seventh mass extinction: in a relatively short amount of time, significant amounts of animals and plants have died as a consequence of human behaviour (Carpenter & Bishop, 2009). With human-induced problems like climate change, deforestation, fishing, and general pollution of the planet, many species are found on the border of extinction. Revolutionary gene-editing tools present a new hope to not only counteract the environmental effects of climate change, but also restore the overall biological balance of the planet by cloning animals or plants in the laboratory. This, of course, would require more extensive research and regulation combining the efforts of scientists and governments, but it nevertheless opens up a new direction for deriving solutions to existing problems of humanity.

Bibliographical References

Alphey, L. (2016). Can CRISPR-Cas9 gene drives curb malaria? Nature Biotechnology, 34(2), 149–150. https://doi.org/10.1038/nbt.3473

Ben-Amar, A., Daldoul, S., M. Reustle, G., Krczal, G., & Mliki, A. (2016). Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics. Current Genomics, 17(6), 460–475. https://doi.org/10.2174/1389202917666160520102827

Callaway, E. (2023). What it would take to bring back the dodo. Nature, 614(7948), 402–402. https://doi.org/10.1038/d41586-023-00379-5

Carpenter, P. A., & Bishop, P. C. (2009). The seventh mass extinction: Human-caused events contribute to a fatal consequence. Futures, 41(10), 715–722. https://doi.org/10.1016/j.futures.2009.07.008

Chen, Y., Batra, H., Dong, J., Chen, C., Rao, V. B., & Tao, P. (2019). Genetic Engineering of Bacteriophages Against Infectious Diseases. Frontiers in Microbiology, 10(MAY). https://doi.org/10.3389/fmicb.2019.00954

Dodo, H. W., Konan, K. N., Chen, F. C., Egnin, M., & Viquez, O. M. (2008). Alleviating peanut allergy using genetic engineering: the silencing of the immunodominant allergen Ara h 2 leads to its significant reduction and a decrease in peanut allergenicity. Plant Biotechnology Journal, 6(2), 135–145. https://doi.org/10.1111/j.1467-7652.2007.00292.x

Gurumurthy, C. B., Grati, M., Ohtsuka, M., Schilit, S. L. P., Quadros, R. M., & Liu, X. Z. (2016). CRISPR: a versatile tool for both forward and reverse genetics research. Human Genetics, 135(9), 971–976. https://doi.org/10.1007/s00439-016-1704-4

Klein, C. G., Pisani, D., Field, D. J., Lakin, R., Wills, M. A., & Longrich, N. R. (2021). Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nature Communications, 12(1), 5335. https://doi.org/10.1038/s41467-021-25136-y

Murray, C. J., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F., Hackett, S., Haines-Woodhouse, G., Kashef Hamadani, B. H., Kumaran, E. A. P., McManigal, B., … Naghavi, M. (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0

Nakagawa, R., Kannan, S., Altae-Tran, H., Takeda, S. N., Tomita, A., Hirano, H., Kusakizako, T., Nishizawa, T., Yamashita, K., Zhang, F., Nishimasu, H., & Nureki, O. (2022). Structure and engineering of the minimal type VI CRISPR-Cas13bt3. Molecular Cell, 82(17), 3178-3192.e5. https://doi.org/10.1016/j.molcel.2022.08.001

Rees, D. C., Williams, T. N., & Gladwin, M. T. (2018). Sickle-cell disease. Www.Thelancet.Com, 376, 2018–2049. https://doi.org/10.1016/S0140

Wang, G.-H., Gamez, S., Raban, R. R., Marshall, J. M., Alphey, L., Li, M., Rasgon, J. L., & Akbari, O. S. (2021). Combating mosquito-borne diseases using genetic control technologies. Nature Communications, 12(1), 4388. https://doi.org/10.1038/s41467-021-24654-z

Visual Sources