In my final few posts, I will focus on the future of cancer treatment. Over the course of my series of posts, I discussed what scientists have learned about the genetic basis of disease, how these findings have led to the development of targeted therapies, and how the sequencing revolution has enabled the personalization of these therapies. There are, however, emerging technologies that are so new, they have not yet been implemented in cancer treatment despite their immense potential for applications in the field. One of these technologies, genome editing, is becoming increasingly important in every corner of biological research due to the use of a new tool called CRISPR, short for Clustered Regularly Interspersed Short Palindromic Repeats. While its potential has not yet been fully realized, CRISPR is bound to change the face of cancer therapies. But what is genome editing?
Genome editing is a technique that has gained traction in biological research over the past decade. This term encompasses the use of different tools and techniques to selectively change DNA sequences. The genome is the complete package of DNA we inherit from our parents and is contained in each cell in our bodies. In my previous posts, I equated the genome to a book made up of chromosomes that are akin to chapters and genes that are like sentences. The DNA sequence itself is the letters that make up these larger components. Genome editing, thus, is a way to change specific letters in the book in order to alter the words and sentences.
Changing the letters in the genome, however, is not as trivial as erasing pencil on paper. In The Double-Edged Sword of Mutation, I discussed that letters can be randomly changed, as DNA sequences are copied. Later, in BRCA: Bracing the Genome, I discussed how mutations can also be introduced through the repair of DNA breaks and other types of damage in the genome. Scientists are able to exploit the errors that can occur during these processes in order to alter the genome sequence in a specific way. The use of these processes as genetic tools has existed for decades in model organisms such as budding yeast and fruit flies. Genome editing technologies, however, make the process easier and more precise in human cells and other organisms that have historically been difficult to genetically manipulate.
CRISPR is the most well-known genome editing tool and was developed in 2013. Prior to CRISPR, other tools called TALENS and Zinc Finger Nucleases were beginning to gain traction. These other tools, however, were costly, and not as versatile as CRISPR. The genome-editing trend, therefore, exploded with the development of CRISPR because of its low cost, simplicity, and improved accuracy over the other tools.
Much like the exploitation of error-prone sequencing and DNA repair processes, CRISPR is a natural phenomenon, which scientists harnessed for the purpose of genome editing. CRISPR was discovered in bacteria and is thought to be an immune mechanism to fend off viral invaders. Researchers found that certain bacteria contained regions in their genome that had short, unique DNA sequences that were separated by a repeated sequence. This repeated sequence, researchers found, came from the bacterial genome, but the unique intervening sequences did not. These sequences, instead, came from viruses.
The discovery of the CRISPR pattern in bacteria led to the identification of a group of proteins, called Cas, that mediate the CRISPR process by adding the viral sequences to the bacterial genome. The short viral DNA sequence that is added to the bacterial genome acts as a "memory," allowing the bacteria to recognize and kill the virus if it returns. Upon reinfection of a bacterium by a virus, the protein Cas9 uses the memory DNA to locate and cut the viral DNA so that the virus can no longer replicate and spread.
The CRISPR genome-editing tool utilizes Cas9, which acts like a pair of scissors that is able to locate and cut precise DNA sequences. By paring with a unique sequence of RNA (which is a copy of a DNA sequence) Cas9 is guided to the corresponding DNA sequence in the genome. The guiding RNA then binds the DNA, and Cas9 cuts the DNA strands. Once Cas9 creates breaks in the DNA, many different outcomes can occur. Cutting the DNA by Cas9 sends a distress signal to the cell, stimulating the DNA repair process, similar to what I described in BRCA: Bracing the Genome. Cells can repair DNA breaks either through the error-prone non-homologous end-joining process or the homologous recombination process that can swap out one DNA sequence for another. This gives scientists the option of utilizing the DNA repair processes to either delete DNA sequences or insert new DNA at the spot where the cut is made by Cas9, depending on the method of DNA repair. Deleting DNA sequences through this process can inactivate the function of a gene, while inserting a DNA sequence by replacing a mutated sequence with a non-mutated sequence can restore function to a gene that was previously inactivated.
While the CRISPR-Cas9 system has been used in a multitude of research studies around the world since its development in 2013, it has not yet been utilized long enough to be implemented widely in clinical research. While a few clinical trials are in progress in China, there are not any currently underway in the United States. One of the reasons the U.S. has been reluctant to approve clinical trials is due to debate about the safety of CRISPR in humans.
The use of CRISPR has stirred up controversy since its development as a genetic tool. There are fears that the ease of use will lead to its misuse or that introducing foreign DNA and proteins into human cells will have negative repercussions. These concerns, however, are not unique to the CRISPR system. Controversy has surrounded ethical topics such as the use of genetically modified organisms and the selection of embryos based on their genetic makeup prior to the development of CRISPR for genome editing. Because CRISPR is so new and restrictions have not been placed on applications of its use, there are fears that misuse will be more widespread. The successful use of CRISPR, however, still requires detailed understanding of the genetic basis of biological processes. Thus, what is likely preventing intentional misuse of CRISPR and other genetic tools at this point is the lack of detailed understanding, collectively, of many biological processes.
More realistic worries about the use of CRISPR are related to its accuracy in targeting DNA sequences and the repercussions of unintentionally editing the wrong part of the genome or the wrong cells in the body. Many of these off-target effects are not unique to the CRISPR gene editing system and are also concerns with many types of molecular biology techniques that alter cell function. As has occurred with other genetic tools over decades of use, over time scientists will gain a better understanding of the weaknesses of CRISPR and how to control or eliminate them.
As CRISPR technology is validated and methods for eliminating off-target effects are developed, CRISPR will have immense potential for cancer therapy. Gene-therapeutic applications of CRISPR could replace mutated cancer susceptibility genes such as BRCA1 or BRCA2 with their non-mutated counterparts and could prevent the development of cancer. CRISPR-based therapeutics could, alternatively, treat existing cancers by turning off cancer-promoting pathways or modifying immune cells to target cancer cells. While drugs such as PARP inhibitors can be used to treat cancers with known genetic susceptibility, CRISPR could be a faster way to target other cancers that do not yet have drug-treatments.
In summary, CRISPR is one of the most promising genetic tools driving the genome-editing revolution. Like many molecular tools, it was harnessed from a natural process utilizing the bacterial protein, Cas9. By targeting and cutting specific DNA sequences, scientists have exploited the DNA repair process to either insert or delete DNA sequences. As a result of the versatility in targeting any DNA sequence in the genome, CRISPR has the potential to be used as a therapeutic agent for genetic diseases. One of the bottlenecks to being able to successfully treat many diseases including cancer is the identification of the underlying genetic components of disease. Until those contributions have been determined, there is a limit to what scientists can edit with CRISPR in order to get a desired outcome