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Everything You Need to Know About Genome Editing – Interesting Engineering

Posted: December 9, 2020 at 12:51 am

Every cell in your body has around 3 billion base pairs of DNA code inside it. Just a few small errors in this code could leave someone with a debilitating illness. Molecular biologist Eric Olsen has described it as equivalent to misspelling one word in a stack of one thousand bibles, and this tiny typo could put a child in a wheelchair for life.

Researchers have already identified DNA errors as the cause of nearly 7,000 diseases. Thankfully, the growing world of genome editing could be the "spell-checker" needed to detect and eventually fix these problems.

Genome editing is often equated with designer babies and CRISPR/Cas9. However, the world of genome editing is far more diverse and complex and goes well beyond just CRISPR, which is only the latest in a long line of editing "tools". Genome engineering is a type of genetic engineering in which DNA is inserted, deleted, modified, or replaced in the genome of a living organism.

It is an incredibly powerful tool with tremendous potential in the field of medicine. In its simplest form, it is a way of making specific changes to the DNA of an organism. It's similar to editing the code in a piece of computer software.

There is a reason why there is a lot of hype around gene editing, and you should be excited too. Genome editing could potentially be used to treat major degenerative diseases and fix simple genetic conditions like muscular dystrophy. It may one day soon be used to grow new human organs in pigs, combat the constant demand for organ transplants, and potentially turn human reproduction on its head, yes, we're talking about using it to engineer entire populations.

We are still a ways away from the movie Gattaca, or Aldous Huxley's Brave New World. Nonetheless, real-world gene engineering poses some very interesting ethical questions. Today we are going to look at the history of genome editing, new methods like CRISPR, as well as alternatives, and look at some of the ethical questions currently plaguing this medical tool.

Okay, to review, genome editing or gene editing is a relatively new method that lets scientists change the DNA from bacteria to animals. These "edits" could potentially lead to changes in physical traits like eye color, or, more importantly, to cure certain diseases. Genome editing has already been used in agriculture to modify crops to improve their yields and increase their resistance to disease and drought.

There are many different methods and technologies used to edit DNA. Nonetheless, most of these technologies generally act like the "cutting" and "pasting" functions on your computer, allowing scientists to alter the DNA at a specific spot in an organisms' genome. Though much of the hype around gene editing centers around its power to engineer humans, the main application of genome editing so far has been in plants and some animals in lab settings.

Once it was realized in the 1940s that DNA was responsible for heredity, and once the structure of the DNA molecule was elucidated in the 1950s,researchers realized that errors in this genetic code were responsible for many diseases and inherited conditions.

The question that followed was an obvious one. Could these errors be corrected? This question led to the emergence of genetic engineering in the 1970s, where new genetic code was introduced into organisms' DNA. However, this technology was not initially capable of inserting the new material in a highly targeted way.

One early example of targeting genes to certain sites within a genome of an organism usedhomologous recombination. This method involves the construction of a sort of template that matched the targeted genome sequence, and relied on the normal cell processes to insert this template at the correct location. The method was successfully used to introduce genetic modifications in mice using embryonic stem cells.

Another early method used conditional targeting using enzymes calledsite-specific recombinases(SSR). These techniques were able toknock out or switch on genes only in certain cells and ultimately allowed researchers to induce recombination under certain conditions, allowing genes to be knocked out or expressed at particular times or at particular stages of development.

The key to genome editing is creating a double-stranded break(DSB) in the genome at a specific point and removing the erroneous part of the genetic code. Enzymes are then used to repair the break, rejoining the ends of the DNA or to insert the missing correct sequences in the correct location. However, while certainenzymes are effective at cutting DNA, they generally cut at several multiple sites - potentially removing DNA that researchers do not want removed. To overcome this challenge, several types of nucleases (enzymes) have been created. These are called Zinc finger nucleases (ZFNs), transcription-activator like effector nucleases (TALEN), meganucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9).

Meganucleases werediscovered in the late 1980s, they canrecognize and cut DNA sequences of between 14 and 40 base pairs. However, it can be difficult to engineer nucleases that will cut the DNA at the exact site needed. Recently, a library of sorts has been created that has allowed scientists to more easily create meganucleases that will cut in specific locations. For example, there are now meganucleases able to remove mutations to the human XPC gene which causeXeroderma pigmentosum, a disorder that predisposes the patients to skin cancer and burns when exposed to UV light.

In the 1990s, scientists used zinc-finger nucleases to improve existing gene-editing techniques. These synthetic proteins are used for gene targeting and are composed of DNA-cutting endonuclease domains fused to zinc finger domains engineered to bind a specific DNA sequence. They can be used to add or delete cut sites in the genomes of cells. Though this method has been dramatically improved, the success rate is still only about 10 percent. Even more so, this gene-editing method is costly and time-consuming to design.

Transcription activator-like effector nucleases (TALEN) share some similarities to Zinc-finger nucleases. Developed in 2009, TALENs are engineered from proteins found in nature and are capable of binding to specific DNA sequences. And while their effectiveness and efficiency parallel ZFN, they are far easier to engineer.

While ZFN and TALEN do offer effective genome editing, one drawback is that they are both time-consuming and expensive to develop. And, the process of engineering proteins is prone to error. CRISPR is so revolutionary in gene editing realms because it offers scientists a faster and simpler way to edit the genome, "with little assembly required." CRISPR/Cas9 was already on the radar of researchers in the 1990s, but its full potential was not realized until recent years.

CRISPR/Cas9 is a powerful new gene-editing technology developed separately in around 2012 by scientists Feng Zhang, Jennifer Doudna, and Emmanuelle Charpentier.

CRISPR can recognize specific genome sequences and cut them often utilizing the Cas9 protein.

CRISPR technology is based on a defense mechanism that bacteria use to fight viruses. Viruses attack cells by using the cells' own machinery to create replicas of themselves. Eventually, the cell bursts and the virus copies are released into the organism to infect new cells. However, bacteria have evolved a way to fight back by cutting up the virus' DNA. If a bacteria survives a virus attack, they copy pieces of that virus' DNA and incorporate these into its own genomes. These copies are used like mugshots to allow the bacteria to identify harmful viruses.

To keep track of this collection of "mugshots" and to keep them separate from the bacteria's own DNA, repetitive sequences of molecules are placed around each sequence that was taken from a virus. When a bacteria comes up against a virus with a sequence in its collection, the bacteria sends an enzyme to cut apart and destroy anything that matches the genetic mugshot. CRISPR allows scientists to use a similar approach, often using the protein Cas9 to cut and replace specific gene sequences.

The CRISPR technique allows scientists to quickly and efficiently alter almost any gene in any plant or animal at a low cost. Researchers already have used the technique to correct genetic diseases in animals, grow crops more resilient to a certain climate, alter pig organs for easier human transplantation, sterilize mosquitos for disease prevention, and add muscle mass to beagles.

Scientists are also able to use CRISPR to create short RNA templates that match a targeted sequence in the genome, making the process of editing far easier, efficient, cheaper, and quicker. CRISPR is currently being used to develop treatments for HIV, Duchenne muscular dystrophy, some types of blindness, and Lyme disease just to name a few.

"CRISPR is incredibly powerful. It has already brought a revolution to the day-to-day life in most laboratories. I am very hopeful that over the next decade gene editing will transition from being a primarily research tool to something that enables new treatments in the clinic,"saidNeville Sanjana, of the New York Genome Center and an assistant professor of biology, neuroscience, and physiology at New York University.

Gene-editingtools like CRISPRcould give scientists the keys to the DNA kingdom, allowing us to find "molecular mistakes" and remove them. According to Nicola Patron, a molecular and synthetic biologist at the Earlham Institute in the UK, "We are getting to a point where we can investigate different combinations of genes, control when, where, and how much they are expressed, and investigate the roles of individual bases of DNA. Understanding what DNA sequences do is what enables us to solve problems in every field of biology from curing human diseases, to growing enough healthy food, to discovering and making new medicines, to understand why some species are going extinct."

Researchers could one day remove malaria from mosquitoes. Researchers have already created mosquitoes that are resistant to malaria by deleting a specific segment of mosquitoes' DNA. Neurodegenerative diseases like Alzheimer's and Parkinson's could potentially become a thing of the past. Scientists are already working on CRISPR-based platforms to identify the genes controlling the cellular processes that lead to neurodegenerative diseases. In 2017, researchers used CRISPR to shut down the HIV virus' ability to replicate, eliminating the HIV virus from infected cells.

In 2016, a lung cancer patient in China became the first human to receive an injection of cells that had been modified using CRISPR. Researchers used CRISPR to disable a gene used by the cancer cells to divide and multiply. Without the gene, researchers hope the cancer cells will not multiply.

From agriculture to pharmaceuticals, gene editing could one day help us build a better world.

Yes and no. Designer babies seem to lead the conversation when discussing CRISPR. Ethical questions like, "Is it okay to use gene therapy on an embryo when it is impossible to get permission from the embryo for treatment?" or "What if gene therapies are too expensive and only wealthy people can access and afford them?" lay at the core of most people's concerns.

What if people use these tools to improve a child's athletic ability or height rather than use it for treating diseases?

Would this lead to genetic discrimination? Though researchers are still navigating the arguments for and against, gene editing in humans has already begun.

The US, China, andthe UKhave approved gene editing in humans for research purposes only.

Even popular gene-editing tools like CRISPR are still not perfect. In some cases, the gene-editing tools make cuts in the wrong places, and researchers are still not 100% sure how that will affect people. Properly addressing the ethical concerns and ensuring gene editing safety are still two massive mountains that scientists need to climb before we see mainstream genome treatments.

In her book, A Crack in Creation: The New Power to Control Evolution,Jennifer A. Doudas paints us a picture of a gene-edited world, stating, "Tomatoes that can sit in the pantry slowly ripening for months without rotting. Plants that can weather climate change better. Mosquitoes that are unable to transmit malaria. Ultra-muscular dogs that make fearsome partners for police and soldiers. Cows that no longer grow horns."

She adds: "These organisms might sound far-fetched, but in fact, they already exist, thanks to gene editing. And they're only the beginning. As I write this, the world around us is being revolutionized by CRISPR, whether we're ready for it or not."

It does not sound too bad, right? What is your opinion on gene-editing? How will it change the world?

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Everything You Need to Know About Genome Editing - Interesting Engineering

Recommendation and review posted by G. Smith