Controversial gene-editing tool CRISPR “could give rise to cancer”, worrying studies find

It might sound like a cereal brand but CRISPR stands to be one of the most significant revolutions in genetics during our lifetime. In recent months, stories have emerged about researchers using CRISPR-Cas proteins to effectively edit the genetic sequences of DNA, kill HIV, “eat Zika like Pac-man” and store a GIF in the DNA of bacteria. 

Yet, despite CRISPR’s potential, it is an incredibly controversial procedure. It requires strands of DNA to be cut and completely altered in order to change a person’s genetic make up, and two new studies have linked such gene-editing technology to a rise in cancer.

The papers, one by Novartis and the other by the Karolinska Institute, published in Nature Medicine, conclude that gene therapy techniques may weaken a person’s ability to fight off tumours, and “could give rise to cancer, raising concerns about for the safety of CRISPR-based gene therapies.”

Let’s back up a little though.

 The two papers focused on the gene p53. Previous research has found that certain human tumours can’t develop if the p53 gene is working as it should. As a result, p53 acts as a natural defense mechanism to protect the genome from the kind of changes made by CRISPR-Cas9. When CRISPR-Cas9 is used to edit a person’s genetic makeup, the p53 gene jumps to its defense and effectively kills the edited cells by causing them to self-destruct. In fact, it’s this gene that has delayed the progress and effectiveness of the CRISPR technique in a number of trials. 

However, in cases where CRISPR-Cas9 has successfully made edits to a person’s genome, it suggests that the particular cell’s p53 gene is faulty or dysfunctional. This, in turn, can be linked to the body being less able to fight off cancer. In particular, a faulty p53 could cause cells to grow “uncontrollably and become cancerous”, and has been linked to instances of ovarian, colon and rectum cancer. 

“By picking cells that have successfully repaired the damaged gene we intended to fix, we might inadvertently also pick cells without functional p53,” study author Emma Haapaniemi from the Karolinska Institute explained. “If transplanted into a patient, as in gene therapy for inherited diseases, such cells could give rise to cancer, raising concerns for the safety of CRISPR-based gene therapies.”

It should be noted, however, that having a link to cancer is not the same as causing cancer and the results in these two studies are what’s known as “preliminary,” meaning further work is needed to either strengthen or dismiss the findings. The researchers are even quick to distance themselves from saying CRISPR is “dangerous.” Instead, they raise valid issues and advise companies and scientists storming ahead with clinical trials to be mindful of the link.

The studies also focus on a very particular type of CRISPR editing technique – the Cas-9 protein used for correcting diseased DNA by inserting “healthy”, edited DNA – and further work is needed to see if other forms of gene editing generate similar concerns. Indeed, in an attempt to tackle similar, previous criticisms, researchers from the Salk Institute recently reported a workaround. Rather than editing genes, their so-called epigenetic (or “above the gene”) CRISPR method would see genes switched on or off, rather than being cut. 

By modifying the epigenome, scientists were able to control a gene’s behaviour without modifying any DNA directly; gene modification rather than gene editing. In trials on mice, the scientists reversed symptoms of kidney disease, Type 1 diabetes, and a form of muscular dystrophy. It also has potential for eradicating Alzheimer’s. 

What is CRISPR-Cas9?

CRISPR-Cas9 is a genome editing tool that’s able to “cut” DNA in a targeted fashion, allowing scientists to accurately edit the building blocks of life. You’ll likely see it mentioned alongside the slightly-less-famous duo of CRISPR-Cas1 and CRISPR-Cas2 – both of which splice “cut” pieces of DNA into a bacteria’s own genome (more on that later). 

Cas9 was actually first observed in the 1980s as part of single-celled bacteria’s defence mechanisms, which ensure that the cells are able to remove unwanted intruders. Scientists have found that, by adapting the technology, they are able to target genome sequences with unprecedented speed, precision, and accuracy.

Picture CRISPR-Cas9 as like a “find and replace” search in a computer document, only instead of words, you’re editing genetic sequences. Accurately modifying DNA is a scientific holy grail, and the potential is enormous. It could be used to eradicate diseases – even hereditary ones such as cystic fibrosis, sickle-cell anemia and Huntington’s could become a thing of the past.

The name CRISPR is an acronym for the less catchy “clustered regularly interspaced short palindromic repeats”. The “Cas” part refers to “CRISPR associated”.

CRISPR-Cas9: How does it work?

CRISPR is part of certain bacteria’s naturally occurring defences. When a bacteria detects an invading virus, it is able to copy and blend segments of the foreign DNA into its own genome around CRISPR. Cas9 does the cutting, while Cas1 and Cas2 insert the exterior DNA into the cell’s genome. 

The next time the virus is spotted, CRISPR has an exact copy of the genome sequence to look out for, which is where the Cas protein comes in: it can cut the DNA up, and disable unwanted genes with incredible accuracy.

Or, as Carl Zimmer explains: “As the CRISPR region fills with virus DNA, it becomes a molecular most-wanted gallery, representing the enemies the microbe has encountered. The microbe can then use this viral DNA to turn Cas enzymes into precision-guided weapons. The microbe copies the genetic material in each spacer into an RNA molecule. Cas enzymes then take up one of the RNA molecules and cradle it. Together, the viral RNA and the Cas enzymes drift through the cell. If they encounter genetic material from a virus that matches the CRISPR RNA, the RNA latches on tightly. The Cas enzymes then chop the DNA in two, preventing the virus from replicating.”

In 2012, scientists from the University of California, Berkeley, published a groundbreaking paper showing they were able to “reprogramme” the CRISPR-Cas immune system to edit genes at will. CRISPR-Cas9 uses a specific Cas protein and a hybrid RNA that can identify and edit any gene sequence. The possibilities are huge.

In short, CRISPR lists the DNA sequences to target, and then Cas9 does the cutting. Scientists just need to programme CRISPR with the right code, and Cas9 does the rest.

This could also apply to “faulty” genes – sections currently causing problems could be removed with CRISPR-Cas9, and then replaced with healthy genetic code, theoretically solving the problem.

CRISPR-Cas9: Has it been used on humans?

Yes, in China. Using human embryos sourced from a fertility clinic, scientists tried to use CRISPR-Cas9 to edit a gene that causes beta thalassemia in every cell. It should be noted that the donor embryos used were “non-viable”, and could not have resulted in a live birth.

In any case, it failed, and failed quite badly: 86 embryos were injected, and after 48 hours and around eight cells grown, 71 survived, and 54 of those were genetically tested. Just 28 had been successfully spliced, and very few contained the genetic material the researchers intended. “If you want to do it in normal embryos, you need to be close to 100%,” lead researcher Jungiu Huang told Nature. “That’s why we stopped. We still think it’s too immature.”

On top of that, it’s extremely likely more undocumented damage was done. As the New York Times explains: “The Chinese researchers point out that in their experiment gene editing almost certainly caused more extensive damage than they documented; they did not examine the entire genomes of the embryo cells.”

As you might imagine, it caused a huge amount of controversy in the scientific community.

In November 2016, another group of Chinese scientists became the first to use CRISPR-Cas9 on an adult human, injecting a lung cancer sufferer with the patient’s immune cells modified by CRISPR to disable the PD-1 protein, theoretically making the patient’s body fight back against the cancer. 

Then, in a study published on 3 August, scientists successfully ‘edited’ human embryos, removing the faulty segment of DNA that can lead to hereditary heart disease. It was a landmark achievement and provided avenues into potentially preventing around 10,000 single mutation genetic disorders (i.e. diseases caused by a single faulty gene) in future humans. 

CRISPR-Cas9 and ethics

Even though the Chinese scientists used embryos that were not going to develop into life, there are real ethical concerns about experimenting on human embryos – indeed, just a month before the Chinese research was published, a group of American scientists urged the world not to do so.

Part of this comes down to how immature the technology is – remember that it’s only been in active use since 2012, and it would be astonishing if it was fully matured at this point. Scientists warned that it was too misunderstood and dangerous to use on humans at this point, and the Chinese research certainly vindicates this concern. Even if it worked flawlessly, there are concerns that unforeseen consequences could occur over generations.

But, even if it were 100% safe and successful, there are other ethical concerns: while nobody argues that we should hold back the potential of wiping out killer genetic diseases such as Huntington’s and cystic fibrosis, CRISPR-Cas9 potentially offers the opportunity to change anything about a person. As long as the genetic sequence is identified, in theory, it can be edited.

It’s one thing to remove life-impacting diseases before birth – it’s quite another for parents to be able to design their babies to be stronger, faster or better looking. Even if you accept that this is something people should be allowed to do, the chances are this would be heavily commercialised, ensuring only the rich could afford all the extra life advantages this would afford, massively affecting inequality.

CRISPR-Cas9: What has been done so far?

Of course, these ethical questions are a million miles away when the only recorded embryonic human experiment caused such a high-profile set-back. However, CRISPR-Cas9 is now showing extremely promising results in smaller tests.

Examples include HIV infection prevention in human cells, curing genetic mouse diseases and a pair of monkeys born with targeted mutations. 

CRISPR is also emerging as an effective means to store data within DNA. In March 2017, a pair of researchers at the New York Genome Centre published a report in the Science journal, detailing methods for storing compressed files in DNA molecules.  With the help of an algorithm for translating the files into a binary code that can be mapped onto the DNA’s nucleotide bases, the researchers were able to encode the total of six files: a 1948 academic paper, a Pioneer plaque, an operating system, a virus, the 1895 film L’Arrivée d’un train en gare de La Ciotat…and a $50 Amazon giftcard.

A few months later, a team of scientists at Harvard Medical School encoded a looping video clip into the DNA of a living E.Coli bacteria cell. The aim is to develop a system for making “molecular recorders” – DNA that’s capable of recording its own information from its surroundings. This could be used in everything from monitoring soil pollution, to revolutionising our understanding of neurological activity.

As part of DARPA’s Safe Genes program, the seven teams include a team led by Dr. Amit Choudhary at Harvard Medical School that is developing ways to control malaria-spreading mosquitoes, a second Harvard Medical School team looking to use CRISPR to detect and reverse mutations caused by radiation. A North Carolina State University team led by Dr. John Godwin aims to target gene drive systems in rats to manage invasive species, while the University of California, Berkeley want to use CRISPR to target Zika and Ebola viruses. The full list of projects and team details are available from DARPA’s website.

More recently, structural biologist Osamu Nureki from the University of Tokyo shared incredible footage of CRISPR editing DNA in real time which formed part of his team’s recent paper, published in the journal Nature Communications. The clip below shows CRISPR “searching” DNA before making its edits. You can see a strand of DNA becoming disconnected. 

The footage was originally shown to attendees of the CRISPR 2017 conference that took place in June. The paper was submitted following this conference and was published on 10 November. 

CRISPR-Cas9: Will it be coming to the UK?

Yes. Stem cell researchers in the UK sought permission to modify human embryos in an attempt to understand early human development, and reduce the likelihood of miscarriage. In February 2016, the Human Fertilisation and Embryology Authority (HFEA) granted permission.

CRISPR-Cas9: Why is CRISPR bad? 

As mentioned previously, Cas9 can only recognise genetic sequences of around 20 bases long, meaning that longer sequences cannot be targeted. More significantly, the enzyme still sometimes cuts in the wrong place. Figuring out why this is will be a significant breakthrough in itself – fixing it will be even bigger.

Then, of course, there’s the issue that CRISPR didn’t work terribly well in human embryos, and its more recent links to cancer. 

CRISPR-Cas9: Who owns it?

That isn’t a simple question to answer. It’s subject to an ongoing patent battle – surprisingly, given CRISPR is naturally occurring in certain bacteria.

Technology Review explains that, although CRISPR-Cas9 was first described in Science in 2012 by Jennifer Doudna from UC Berkeley, Feng Zhang from the Broad Institute won a patent on the technique by submitting lab notebooks proving he’d invented it first.

“First to file” patent rights means that this should be granted to Doudna, but the decision could have been decided based on “first to invent” rules, which would have favoured Zhang. In the end, the case was resolved in February 2017, when the US Patent Trial and Appeal Board resolved that UC Berkeley would be granted the patent for the use of CRISPR-Cas9 in any living cell, while Broad would get it in any eukaryotic cell – which is to say cells in plants and animals. 

Images: Petra B Fritz, VeeDunn, NIH Image Gallery, and Steve Jurvetson used under Creative Commons