You might be resistant to CRISPR-Cas9 – but there are still ways around it

You might be resistant to CRISPR-Cas9 – but there are still ways around it

January 14, 2018 0 By Santiago
Reading Time: 6 minutes

It looks like there could be a setback for CRISPR-Cas9 as a gene therapy option for humans. Last year ended well for the gene-editing tool, and we got one step closer to using it as a treatment for diseases. The expectations were high, to say the least. But now, according to a recent publication our immune system could render future CRISPR-Cas9 treatments ineffective. Humans might be resistant to CRISPR-Cas9 and it could even harm us.

Can you believe it? CRISPR-Cas9, the king of the genome editing tools, allowing scientists to manipulate genes since 2013, was riding the big Kahuna and was controlling it up until now. Everything looked promising and now this. You can imagine that it left the faces of some scientists and other random aficionados looking like nesting boxes. A total backlash…

But the question is, how worried should we be? Is this the end of CRISPR-Cas9 as a potential gene therapy? Has doomsday finally arrived? Let’s calm down for now and have a look at the problem in a Q&A kind of way. What really happened, what are the implications and how can this be solved? Let’s start then:


Yes, CRISPR-Cas9. It’s a genome editing tool that can be used to cut genes or other sequences of your choice in the DNA (lately you can even cut RNA with it, but let’s focus and talk only about DNA-cutting for now).

The tool is derived from the bacterial immune system. Simply put, it consists of a protein that can cut DNA, but it needs to be guided to the right spot. This is achieved by coupling the cutting protein to a small module that guides the cutting protein to the right sequence; a so-called guide RNA or guide for short. Once targeted, the DNA sequence can be cut at that specific spot which can lead to mutations, many times resulting in a total silencing of its expression.

Researchers can design guides that target almost anywhere in the DNA. So, obviously it’s useful on the lab bench. But what if we could use the tool as a therapy? What if we could change sequences that lead to diseases? This is the big idea right now and we’re pretty close to such solutions.

CRISPR-Cas9 as therapeutic tool? 

Again, yes. Beginning of last year, the company CRISPR Therapeutics applied to perform clinical trials with a CRISPR treatment against sickle cell disease and β thalasemia. Patients with these conditions have genetic mutations on a gene that expresses a subunit of adult haemoglobin. The mutation affects the oxygen transport by the blood cells.

The idea is to use CRISPR-Cas9 to target and silence another gene that represses the production of fetal haemoglobin, which is produced early in life. By allowing the fetal haemoglobin to be expressed again, the oxygen transport can be restored. No more nasty symptoms caused by these conditions.

So, what’s the problem now?

A recent publication demonstrated that some people have immunity against the protein that cuts DNA, called Cas9. This means that Cas9 is recognised as a pathogen by your immune system.

It goes from being the king of the bar to that drunk that isn’t supposed to have another drink, because he’s annoying everyone already, yet takes his chances and eventually gets kicked out by security (the immune system). 

Here’s the root of the problem: between 20% and 40% of people have developed antibodies and/or immune cells against at least one of the two bacterial strains Streptococcus pyogenes (S. pyogenes) and Streptococcus aureus (S. aureus) respectively. The most common forms of Cas9 proteins, SpCas9 and SaCas9, are (as the names suggest already) derived from these two bacteria.

Because of this, Cas9 risks to be kicked out of the bar (i.e. your body. Yes, your body is a bar, deal with it). To add to that, in the worst-case scenario, a cellular immune response could lead to systemic inflammatory responses. This last part is bad and can cause overall toxicity in the body.

Imagine the security guard now starting to beat up the rest of the guests and trashing the place, just because of this one drunk.

Why are some resistant to CRISPR-Cas9?

Apart from the innate immune system, humans also have a so called adaptive immune system. Whenever a pathogen is recognised and killed by your immune cells, a sort of “memory” is formed. This memory allows your immune system to remember and act fast next time the same pathogen infects your body. B-cells, T-cells and antibodies are all part of this adaptive immune system.

Since some people have been exposed to S. pyogenes and/or S. aureus in real life, there is a risk that we also developed an immunogenic memory and response against these. “Risk” is maybe not the right word in general terms since it’s often a good thing that we have this surveillance system. But it is a risk if you would want to undergo a CRISPR gene therapy in the future, and the only options are using SpCas9 and SaCas9.

Why is this relevant?

Easy, people being resistant to or getting sick from a therapy is bad for business; and for people of course…

Is this the end of CRISPR-Cas9?

No. For several reasons, but let’s first be clear that this does NOT impact ex vivo, in vitro or animal experiments in research. High-five lab-rats! You can keep on using this to study gene, protein and cell functions (you lucky bastards…).

The finding only affects future CRISPR-Cas9 gene therapy in multicellular organisms and I’m mostly thinking humans now. However, there’s still hope. Here are some points that can save future gene therapy with CRISPR-Cas9. Because believe me, this isn’t over.

The published study is not confirmed yet

First of all, the above-mentioned paper was published in a preprint source called BioRxiv. It has increased in popularity because now researchers can publish ongoing or unfinished work to the public. The problem is that it lacks peer review, which means that it’s not evaluated by other scientists.

In other words, before these findings are confirmed by other researchers this is still only one observation. And it might be 100% accurate, but then again, it might not be.

BioExiv is an open-access preprint server. Source: bioRxiv; Author: Cold Spring Harbor Laboratory

The CRISPR-Cas9 gene therapy tool can be further optimised

Let’s look at the bright side for a second. This whole immune system issue presents us with a chance to further develop the CRISPR tool and optimise it for future clinical trials. Obstacles and difficulties will appear, just as with any other project. But there’s nothing strange with that, we cannot get it right immediately. Several tweaks might be necessary before it can be successfully introduced as treatment for humans. We have the chance to improve it.

Other bacterial strains

Resistant to CRISPR-Cas9 other bacteria

Bacteria under a microscope.

This one is possible. Since the findings only are relevant for Cas9 from two bacteria strains (S aeurus and S pyogenes), a solution could be to use the Cas cutting-proteins from other bacteria. A bacterium that humans have never been naturally exposed to. Your immune system would have no clue about the existence of this one and would not react to it as a pathogen. Here’s an interesting option: how about bacteria living in hydrothermal vents?

Other technologies can prove valuable

This little “speedbump” can also emphasise other, maybe better suited technologies. Could it for example be time for CRISPR’s main rival TALEN to get back on stage? TALEN is a different type of genome editing tool, a bit tougher to design and produce. It was more or less abandoned by the scientific community as soon as CRISPR-Cas9 showed its face.

I’m not saying it’s ready for use as a treatment and there are probably other back-up options to be considered. Not to offend the all-in CRISPR enthusiasts, but this could allow TALEN to get cleaned, improved and to get out of its lonely bachelor room. The more options we have the better.

Repressing the immune system

Another option is the use of immunosuppressants before CRISPR gene therapy. A suppressed immune system cannot recognise the Cas9. Of course, this could result in other complications such as infection risks, but it’s an idea at least.

Check immune response status before gene therapy

Maybe it’s possible to analyse the patient’s’ immune profile before initiating clinical trials or future therapies. I don’t know. Could this be an option?

You see, hope is not up. As always with CRISPR nowadays people become so sensitive about the tiniest setback. It can be mind-blowing to observe how CRISPR can sometimes be treated as a miracle cure for everything. A science Jesus. There’s no patience with it either. Calm down people, give it time and we will be able to get the most out of it.

I started working with CRISPR-Cas9 in 2013 myself. I’m not bragging, just saying. But I also remember a couple of the smug comments from some colleagues when the first reports managed to show the possible off-target effect of CRISPR: “So, this is the end of your project then?” Colleague, please… Look where CRISPR is now.

Let’s not prepare the tombstone for CRISPR gene therapy just yet. Just like punk, CRISPR is not dead. So, until next time, keep rocking.

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