The Trouble With CRISPR – Strand

CRISPR is a catchy acronym that originally described a naturally occurring gene editing tool, derived from a bacterial defense mechanism against viruses. Its the name on everybodys lips in the intersecting realms of science, medicine, ethics, and politics. From the moment of its discovery, CRISPR-Cas9 looked like a miraculous solution to all of the problems that gene editing efforts have experienced over decades of trial and error. This revolutionary new gene editing technique has opened the doors to both massive scientific progress and ethical controversy. Now more than ever, were seeing that CRISPR still has massive kinks to work out. Can we ever fully understand the social and scientific implications of gene editing, and should we use it in humans before we learn how to properly harness it?

What is gene editing?

The 20th century saw genetic scientists increasingly focus their pursuits on the sub-microscopic. As science delved deeper into the human body in an attempt to uncover the molecular minutiae of life, the possibility of reaching into the cell and manipulating its genetic material began to look more and more real. Even by the 1950s, evidence had been mounting for decades that deoxyribonucleic acid (DNA), an unassuming molecule residing in a central cellular compartment called the nucleus, was the physical genetic material that passed information from parent to child. Finally, in 1953, landmark work by Kings College biochemist Rosalind Franklin allowed Cambridge researchers to reveal the structure of DNA and confirm its role in heredity once and for all.

Starting from a hesitant foundation, molecular genetics exploded in both scope and popularity over subsequent decades. With the secrets of heredity increasingly out in the open, human ambition demanded that we try to bend DNA to our willand now we can. These days, targeted gene editing techniques revolve around artificially-engineered molecular tools known as nucleases, whose earliest use was in 1996not even 50 years after the discovery of DNAs structure. Engineered nucleases are often described as molecular scissors. Fundamentally, they have two main parts: one part that finds and grabs onto the target DNA within a cell, and one part that snips a piece out of that DNA.

How CRISPR works

CRISPR is similar to other directed nucleases, but its much better at its job. The CRISPR part is secondary to the systems gene editing applications; the truly important discovery, which Jennifer Doudna made in 2012, was a protein that she called CRISPR-associated protein 9, or Cas9. This protein is the nuclease tool, the pair of molecular scissors that finds, sticks to, and snips target DNAand its more accurate than anything weve ever seen before.

In bacteria, CRISPR is a section of the genome that acts as an immune memory, storing little snippets of different viruses genetic material as DNA after failed infections, like trophies. When a once-active virus attempts to invade a bacterium, the mobile helper Cas9 copies down the relevant snippet from CRISPR in the form of ribonucleic acid, or RNA. RNA is a molecule thats virtually identical to DNA, except for one extra oxygen atom. Because of this property, the RNA sequence that Cas9 holds can pair exactly, nucleotide by nucleotide, with the viral targets DNA, making it extremely efficient at finding that DNA. With a freshly transcribed RNA guide, the bacterium can deploy Cas9 to findand cut outthe corresponding section of viral genetic material, rendering the attacker harmless.

The existence of CRISPR in bacteria was old news by 2012, but Doudnas discovery of Cas9s function was revolutionary. With a little creativity and ingenuity, such a simple and accurate nuclease can be modified to be much more than just a pair of scissors. Using synthetic RNA guides and certain tweaks, Cas9 can be used to remove specific genes, cause new insertions to genomes, tag DNA sequences with fluorescent probes, and much more.

The possibilities seem endless.What if we could go into the body of a human affected by a hereditary disease and change that persons DNA to cure them? What if we could modify reproductive germ cells in human bodies (which give rise to sperm and eggs), or make targeted genetic edits in the very first cell of an embryo? Nine months of division and multiplication later, that cell would give rise to a human being whose very nature has been deliberately tweakedand their childrens nature, and their childrens. With the accuracy and accessibility of the CRISPR/Cas9 system, these ideas arent hypotheticals. In 2019, CRISPR edits in bone marrow stem cells were successfully used to cure sickle cell anemia in a Mississippi woman. Beta thalassaemia, another genetic disease of the blood, has also been treated this way. In 2018, Chinese scientist He Jiankui even claimed that he had conferred HIV immunity upon twin girls using embryonic editing.

CRISPRs complications

At first glance, CRISPR looks like a miraclebut it isnt perfect. What if some cells were affected by edits, but others werent, creating a strange genetic mosaic in a human body? What if, in trying to modify a specific gene, we accidentally hit a different section of DNA nearby? What if we got the right gene, but it also affected a different part of the body that we didnt know about?

These problems arent hypotheticals either. So-called mosaicism and off-target editing are huge concerns among CRISPR scientists. Mosaicism is of particular concern in embryonic editing. Though CRISPR injections are carried out when an embryo is single-celled, CRISPR doesnt always appear to work until after several rounds of cell divisionand it doesnt work in every cell. If not all the cells in the body are affected by gene editing that is intended to eliminate a genetic disease, the disease could remain in the body. It may be possible to combat mosaicism with faster gene editing (so that cells dont replicate before theyve had a chance to become CRISPR-modified), altering sperm and egg cells before they meet to form an embryo, and developing more precise CRISPR gene editing which is in itself a challenge, thanks to off-target editing.

In nature, a little bit of off-target editing could actually make the CRISPR-Cas9 defense system stronger with the principle of redundancy. Flexibility in the form of imprecision could allow a bacterium to neutralize viruses whose exact genetic sequences have not yet been encountered: viruses related to, but not identical to, previous attackers. In clinical and therapeutic applications, on the other hand, precision is everything. And unfortunately, as time passes, CRISPRs level of precision seems further and further off. Preprints released just this year reveal that the frequency and magnitude of CRISPRs off-target edits in human cells may be worse than we had previously known. Large proportions of cells with massive unwanted DNA deletions, losses of entire chromosomes in experimental embryos, and shuffling of genetic sequences were observed.

Of course, not only do scientists need to avoid off-target edits, but they also need to know when such undesired edits have occurred. Off-target effects can be detected by genome sequencing and computer prediction tools, but theres no perfect way to do it yetthere may still be editing misses that were, well, missing. Off-target edits themselves could be minimized by altering the RNA transcript that Cas9 carries to make it more accurate, altering Cas9 itself, or reducing the actual amount of Cas9 protein released into the cell (though this could also reduce on-target effects). Replacing Cas9 itself with other Cas variants, like smaller and more easily deliverable CasX and CasY proteins, is a promising possibility for more efficient editing, but these candidates still run into many of the same problems as Cas9. More strategies are constantly being discovered, proposed, and explored, but were still nowhere near perfect.

Perhaps most importantly, even barring any purely technical problems, is that humans remain in sheer ignorance of much of the extent and consequences of pleiotropy, a phenomenon where a genes presence or deletion has more than one effect in the human body. Even genes whose function we think we know well might have totally unexpected additional functions. On the other side of the coin, we dont have a comprehensive understanding of how many different genetic contributors there are to any given trait or disease, much less where they lie in the genome. We dont understand the way that thousands of variations across the entire genome contribute to appearance, personality, and health. Assuming that some genes are good and others are bad is morally dangerous, and scientifically reprehensible. In reality, we are not ready for genetic determinism, and may never be.

A great responsibility

Humanity has discovered a great power, but we all know what comes with great power. Questions of which edits are necessary for health (is mild Harlequin syndrome a disease or a cosmetic concern?), whether edits are ethical (should autism and homosexuality be considered curable conditions?), and the possibility of designer babies, among others, are pertinent and require thorough discussion. We also need to realize that making these types of changes isnt our decision until we can get CRISPR right, and understand the genome well enough to target particular phenotypes. Though most scientists are aware of the difficulties of CRISPR and its use is generally tightly regulated, some scientistsand laypeopleare less careful. He Jiankuis apparent miracle HIV cure led to his arrest and imprisonment for unapproved and unethical practice. Its no great surprise that his work likely fell prey to off-target effects and mosaicism; even if he got it right, his intended change could alter cognitive function, and who knows what else?

Non-scientists are getting involved too: in 2018, self-proclaimed biohacker Josiah Zayner publicly injected his own arm with what he claimed was muscle-enhancing CRISPR. Though Zayner is one of the most vocal, hes not the only one of his kind. Quieter biohackers, untrained people without a scientific background or a good understanding of how CRISPR can go wrong, are attempting to edit themselves and even their pets.

Laypeople have an unquestionable place in science: the scientific discipline needs fresh perspectives and creativity that stuffy academics cant offer. CRISPR is still in its infancy, though. Before we know much, much more about its capabilities and consequences, there can be no place for black market gene editing kits, rogue scientists altering human embryonic and germline DNA, or basement geneticists injecting Cas9 into their dogs. Who can say what effects these interventions might have, not just on edited individuals, but on the futures of entire species?

Some say that gene editing is an act of hubris, destined to backfire spectacularly and horrendously. Others believe that its our responsibility to use CRISPR to improve lives. Which of these opinions is true depends on how science walks a narrow tightrope, though Im inclined to agree with the latterand add that our responsibility is not just to master gene editing, but to make clear and public its many faults and failings. The truth, in all its complexity, needs to overcome pop sciences oversimplification and sensationalism. Promising new advances and techniques are on the horizon, but we have a long way to go. Gene editing is no joke; humanity is playing with fire. With an incredibly accurate and accessible nuclease making its way into labs and garages across the world (while its flaws continue to be uncovered year by year), it is more important than ever for the world to understand and discuss the long-reaching consequences and responsible use of gene editing technology. CRISPR is not a miracle, but gene editing may very well be the future of humanityand its on us to keep it under control.

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The Trouble With CRISPR – Strand