Weekend Roundup: Gene Editing

The promise and peril of CRISPR and the ability to alter our genes at will

The covid-19 pandemic reached a turning point in 2021 with the widespread deployment of vaccines that reduced the severity of the virus, especially in highly vulnerable people. However, their arrival was predictably accompanied by numerous conspiracy theories, ranging from the claim that vaccines contained microchips to the notion that the mRNA vaccine technology can alter your DNA (fact check: no it doesn’t). That back and forth battle over nonsensical claims obscures that different bioengineering techniques DO allow us to edit genes.

Five years ago, the Chinese scientist He Jiankui announced—to great controversy, to put it mildly—that he had performed the first gene editing in live human embryos. He claimed to have been trying to protect the children from contracting HIV from their father by modifying the receptor the virus uses to enter cells (CCR5) with a technique called CRISPR. He’s attempt was widely viewed as reckless, proceeding too quickly, breaking international mores about human experimentation, proceeding without informed consent or regulatory approval, and with sloppy methodology that calls into question whether his use of CRISPR worked the way he intended. The twins, pseudonymously dubbed Lulu and Nana, were born apparently healthy, although the long-term consequences of their genetic change remains to be seen over time.

You may have heard a lot about CRISPR in the last few years. Its a tool that scientists can use to edit DNA. To help you understand how it works, I asked ChatGPT to explain it in basic terms (hey, nothing like a call-back to a previous article, right?):

CRISPR gene editing is a new way for scientists to make changes to genes in living things. It uses a special tool called CRISPR/Cas9 that can find and cut a specific piece of DNA, which is like the instruction manual for how an organism grows and works.

Here's how it works: First, scientists design a guide RNA that matches the DNA sequence they want to change. The guide RNA helps the CRISPR/Cas9 tool find the right spot in the DNA. Once the tool has found the right spot, it cuts the DNA. Then, the cell's natural repair process kicks in and can either fix the DNA or make changes to it.

With CRISPR, scientists can change the DNA in a living thing in a very precise way. This can be useful for many things, like helping plants resist disease or making medicine to treat genetic diseases in humans. It's still a new technology, so scientists are still learning about how to use it safely and effectively.

CRISPR as a technology has become relatively cheap and easy for scientists to use. However, “the Devil is in the details,” and there are large questions around the ethics, safety, and societal implications of using this technique to modify either adults (“somatic cell” changes, where the edits won’t be heritable) or reproductive cells or embryos (so-called “germ line” edits, which will make the changes permanent and heritable). Here are some thought-provoking articles on where gene editing is and where it may be going.

CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia

One of the strongest arguments in favor of pursuing gene editing is using it in adults (in a way that doesn’t pass down to children) to treat diseases of terrible suffering. In 2021, a landmark study in the New England Journal of Medicine showed that CRISPR could be successfully used to cure patients with the terrible blood diseases sickle cell anemia and thalassemia. From the abstract:

Transfusion-dependent β-thalassemia (TDT) and sickle cell disease (SCD) are severe monogenic diseases with severe and potentially life-threatening manifestations. BCL11A is a transcription factor that represses γ-globin expression and fetal hemoglobin in erythroid cells. We performed electroporation of CD34+ hematopoietic stem and progenitor cells obtained from healthy donors, with CRISPR-Cas9 targeting the BCL11A erythroid-specific enhancer. Approximately 80% of the alleles at this locus were modified, with no evidence of off-target editing. After undergoing myeloablation, two patients — one with TDT and the other with SCD — received autologous CD34+ cells edited with CRISPR-Cas9 targeting the same BCL11A enhancer. More than a year later, both patients had high levels of allelic editing in bone marrow and blood, increases in fetal hemoglobin that were distributed pancellularly, transfusion independence, and (in the patient with SCD) elimination of vaso-occlusive episodes. (Funded by CRISPR Therapeutics and Vertex Pharmaceuticals; ClinicalTrials.gov numbers, NCT03655678. opens in new tab for CLIMB THAL-111 and NCT03745287. opens in new tab for CLIMB SCD-121.)

Basically, these researchers and doctors obtained bone marrow stem cells and used CRISPR to repair the faulty gene that produces abnormal red blood cells, and infused the modified stem cells back into the patients. Follow-up a year later found that these patients still produced high-levels of the altered gene in their newly normalized red blood cells, no longer experience anemia or other symptoms, and no longer required transfusions or related therapies. This represents an amazing breakthrough in not only treating, but CURING, a disease that results in enormous suffering and high costs for patients, and disproportionately affects people of color.

More CRISPR In Human Subjects

This article in Science discusses another recent newsworthy gene-editing trial going on: using CRISPR to change the faulty gene PCSK9 to try and prevent myocardial infarctions, or heart attacks. The PCSK9 gene encodes a receptor for low-density lipoprotein (LDL) cholesterol, and when mutated, causes familial hypercholesterolemia. These patients develop extraordinarily high cholesterol early in life despite diet and exercise and suffer frequent heart attacks. There are drugs that target this receptor, but they are expensive and must be taken for life. Derek Lowe of Science explains:

That whacking (technical term there) is being done in Verve's case by using CRISPR base-editing technology to make a specific A-to-G change in the PCSK9 gene. That site was picked because it's not similar to anything else in the genome (so the guide RNA should take the machinery only to the place where it's being targeted), and once that single-base change is made, the expression of the PCSK9 gene will be altered at the first exon/intron boundry. That will lead to "read-through" for some of intron 1, adding a few completely unnecessary and totally disruptive amino acids to the exon 1 piece of the actual PCSK9 protein, which will leave the affected liver cells with no real PCSK9 function at all. This editing will remain for the rest of these cells' lifetimes and be passed on after mitosis: in theory, this will be a one-and-done therapy, but we'll see what happens in practice. The patients will not, though, be passing this on to their children, since this won't be editing the germ line - rather, they should just end up with permanently altered livers.

The Verve team first demonstrated this in primate studies, and I wrote about those in detail here. That was the first example of such base-editing technology in such a species, as opposed to "classic CRISPR", which goes through double-strand DNA breaks and can lead to undesired effects. And here it is in humans: the first patient has been dosed. The therapy, Verve-101, is a lipid nanoparticle formulation of mRNA to code for the needed CRISPR enzymes and a guide RNA to send them to the right spot on the genome. PCSK9's expression is heavily biased towards the liver to start with, so that makes it a perfect candidate for this sort of thing, because if you infuse LNP formulations that's where all the particles are going to pile up anyway. The same goes for the siRNA therapy, for that matter, and the earlier attempts at antisense PCSK9 treatment as well. Getting these things to work somewhere other than in the liver, now that's more of a challenge, so what we're seeing now is the low-hanging fruit. Which is fine - it's a great test bed for such ideas in general. I should note that there are other CRISPR therapies being tried in humans right now, but these are generally using earlier CRISPR techniques and/or doing the gene modification outside the patients' bodies, with later injection or transplants of modified cells (as in the sickle cell anemia trials going on now).

The CEO of Verve Therapeutics is cardiologist Dr. Sekar Kathiresan. He founded the company after a career in academia to try and use gene editing to cure heart attacks. He had personal experience with the disease after losing his brother to a myocardial infarction. Early animal studies using Verve’s gene therapy approach have been promising in terms of both safety and efficacy. Human clinical trials have begun in the UK and New Zealand, but for now have been paused in the US. Only time will tell whether or not this will succeed, but it is tantalizing to think that in a few decades, we may be living in an era where we have eradicated one of the major killers of modern man: heart attacks.

Forthcoming genetic therapies raise serious ethical questions, experts warn

So far, we have focused on gene editing in terms of treating disease and the biological science behind it. I’d like to zoom out and provide some context on the potential ethical and philosophical questions, many of which will be debated at the Third International Summit on Human Genome Editing. One concern is that the extremely high cost of treatments (early estimates suggest they may exceed $1 million per patient!) will create huge disparities in patient care and outcomes. Another is that there will inevitably be a temptation in the future to alter not just genes to prevent disease, but to select for superficial appearance like eye or skin color, or advantageous traits, such as increased muscle mass, height, or even intelligence. This raises the obvious specter of 20th century eugenics, as well as dystopian futures of a two-tier system of not only socioeconomic but also genetic stratifications:

The same technology paves the way for therapies to enhance healthy humans, to make them faster, smarter, stronger, or more resistant to disease, though enhancement is trickier than mending single faulty genes, according to Professor Ewan Birney, joint director of the European Bioinformatics Institute near Cambridge. “It is far, far harder to know the edits which will ‘improve’ rather than ‘fix’,” he said.

Regardless, some see it as inevitable. Professor Mayana Zatz at the University of São Paulo, Brazil and founder of the Brazilian Association of Muscular Dystrophy, said she was “absolutely against editing genes for enhancement”, but added: “There will always be people ready to pay for it in private clinics and it will be difficult to stop.” Baylis believes genetic enhancement is “inevitable” because so many of us are “crass capitalists, eager to embrace biocapitalism”.

There is also a great episode of the Ezra Klein Show podcast on this topic, and in fact he frames CRISPR as humanity’s “awesome, terrifying takeover of evolution. Definitely worth a listen!

Book Recommendation: “The Gene: An Intimate History”

Finally, I want to recommend a book to you: “The Gene” by Dr. Siddhartha Mukherjee. Written by a physician-scientist specializing in oncology, this book is a tour de force that takes readers through the history of genetics from Gregor Mendel experimenting with pea cross breeding in his monastery to the discovery of the double helix by Watson, Crick and Franklin to current techniques like CRISPR and others. Dr. Mukherjee explains the difference between genetic patterns that almost certainly guarantee an outcome (say the mutation for Huntington’s Disease) to those that are multifactorial, and heavily influenced by the environment (say, intelligence, heart disease, diabetes, many forms of mental illness, etc). He does not shy away from the legacy of eugenics in some of these topics, and discusses the tricky ethical dilemmas of whether or not to use some of these technologies, and how. Finally, throughout the book, he stays grounded to the personal: weaving in the stories of multiple family members who developed schizophrenia following the Partition in India and Bangladesh, and meditations on what parts of that were set in genes and what was the result of history and chance.

Bonus: Mukherjee’s newest book “The Song of the Cell: An Exploration of Medicine and the New Human” is also excellent, and serves as a primer for basic cell biology for the curious generalist. He briefly touches on several of the gene therapy trials above within.