George Church, PhD, has been a towering figure in genomics for more than three decades, dating back to the early days of DNA sequencing and the inception of the Human Genome Project. Since then, his interests and influence have spread to systems and synthetic biology, genome editing, next-gen sequencing technology, and personal and consumer genomics. His group remains among the most creative of research labs, pushing CRISPR to the boundaries of areas including multiplexing technology, de-extinction, xenotransplantation, and gene drives.
Church recently sat down with Kevin Davies at Harvard Medical School to sample some of the many research highlights and ethical quandaries posed by his lab’s endeavors. (The interview has been edited for length and clarity.)
DAVIES: What are some of the key things that are going on in the Church Lab at the moment?
CHURCH: I think the theme is technology development—radical, enabling, transformative technologies, if we can. Most of them are paired with some really cool applications, a little out of reach with current technologies. We pair radical technology and radical application.
For example, GP-write is something we’ve been working on for a long time, before it was even named that. The idea is to recode genomes and the application is to make any organism resistant to all viruses, even viruses we’ve never seen before. That is recoding, which we’re doing from bacteria to mammals, humans, and plants.
Another is organoids. We make organs in pigs by making dozens, maybe 80 different changes in their genome, to make them more human-compatible and eliminate their viruses. But we could also make organs from humans. And these are surprising me, how quickly all this is going, and in particular, how you can get definite insights, even diagnostically important insights into very late-onset diseases, like Alzheimer’s, schizophrenia, and bipolar in about two to four weeks, even though the onset should take 20 to 70 years. We’re making mostly brain organoids, but we have vascularized ones, so we are keen on getting good blood flow so we can make bigger organoids.
We’re doing aging reversal. And gene drives, which allow us to cure diseases by dealing with carriers, the animal vectors. We’re also looking at other approaches to Lyme disease, including vaccines and people who are exceptionally resistant, analogous to what we’ve done with HIV.
Encoding data into DNA. The most recent breakthrough there is we encoded a terabyte of developmental data into mice. Every mouse in the colony encodes a fresh terabyte of data, and it only takes a billionth of its body.
DAVIES: You first got into genome editing before you got into CRISPR, correct?
CHURCH: Oh, way, way before. I got into recombinant DNA in the ’70s—our editing is an honorary member of the recombinant DNA family. I was one of the first employees at Biogen, which used recombinant DNA. As soon as I established my lab in 1986, we had two things—one was reading the genomes, the other was writing genomes. We did homologous recombination, which was precise editing.
Since then, we’ve gotten grade inflation and distortion of the word “editing.” But back in the ’80s, when we started working on editing, it meant doing exactly what you wanted—making exact changes, whether they’re big or small. Now it’s like, if you can mangle a gene—I call it genome vandalism—that counts as editing! Most people that are actually editing would be appalled by that definition.
DAVIES: You’ve said that CRISPR-Cas9 almost certainly will not be the last word in gene editing. There’s a lot of excitement recently around base editing [and more recently prime editing]. Do you feel fundamentally that is a better way of going about it?
CHURCH: Definitely. We’ve been involved in the deaminases, the base editors, since before CRISPR… David Liu’s group definitely took it places where we had not gone, and it was fantastic, especially the A-to-G base editor. We pioneer multiplex editing and hene consequent toxicity of CRISPR, whether it is a base editor or not—almost every editor that everybody is using is highly toxic for multiplex editing, which is my obsession, multiplex everything—my middle initial “M”!
So we did the study where we showed that we could get 26,000 edits. Our previous record was 62 edits in the pig, and we did 26,000 in human cells. And that required scrupulously getting rid of every source of nicks—not just double-strand breaks, but even nicks that you didn’t really think were nicks…
All these damages are extremely toxic in a multiplex environment, which I think is where we are going for a lot of applications. It is just that people talk themselves out of it because it just seems like science fiction. But when you’re on an exponential, science fiction becomes science fact while you are blinking. We try to stay a little bit ahead, and so we did this toxicity study, which is now published in bioRxiv.
DAVIES: We recently heard promising clinical data on Victoria Gray, the first American patient dosed for sickle-cell gene editing ex vivo, and Editas is enrolling patients for their LCA10 trial. What are your hopes for the clinical application of CRISPR over the next few years?
CHURCH: It’s great to see gene therapies making it to clinical trials, and even some emerging out of the Phase III trials victorious. Gene therapies hit a major speed bump in 1999, 2000. But now we’re seeing the field blossom. And it’s not just CRISPR, which is mainly subtractive—but also adding a gene that is missing, or too low, the latter as we are doing in our aging reversal studies—adding back genes that drop during aging.
My hopes are to greatly lower the expense. I don’t want my legacy to be the most expensive drugs in history. We’ve brought down the price of reading human genomes from $3 billion now to 600, or even zero dollars [with Veritas & Nebula]. That I am proud of. I’m much more excited about that than I am about my contribution to expensive therapies.
DAVIES: As CRISPR expands into the clinic, there seem to be three potential technical concerns. There’s the off-target question; the antibody question; and the delivery vehicle. Have those been solved for the most part, or are there still major challenges ahead?
CHURCH: I think the off-target problem has been over-stated slightly. I’m partially responsible, because academically, it is a really cool problem that we know how to solve. We and others have published a lot of papers on this. But even in the very first papers, we were getting off-targets that were close to the spontaneous mutation rate. If you’re going to worry about CRISPR, you should also worry about the spontaneous mutation rate—which is very, very low.
The immune question is hard to evaluate, since I think it is more applicable to CRISPRi and regulatory mechanisms than it is to the hit-and-run of editing. It is once and done—that’s the beauty of it. It’s not like many drugs, which you have to take for the rest of your life. From that standpoint, the immune question is exaggerated. We’re working on ways of making completely human-derived editors, for example, human integrases.
I think delivery is definitely the wave of the future. I have two startups just launched, one called Dyno and one called Ally, focused on reducing the immune response. AAV has already very low immune response, but you can take it a bit lower. The side effect of that is, you can get away with lower doses, which brings down the cost and the unintended negative consequences. We’re also working on ways that you can target it better. One of the nice things about LCA10 is, you’re not dosing the whole body, you’re just doing it in the retina. It is the first editing approved for use in vivo.
I would add to your list a fourth issue: CRISPR still does not do its job on target. I think its on-target sins are greater than its off-target sins. The base editors are not perfectly specific for a particular base, and they’re limited to transitions, As to Gs and Cs to Ts. It’s very limiting. They’re not the Holy Grail, which is precise editing. I think we should hold that concept as our actual goal.
DAVIES: Are you against the concept of germline editing? When the technology is ready, and if society gives approval, what might be some of the first genes that would be in the top group of candidates, beyond devastating disease genes?
CHURCH: I’m not even sure about devastating disease genes. I’m not wildly enthusiastic about it, I’m not opposed to it. We should be focusing on outcomes, which is what you’re asking about, rather than method. The outcome is, you don’t want there to be sickle-cell, cystic fibrosis, and thalassemia.
But, as I mentioned earlier, most of these can be cost-effectively dealt with by genetic counseling. IVF is not pleasant. Whether you’re eliminating them by IVF selection or by IVF editing, you still have to do IVF, which is not a pleasant procedure. In fact, many religions would categorize nonimplanted embryos as murder. It is neither ethically nor medically pleasant…
Most genetic diseases you could solve in an IVF clinic. If one of the parents is a double-homozygote for a dominant disease that maybe is partially penetrant, and they make it to reproductive age, but they’re not sure that their kids will, that would be one example. Infertility is another, where there is no other treatment. Germline does have three intrinsic advantages. First, it is better than other delivery systems at reaching all cells in the body. Second, after the first generation it could be free rather than $2 million for somatic gene therapy (so like smallpox an initial investment eventually results in equitable distribution if we work at it). Lastly, germline goes through a single cell while most somatic therapies impact millions of cells any one of which could become cancerous. In a single cell such an event is, a priori, a million times less likely and if derived from a clonal set of cells, could be checked by whole genome sequencing.
DAVIES: You had the cover of Science in 2017 with your company eGenesis and the CRISPR pigs, with 25 endogenous retroviral knockouts. What is the next step?
CHURCH: We’re preparing an article describing the rest of the wish list. This is a collection of everybody that has been working on this for over 20 years. We were latecomers, invited by the pioneers, and we’re very indebted to them. When we published our first CRISPR article in 2013, and they said, “Oh, that’s what we need,” because they’d originally hoped it was one or two genes, but then realized it was much more—on the order of 43 genes. We’ve now engineered in that full wish list.
We’ve already started primate preclinical trials with a nine-month survival so far. We employ an immunosuppression protocol that is completely compatible with current practice for human-to-human transplants.
DAVIES: In your ASGCT 2019 keynote, you joked about being pestered by journalists who want to know about the woolly mammoth project, and you said there’s a lot of work coming along soon. You went to Siberia last year. What was that trip like?
CHURCH: I felt it was overdue. We’ve had a very collaborative relationship with the Zimovs, who are running the most likely initial location for our cold-resistant elephants, if/when we get them—Pleistocene Park. There are two now, one near Moscow, which is more convenient for wealthy and powerful Russians, and one in Chersky, which is where I went. It’s like 50 hours to get there! It’s a beautiful experiment and park; they really have established nearly all the megafauna they need (bison, elk, musk ox, etc.). Just missing a huge herbivore that likes knocking down trees.
In addition to this site-visit, evaluating how far along they were in preparing the park, I also went to get mammoth specimens to develop a new technology for analyzing genomic structure. All the ancient DNA people say you cannot get long-range structure, and I think you can… Whenever I get to do experiments with my own hands, I’m a very happy guy. We dissected six mammoths, and then did the paperwork to get the samples back to the United States. We’ve done some of the experiments on testing. I’m not going to spoil that story but can say that we’re very excited about every aspect of the Siberia trip.
A longer version of this interview can be found in the November/December issue of The CRISPR Journal. The full interview is available in the GuidePost podcast series (available on Spotify, Stitcher, and other podcast platforms).