CRISPR Technologies: Mining Biology

CRISPR Technologies: Mining Biology

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Hello, and welcome to our breakout session, CRISPR Technologies: Mining Biology. I'm Julie Pryor, I'm the communications director at MIT's McGovern Institute for Brain Research and I will be your moderator for this session. Our speakers for today's session are MIT alums Omar Abudayyeh and Jonathan Gootenberg.

Both Omar and Jonathan conducted their PhD work in Feng Zhang's lab at the McGovern Institute and Broad Institute of MIT and Harvard. And they are now inaugural fellows at the McGovern Institute, where they mine the biological world to develop revolutionary new CRISPR tools that both detect and treat human disease. I've had the pleasure of working with Jonathan and Omar for the past several years and I look forward to moderating today's event. Before we begin, I encourage our audience members to submit questions for Jonathan and Omar using the Poll function. To post a question you'll need to click the Polls tab above, and then click Ask a Question.

This session is brief so we'll do our best to answer as many questions as possible. So without further ado, let's get right into it. Jonathan and Omar, so let's start first by defining the term CRISPR. What exactly is CRISPR? Yeah, I guess I will go ahead and share my screen to help answer that question. So let me pull that up.

So can you, I guess, see this? Great. I can. Awesome. Yeah, so, I guess CRISPR has become quite a popular term in culture and society, but what it actually stands for is not as exciting as it sounds.

So we actually have the acronym here, it's quite a mouthful. But what it comes down to is it's really a fancy name for a bunch of repeats that were long ago noticed in bacterial genomes. I think this probably dates back to, like, 1987 when some Japanese researchers were sequencing for alkaline phosphatase genes in bacteria and noticed a bunch of these repeats, like repetitive sequences, kind of like in a sentence if you had the word that just was the same word over and over. And so it's kind of, that would be a weird sentence and in a genome, that's also a weird sequence to kind of observe. So they noted it in a paper and didn't really know any more than just saying, "Eh, we see these repeats," and it actually took a couple decades for scientists to take that observation and actually start to understand what it was. So as people started sequencing everything in the '90s and 2000s, you know, humans and organisms and bacteria and viruses, what they started noticing is these repeats are actually in a lot of different bacteria and they were also, those pieces were also in viruses.

And so people started suspecting, okay, these connections between bacteria and virus might be an immune system and it might be an interplay between bacteria and the viruses to defend the bacteria against the viruses. And so after another couple of decades of work, we now know that these CRISPR repeats, each one of these repeats separates a colored unique sequence and these unique sequences are actually different pieces of bacteria that kind of encode the history of the bacteria's sort of infection over many years, or, you know, bacteria have had these systems for billions of years. So each one of these colors is a different virus that the bacteria was exposed to and it actually became immune to as it took up a piece of the virus and uses it to actually defend against the virus.

That's kind of a long-winded explanation for, you know, CRISPR is basically bacteria's immune defense. Much like how we have antibodies to remember past infections, bacteria have their own system, so, yeah. Great, and so that has been adapted to be this genetic tool that everybody seems to know about now, and so before we get into that, let's just talk briefly about the natural world as a playground for scientists like you guys. When you say that you mine the biological world for tools to treat disease, what does that mean? Yeah, that's a great question. So I think that in biology a lot of the key advances are not made from thin air but we actually draw from a lot of our understanding of the natural world.

And here is just an illustration, this is actually the tree of life around 2015. But if you look at many of the big innovations that have caused and allowed us to make many of these strides in all these different therapies, even this week many therapies have come out, these are actually drawn from natural discoveries. So, as Omar mentioned, CRISPR is this, you know, actually an adaptive immune system in bacteria and it's been turned into a powerful genome editing tool. And it's actually not the first actual naturally occurring thing that has been turned into a genome editing tool. There's a history of other tools called TALENs, meganucleases, and zinc fingers.

These are all actually naturally occurring proteins that have been engineered. And this occurs again and again. Antibodies that are used in cancer treatments or Covid treatments, or many of the innovations that are used to actually understand biology. Many things like optogenetics which Ed Boyden at MIT uses to understand the brain at McGovern, that is actually coming from a natural, actual channel protein in algae.

So again and again we dip into this massive reservoir of biological diversity because this is one of the best ways to interact with biology and these tools that have evolved over billions of years are really good at it. Pretty much better than anything that we can make ourselves. So we find these and then we adapt them for different purposes. And it allows us to really manipulate biology to understand and treat disease in a lot of profound ways. That's great.

So that's a great way to lead into the next question, which is let's talk about CRISPR, this genetic tool, right? What does CRISPR allow us to do and how? Yeah, that's a great question. So, you know, I gave the intro about it's this fancy bacterial defense system for bacteria, but what people realized is because it can actually recognize precise stretches of different viral genomes, there must be a way for it to program itself to recognize diverse sequences. And that's a really important property that could make it useful as a tool. And so to give a little bit of the preface for why we need good gene editing tools. Between the '90s, 2000s, and up until now, sequencing has really taken off. And as we sequence more people, we start to realize that there are a lot of variance in mutations that can be quite harmful.

And here's just a number of genetic diseases we now know can be attributed to a single base and mutation to their proteins. And, of course, genetic differences can actually protect which has, that's actually been the more surprising finding. There are mutations that can make people resistant to HIV, there are mutations that can lower people's risk for Alzheimer's. There's actually been like hundreds of thousands of variances associated with different diseases that people are trying to study now, but that we don't have the right tools to actually study all these hundreds of thousands of mutations.

Here is another example with mutations involved even with plants. So it's not just human health, but you can make plants that grow better in dry environments, that grow more fruit, right? Or even bring back ancestral fruits. Like, why do we only have strawberries, blueberries, raspberries, you know, a handful of berries in the market? There's actually dozens or hundreds of other types of berries, and if you could domesticate them and to actually bring new types of fruits to the market.

So being able to manipulate genomes is a really important thing to do, but we need tools to do it. And much like if you have a book or a document, you need a good search tool because you can't go through hundreds of pages if you need to find one word. And that's very much like the case with the human genome where there's billions of bases and tens of thousands of actual words and sentences. You need a good search tool to sift through all that and manipulate that information. And so what people realized with CRISPR is because it can defend against such diverse sequences, you could actually reprogram the protein to recognize any sequence actually and literally just on your computer you can encode a CRISPR experiment to go against a gene that you might want to mutate or knock out. And in less than a week, you can actually do that experiment as a scientist, which is faster than any other technology.

Previous versions, you know, people could spend their whole PhD or postdoc just tweaking technology to modify a new gene, and CRISPR now literally makes that as easy as less than a week and it usually works, and that's why it's spread to every lab around the world and become, it's basically just a common tool in the tool set, much like you use a pipette or you know, you use something like cell lines. It's, you know, now you have CRISPR. So it's a really exciting time, I guess. So I just want to comment at, you know, having worked with you both for a couple of years now, I learned from you that CRISPR is kind of this umbrella term for a lot of different tools, right? There's many tools in the CRISPR toolkit. Can you talk a little bit about the tools that have been developed from this CRISPR technology? From the original. Yeah, yeah.

CRISPR technology? Yeah, that's a great question. So going back to the theme of biodiversity, or next slide, actually. If we think about. Just my next slide. If we think about Cas9, Cas9 is kind of this, the first genome editing tool that came from CRISPR. Because it was one of the only proteins that was known to be able to do this at the time.

It has a great property, it's a single protein, many of these different CRISPR systems actually involve multiple different proteins and that complexity makes it harder to adapt as a tool. But if you look at the diversity, I know we say that a lot, but this is really a great illustration in front of you. If you actually look where Cas9 is, and next slide, it should illustrate that. Yeah, it's only a small piece of this immense CRISPR diversity. So what we've been working on, I guess for the past five years now, is saying, "What are the things out there can we use for doing genome or other kind of neat applications beyond genome editing even?" And by understanding the diversity, can we engineer that diversity and it'll, a whole toolbox of different things to modify or measure many of the different properties that we want to and develop new therapies and diagnostics. So next slide.

Really it actually enables us to have a large CRISPR toolbox. So this is a little bit of a outline of all the different things that we've found over time. So there you can see, those little scissors in the middle left, that's Cas9.

And it allows you to cut the genome. We've also found new enzymes like Cas12, which is also a genome-editing enzyme. But it cuts in a different way that can have somewhat more precision, and it also allows us to target different places in the genome, as well as Cas13. And Cas13's a very an interesting enzyme because unlike targeting DNA, which Cas9 does, Cas13 actually allows us to bind to RNA. So that RNA strand that's on the right of this image, that's the messenger in your cell.

So it, unlike DNA, it's not permanent. It turns over and there's different strands of RNA in different cells of your body. So it allows us to actually target things that may not be as permanent, so we don't have to worry about potential things where there could be off-targets or other weird things going on.

And it also allows us to actually change different letters. So we developed two technologies that build on Cas13 called REPAIR and RESCUE, that allow us to change single letters in the RNA. That gives us, affords us a lot of precision, but it also allows us to, once again, make changes that may not be permanent.

So if we want to, say, change something temporarily it could afford us the ability to really make just a temporary change to one, not have permanent off-targets, but also to affect a bodily process for just a period of time. That could have advantages if you don't want it forever. So this actually makes this really immense spectrum of tools for changing DNA and RNA.

But we don't only want to change things. So another technology that's come out of this is a searching technology called SHERLOCK. And SHERLOCK is a detection technology.

It can be used for diagnostics. And really what it is, is it uses these programmable aspects of these proteins to bind to the nucleic acids and actually some of these proteins, such as Cas12 and Cas13, when they do that in a test tube they actually become activated. And that activation we can sense with a chemical marker. And what that means is that that is then a diagnostic, because we can program these tools to bind to that DNA or RNA and become activated. We detect that activation and we can say, "Hey, this is in that tube." And there's a lot of great properties to this.

It turns out that the SHERLOCK system is very sensitive and specific, so we can detect as little as a single molecule of DNA or RNA. And we do it very rapidly. And we developed ways to do it with, essentially, with ways that we can freeze dry it, so we can do it at point of care.

And we can detect various viruses. So we can, we've done things to detect detect Zika, and dengue, and, of course, Covid-19. In fact, SHERLOCK can detect this SARS-CoV-2 virus.

And it's a great way to have new approaches for diagnostics. So we really like to see this entire aspect of drawing from nature as a really diverse toolbox that allows us to have many different applications. And some of these have more than others. So this is a nice schematic we like to use.

Cas9 has been around for a while, we think of that at the bottom, the DNA, but Cas13 at the top, this is still a growing toolbox. I think this figure is actually a little outdated, we made it a couple years ago, I'd say there's much more than a single tool there. But all of these different tools together are really changing the way that scientists can do their research, so study the disease pathways, but also how clinicians can do therapies and diagnostics, because it's opened up an entirely new spectrum of micro-medicine. And every single one of these advances that we've talked about today is drawn by basic research into natural diversity, into these amazing bacterial systems.

So we really owe a lot to these little bugs, because they've shown to be pretty much a unending well of different tools that we can use. So, yeah, I think that it's been a pretty wild ride, honestly, to be part of and I think that it will only continue to produce more and more discoveries. Right, I was just going to say, I mean it's exciting to think about what else is actually out there. So a lot of great questions are coming in, actually, so I'd like to turn to a few of the questions that have come in from our viewers.

The first one here is, "Are CRISPR technologies being used to help study ways to stop aging?" Would you have any, Omar, I had to mute you a little bit earlier, so you might need to unmute yourself. There you go. Okay. Yeah, I am going to take off the screen share, too. But I guess the question was are these techniques being used for aging and yeah. I mean, aging is a very complex disease. Now, while people originally thought there was very simple mechanisms for it, now there's probably 10 or 12 different axes that aging can occur.

Among from your shortening of telomeres on DNA, to cells accumulating mutations, and maybe not having properly functioning genes and metabolism. And CRISPR, one way it is being helpful is to help with doing genome-wide screens, taking a very, sort of, high-level approach and saying maybe we don't know what's going on, let's knock out every single protein and gene in a cell and see how it affects a cell's ability to age properly. People are also trying to use it to modulate transcription programs. People already appreciate that with a simple cocktail of Yamanaka factors which really, these transcription factors that can rejuvenate cells. You can deliver those to cell types and rejuvenate them and people are trying to make other CRISPR-based approaches to say, "What are the rejuvenating factors that can systematically be delivered to the animal and actually rejuvenate it, and can those findings be translated to humans?" And interestingly some of these techniques are even being applied in dogs. I think people find dogs to be a great model for aging 'cause you can actually study it within a reasonable amount of time.

It's one of the top things of aging, is you can't, you know, the experiments like for with mice, for example, can take many, many years. So accelerating that sort of feedback cycle is good. And dogs are an interesting use case because they resemble a lot of the features of human aging, but also people want to make their pets live longer.

So there's kind of a (laughs) Yes! Win-win situation there. So, but yeah, I think there's a lot of exciting findings down the road for that, so. Great, thank you, Omar. We had another question before I turn to the, there's a few that have come in that are of sort of a similar theme.

But before I get to that, this one, "Can this technology be used to target cancer cells to stop the rapid mitosis process?" Yeah, now, that's a really fantastic question. And the answer is yes, you can imagine using CRISPR to inactivate genes in cancer. You can target certain essential genes to kill dividing cancer cells. This is a concept generally beyond CRISPR where there are certain dependencies in cancer that, called synthetic lethality, that in inactivation of these genes could lead to the death of the cancer that wouldn't in normal cells. One consideration with using CRISPR to target cancer as a direct therapy to do what I just illustrated, though, is that cancer is a tricky beast to fight. Because if you have dividing cancer cells, you're essentially running the process of evolution in the patient's body.

And if you deliver this very efficient drug and it kills 95% of those cells, you still have 5% of those cells to divide and reconstitute the tumor, which can be problematic. So there are, I think, a couple of approaches where people think about using CRISPR in that direct way, but there are several other ways that people are very actively using CRISPR to understand and fight cancer, and I'll touch upon two of them. One is using that same capacity to inactivate those genes and understand what are these synthetic lethalities, what are these sensitivities that cancer has. But not doing it in the patient, doing it in a dish or doing it with a patient's tumor cells that have been taken out of them and put in a dish. And by studying the cancers in these ways we can nominate new drugs, small molecules, other things that might be more drug-like properties that can then be used.

So in that way it can be a very effective tool for discovering new therapeutics. Not only serving as therapeutic, but as a basic discovery tool. And there are many companies and many different groups using that approach and I think it's a very exciting way to new ways to understand cancer biology and personalized medicine. And one other cool way, very, very interesting way that CRISPR is being used is it's intersecting with a really rapidly evolving field of immuno-oncology.

And immuno-oncology, the general field using the patient's immune system to fight cancer, has become incredibly active. The Nobel Prize was awarded two years ago now. But there's a subset of that where we can use a patient's own cells or use editing outside cells to then target cancer.

So you take the immune cells and you modify them, and then you can put them into a patient and those immune cells can home in on the cancer in that patient to destroy it in collaboration with that patient's own immune system. And CRISPR can be used to actually edit these cells. So to create these cell therapies by changing the genome of these cells to put actual genes inside of them that can allow them to identify the cancer and target and then release stimulating molecules that attract more immune cells to it.

So this is an area that many of the CRISPR companies within a block of MIT, such as CRISPR Therapeutics, and Editas and Intellia are very interested in, being able to make different cell therapies using the power of CRISPR gene editing to do cell editing and cell treatments. And I think that is going to be an area that is already incredibly exciting, but is only going to be growing more so in the next several years. Thank you, Jonathan. Time is flying and we need to wrap up.

So we've got several questions that came in about the ethics of CRISPR technologies. So can you comment at all on recent discoveries that CRISPR may cause unintended changes? It's a big question and you have about three minutes to answer it, so (laughs). I mean, yeah, there's been many, many debates about the ethics of CRISPR. I think the, sort of, National Institutes of Health and the Academy of Science have published a lot on this too. And the main two concerns are around safety and also sort of justice and equity around accessibility to these technologies. The safety one is tough.

I mean, I think, you know there's been a lot of studies that have come out that CRISPR can have off-targets, that, you know, if you are making a CRISPR edit, you know, you're activating damaged, DNA-damaged response pathways in cells that can select for things that you might not want. And I think these papers are really helpful because they guide the scientific community towards like trying to solve these issues. Like, you know, typical pharmaceutical drugs also have toxicity problems, right? You have to do clinical trials, you have to do tox studies. That's the whole point of preclinical development and Phase I trials. You've seen this, right, with the Covid vaccine.

That's why we don't have a vaccine yet, right? You have to do these large trials to make sure they're safe for people. So, you know, gene editing is just no different, it's just a much newer technology and we need to understand it more. And there's already been tremendous progress from people in the field, including work we've done in the past to engineer these proteins, right? To either make them not have off-targets, to make them more specific, to select for cells that don't have any other issues except for the intended edit you want. And so I think, you know, also a lot of the companies that are actually bringing this to patients are also working on these things and making it better and better.

So I think, you know, we're starting to see the first Phase I trials in humans. Editas has a trial, CRISPR Therapeutics has a trial. And so far the results have been quite striking, right.

There haven't been any safety issues so far, and you are seeing like basically curative responses for like sickle cell disease. Which is some of the data that's come out for the CRISPR Therapeutics trial. So I think most people are generally pretty excited to see what comes, but of course you have to take it step-by-step and take it very slowly, right. The first CRISPR paper on human cells was 2013 and seven, eight years later we're still just at the Phase I trials of just the beginning of a couple of diseases. So time will tell where we'll go, but I think people are being careful and that's the right way to do it, so, yeah.

Fantastic, Omar. You did very well in answering a difficult question in just a few minutes. So we've run out of time and I'd like to just thank everyone for joining today.

I'd especially like to thank Jonathan and Omar for their valuable time and expertise. And I encourage you all to join us for our next session with Jonathan and Omar, where we will talk more about the development of CRISPR diagnostics for Covid. The next session begins momentarily and you can find the coordinates for that session in your online agenda. Thanks very much and have a nice evening.

2020-12-18 22:30

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