GRCC Science Talk: Gene Modifications and CRISPR by professor William Faber
摘要
TLDRThe presentation introduces the CRISPR-Cas9 gene editing system, highlighting its use in identifying and cutting DNA sequences in a manner akin to an adaptive immune response in bacteria. Originally derived from bacterial defense mechanisms against viruses, CRISPR's ability to edit DNA has been adapted by scientists for broader applications including treating genetic disorders like sickle cell anemia and cystic fibrosis. The speaker details how CRISPR recognizes DNA sequences using a guide RNA combined with the Cas9 protein to make precise cuts in the genome. However, challenges such as effective delivery into human cells and ethical considerations around genomic editing remain ongoing discussions within the scientific community. The talk also touches on potential uses in diagnostics, agriculture, and disease control, with a focus on balancing technological promises with moral constraints. Key points include the fundamental structure of DNA, RNA, and proteins, and how CRISPR can be an advanced tool for gene disruption and modification.
心得
- 🧬 CRISPR-Cas9 is a gene editing tool derived from bacterial systems.
- 🔬 It uses guide RNA and Cas9 protein to cut specific DNA sequences.
- 🧪 Offers potential treatments for genetic disorders like sickle cell anemia.
- 🤔 Faces ethical debates over the implications of genetic modification.
- 💡 Originally a bacterial defense mechanism against viruses.
- 💊 Promising tool for genetic diagnostics and potential therapies.
- 📈 Has significant implications for agriculture and healthcare fields.
- 🔍 Ongoing development needed for safe human applications.
- 🛠 Combines biology's understanding of DNA/RNA with biotechnological advances.
- 🚫 Potentially controversial applications include designer babies.
时间轴
- 00:00:00 - 00:05:00
The speaker begins by expressing gratitude to Tim for organizing the talk and mentions their background in DNA arrays and recognition. They introduce their interest in CRISPR, despite not being a CRISPR scientist, and highlight its role in identifying unique DNA sequences, touching on their own experience in diagnostic biomolecule analysis.
- 00:05:00 - 00:10:00
The presentation will cover: adaptive immune systems, applications of CRISPR-Cas9, and its limitations. The speaker outlines basic concepts about DNA, RNA, and proteins, noting that proteins perform essential functions in the body. They also briefly describe the structure of DNA/RNA and proteins using simple analogies and visual aids.
- 00:10:00 - 00:15:00
The speaker explains bacteria's ongoing battle with viruses, introducing bacteriophages and their method of injecting DNA into bacteria. This sets the stage for CRISPR's role as an adaptive immune response to these viral threats, evolving over years to protect bacteria from these invasions.
- 00:15:00 - 00:20:00
CRISPR is described as part of a bacterial adaptive immune system, recognizing specific viral DNA sequences and incorporating them into its genome to defend against future attacks. The speaker introduces 'CRISPR' as a repeat sequence pattern in DNA, likening it to a memory of past viral invasions that helps bacteria cut viral DNA accurately.
- 00:20:00 - 00:25:00
The Cas protein's function in the CRISPR system is highlighted, showcasing a practical demonstration with pool noodles to illustrate DNA interaction. This part of the system processes viral DNA into 'spacers' within the CRISPR array, preparing the bacteria to recognize and destroy similar viral sequences in the future.
- 00:25:00 - 00:30:00
The presentation details the formation of pre-CRISPR RNAs from the CRISPR array and explains how these RNAs are used to recognize and cut invading viral DNA. Adaptations enabling bacteria to prevent self-destruction by utilizing specific recognition sequences on viral DNA are discussed.
- 00:30:00 - 00:35:00
The discussion shifts to the applications of CRISPR, particularly in gene editing and disease treatment, using examples like sickle cell anemia and cystic fibrosis. The potential of CRISPR to modify or correct mutations in human genes is emphasized, noting the advanced diagnostic capabilities it provides.
- 00:35:00 - 00:40:00
The speaker explores CRISPR's possible applications in non-human contexts, such as altering mosquito genes to combat malaria. They also discuss potential uses in agriculture and improvements in modifying genes for beneficial traits in livestock.
- 00:40:00 - 00:45:00
Challenges with CRISPR implementation are acknowledged, focusing on delivery complexities in multicellular organisms and the potential for unintended genetic variations. The difficulties in using CRISPR as a precise gene-editing tool, particularly when applied to complex eukaryotic systems, are highlighted.
- 00:45:00 - 00:50:00
Ethical considerations in CRISPR use are discussed, particularly in germline editing, which could lead to designer traits in humans. The ethical implications of CRISPR's power to alleviate or potentially misuse this technology are debated, with a call for careful regulation and international cooperation.
- 00:50:00 - 00:58:34
Concluding the talk, the speaker highlights CRISPR's dual essence as both a powerful diagnostic tool and a means of potential genetic modification. They encourage continued dialogue on the ethical use of CRISPR to prevent misuse and promote its benefits in medical and agricultural fields.
思维导图
常见问题
What is CRISPR?
CRISPR stands for "Clustered Regularly Interspaced Short Palindromic Repeats," a system in bacteria that acts as an adaptive immune mechanism by identifying and cutting foreign DNA.
How does the CRISPR-Cas9 system work?
The CRISPR-Cas9 system uses a guide RNA to identify and bind a specific DNA sequence, where the Cas9 protein then makes a cut, effectively disabling the targeted DNA sequence.
What are some potential applications of CRISPR?
CRISPR can be used for gene editing to correct mutations, develop treatments for genetic diseases such as sickle cell anemia and cystic fibrosis, and even modify organisms like mosquitoes to control disease spread.
What are the ethical issues surrounding CRISPR?
Ethical issues include the potential for designer babies, accessibility, control over gene editing rights, and the implications of modifying human embryos.
What are the limitations of CRISPR technology?
Limitations include the challenges of delivering CRISPR into human cells, potential off-target effects, and the unpredictability of DNA repair post-editing.
What is the significance of the PAM sequence in CRISPR?
The PAM (Protospacer Adjacent Motif) sequence is crucial for identifying and cutting the correct DNA sequence, preventing the system from cutting its own DNA.
Can CRISPR be used in cancer treatment?
CRISPR holds potential for cancer treatment by potentially correcting mutations in tumor suppressor genes, though research is still ongoing.
What role does Cas9 play in the CRISPR system?
Cas9 is a protein that binds to the guide RNA, recognizing and cutting specific DNA sequences as dictated by the CRISPR process.
Can CRISPR be used to create vaccines?
While CRISPR's use in direct vaccine creation is uncertain, it can potentially be used to alter immune responses or identify viral components for diagnostics.
How does CRISPR relate to epigenetics?
CRISPR can potentially be used to demethylate DNA regions, affecting gene expression, although this application is still under exploration.
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- 00:00:00(applause)
- 00:00:02>> Yeah.
- 00:00:04All right.
- 00:00:06Well, thanks for coming.
- 00:00:08Some of my students are here, and that's just voluntary,
- 00:00:11which is amazing.
- 00:00:12So...
- 00:00:15So I wanna thank Tim for actually putting these together.
- 00:00:22You know, you get used to kinda doing the same thing
- 00:00:24over and over again.
- 00:00:25And you-- and I think it's neat to actually have something
- 00:00:29to talk about that-- I'm not a CRISPR scientist.
- 00:00:32I will tell you a little bit about what I do.
- 00:00:35But reading about it over the last past year
- 00:00:37and doing honors projects with students
- 00:00:40has really given me an opportunity
- 00:00:42to just kind of expand my mind,
- 00:00:44which, without people like Tim pushing us constantly,
- 00:00:48like, almost annoyingly... (laughing)
- 00:00:52even when I was sitting up here,
- 00:00:54he was trying to get another talk next year.
- 00:00:55So, but anyways, I think it's good.
- 00:00:59I think it's good for all of us to be thinking
- 00:01:01about new things.
- 00:01:02So first of all, why am I interested in this topic?
- 00:01:07Well, when I was in graduate school,
- 00:01:09one of the things I worked on was
- 00:01:10I did work on DNA arrays for different organisms.
- 00:01:14And I looked at recognition for DNA.
- 00:01:17And one of the things that we'll talk about today
- 00:01:19with CRISPR is that one of the things
- 00:01:21that makes it unique is it identifies
- 00:01:23unique sequences of DNA.
- 00:01:25And so, I have a past background of doing amplification
- 00:01:29and recognition of big biomolecules,
- 00:01:32and then trying to analyze them in the gas phase.
- 00:01:35So we were doing more diagnostic components with DNA.
- 00:01:39I've worked a little bit with some students
- 00:01:43and faculty out at Hope looking at doing mutations
- 00:01:46in genes and seeing how those ultimately affect an organism,
- 00:01:52and so, protein modifications.
- 00:01:54And then, I have a couple students here
- 00:01:56that did honors projects in reading this book.
- 00:02:00I found this a couple years ago--
- 00:02:01it's "A Crack in Creation."
- 00:02:03I know a few of you have read this,
- 00:02:05and it is about scientist Jennifer Doudna
- 00:02:08out at Berkeley that helped develop this tool.
- 00:02:13And she's an RNA chemist.
- 00:02:15And so, it's not like she knows bacteria
- 00:02:17or different things.
- 00:02:18She looks at structures of RNA molecules.
- 00:02:21So, and I just think it's kind of an interesting story.
- 00:02:25So if you read what I wanted to cover today,
- 00:02:29it was really looking at how this process came about,
- 00:02:32and then talking about, like,
- 00:02:33"What are some of the applications?"
- 00:02:36And so, you can ask me questions,
- 00:02:38you can comment at the end.
- 00:02:40Maybe you know something I don't know, I hope.
- 00:02:42Or you can say, like, that was the most ridiculous thing.
- 00:02:45This is actually true.
- 00:02:47So-- but I'm gonna kinda take you through this process.
- 00:02:51And you-- this has been showing up in our news
- 00:02:56over and over again, this concept of gene modification
- 00:02:59and CRISPR.
- 00:03:00And some of the things that goes on in science
- 00:03:04is when a new technique is developed,
- 00:03:07there are patent disputes.
- 00:03:08And so, you look at some of the high-power researchers
- 00:03:12in CRISPR out at Berkeley or MIT,
- 00:03:15and they fight over the uses of these things.
- 00:03:17And it's because these have strong diagnostic tools.
- 00:03:21That means money's gonna probably be made.
- 00:03:24And so, modifications around this.
- 00:03:26So people are kinda vying for patents around this.
- 00:03:29So you see it in the news around patents.
- 00:03:32If you were at the end of the year last year,
- 00:03:34you might've seen that a scientist in China
- 00:03:38had modified some embryos so that they were HIV-resistant.
- 00:03:45And so, I'll talk about that a little bit.
- 00:03:47That's a little bit controversial.
- 00:03:50And then, like I said, with patents come stocks.
- 00:03:54And you will-- I know some people that have owned these,
- 00:03:57and it's an emotional roller coaster
- 00:03:59if you own any stock around CRISPR,
- 00:04:02because it goes up and down with FDA approvals.
- 00:04:05And so, we'll talk about some of the limitations of it, too.
- 00:04:08And I'm not gonna give you stock tips, though.
- 00:04:12But what I'd like-- so the outline
- 00:04:14for my presentation is I am gonna give you
- 00:04:16a quick overview of biochemistry.
- 00:04:19And it's just so that when I talk about this system
- 00:04:22and I talk about nucleic acids or amino acids,
- 00:04:26you know what I'm-- you can at least reference back to this.
- 00:04:29And if you do wanna copy this,
- 00:04:30I'm happy to send this to you,
- 00:04:31'cause I know probably in your pastime,
- 00:04:33that's what you wanna review, is this talk.
- 00:04:36(chuckling) But I will say
- 00:04:38that I have sat through many of these.
- 00:04:40My hope is that you take like one or two things home with you.
- 00:04:44And I'll try and be short,
- 00:04:46'cause everybody loves when these get out early,
- 00:04:48and you get a cookie, it's great.
- 00:04:50So I am gonna talk a little bit about bacteria.
- 00:04:53I'm not a biologist, but-- and bacteriophage.
- 00:04:57A few definitions, because I think
- 00:04:59you can get caught up in the terminology.
- 00:05:02Adaptive immune system, I'll explain that
- 00:05:04when we get to it.
- 00:05:05And then, what are some of these applications
- 00:05:07of this CRISPR-Cas9 system?
- 00:05:10And it's fascinating.
- 00:05:14And I am gonna talk about a lot of the limitations, too,
- 00:05:17because I don't-- I--
- 00:05:20it's like any drug delivery.
- 00:05:21Getting it to cells is tricky.
- 00:05:23And so, we'll chat about that.
- 00:05:25So you know, if you've taken a general biology class
- 00:05:28or a chemistry class before, that DNA--
- 00:05:31if you ask even a little kid what DNA is,
- 00:05:34they'll say it's what makes us "us," right?
- 00:05:37And we know that from a genetic perspective,
- 00:05:41DNA codes for genes, right, and those genes
- 00:05:44can be transcribed to RNA,
- 00:05:46which is a compound that can ultimately be used
- 00:05:49and translated into proteins, okay?
- 00:05:52And proteins are what carry oxygen around our blood,
- 00:05:56they break down hydrogen peroxide in our body.
- 00:05:59All the systems that you've learned
- 00:06:01around glycolysis and the Krebs cycle,
- 00:06:03they all have a component in them.
- 00:06:05So I'm gonna talk about DNA and RNA and proteins,
- 00:06:08'cause they're all involved in this process, okay?
- 00:06:12So nucleic acids, that's where we're gonna start.
- 00:06:15And we have to have some molecules up here,
- 00:06:16because when you think of DNA,
- 00:06:19that's what you're used to, right?
- 00:06:20Seeing the double helix and the kind of two rungs of the DNA.
- 00:06:25But you know that it is made up of those four bases--
- 00:06:27adenine, thymine, guanine, and cytosine.
- 00:06:31And they pair up really specifically.
- 00:06:33And that's sort of the crux of this technique
- 00:06:36is something has to make sure that they pair up,
- 00:06:38when DNA pairs up with each other.
- 00:06:40When we recognize DNA,
- 00:06:42it's because of those As and Ts and Cs and Gs, okay?
- 00:06:47Nucleic acids can be in the form of RNA, as well.
- 00:06:50So DNA gets coded to RNA.
- 00:06:52And usually we think of this as single-stranded.
- 00:06:56But it's way more complex than that.
- 00:06:58The RNA folds up into proteins-- or excuse me,
- 00:07:00folds up into structures like this one right here,
- 00:07:03which certainly looks like it's paired up with one another.
- 00:07:07And it's why Professor Doudna actually got involved in this,
- 00:07:11because there is a lot of RNA kind of super--
- 00:07:14that secondary-type structure there, okay?
- 00:07:17So nucleic acids, RNA, and DNA.
- 00:07:21And then, when you think about proteins,
- 00:07:23and I'm gonna stop with the biochemistry here in a minute,
- 00:07:27amino acid chains are proteins.
- 00:07:29So that DNA codes for RNA, which codes for a protein.
- 00:07:33And proteins are made up of these simple little
- 00:07:36amino acids, long chains of them.
- 00:07:38In fact, the Cas9 system, the gene editing tool
- 00:07:42that I'm gonna talk about,
- 00:07:43actually has about a little over 1,300 of these,
- 00:07:47so 1,300 of these strung in a row.
- 00:07:51And so, that gets untenable from a chemicals perspective.
- 00:07:56It's hard to, say, show you 1,300 times 10
- 00:08:02or 130,000, 140,000 atoms.
- 00:08:05So we use cartoons.
- 00:08:07And you've probably seen those before,
- 00:08:09kinda those alpha helices
- 00:08:11and those sheets, those beta sheets.
- 00:08:13And the structures that I'm gonna show you
- 00:08:15are gonna be more like cartoons
- 00:08:17than they are gonna be like, sadly,
- 00:08:19than like atoms strung together, okay?
- 00:08:23Again, it's why people love biology,
- 00:08:25and then they come to chemistry
- 00:08:27and they see this, and they're like,
- 00:08:28"Can we do this again?"
- 00:08:30So here's a couple protein structures.
- 00:08:34And you know they're cartoons!
- 00:08:35They're cartoons of those alpha helices
- 00:08:38and those beta sheets.
- 00:08:39This is hemoglobin.
- 00:08:40It's kind of a low-resolution picture.
- 00:08:42This is a beautiful complex between a protein
- 00:08:45and a piece of DNA.
- 00:08:47And you can see the characteristic double helix
- 00:08:50right across the top, and then the protein over it.
- 00:08:53And I'll come back to that structure again here.
- 00:08:55I'll actually come back to both of these.
- 00:08:58So there is-- so we know we have our biomolecules,
- 00:09:03our big biomolecules of RNA and DNA and proteins.
- 00:09:07But this story sort of begins with bacteria.
- 00:09:09And over 20 years ago, I thought this
- 00:09:12was an interesting statement about bacteria.
- 00:09:15It says they don't have easy lives, right?
- 00:09:17So we eat them, and we break them down in our immune system,
- 00:09:22and I read that half the bacteria die every day,
- 00:09:27every couple days.
- 00:09:28And I've talked to a few of you about that.
- 00:09:30I'm not sure it's true.
- 00:09:31But I like the idea of it, that they're under attack.
- 00:09:35The point isn't whether or not that's statistically correct,
- 00:09:38'cause some are growing faster and some are growing slower.
- 00:09:40The fact is bacteria are under attack, right?
- 00:09:44They're under attack by our guts,
- 00:09:47as well as these viruses that exist
- 00:09:49just to break them apart and use them, really.
- 00:09:54So when you think about a virus, a bacteriophage,
- 00:09:59they land on the surface of a bacteria.
- 00:10:01And they kinda look like that cool land rover, right?
- 00:10:04Right here.
- 00:10:05And here's a nice little structure of them.
- 00:10:08And they-- if you know anything about a virus,
- 00:10:11they insert their DNA into that bacteria.
- 00:10:14And then, they use it to make more of themselves, right?
- 00:10:18And then, they lyse open and take advantage of it.
- 00:10:20So you know that the cell fate when a virus is on it
- 00:10:24is going to be death, right?
- 00:10:26It's going to use it, it's gonna burst it open,
- 00:10:29and spew out a bunch of itself again.
- 00:10:32And so, what has happened over years of evolution
- 00:10:35is it's developed a system to combat these things
- 00:10:39when they come onto their surface
- 00:10:41and inject their DNA.
- 00:10:43And that's where CRISPR comes in.
- 00:10:45What I like about this is it was over 20 years ago
- 00:10:48when it was first identified, this CRISPR system.
- 00:10:51And so, I have-- I'm gonna use pool noodles to do this,
- 00:10:55because it's a visual.
- 00:10:56And that's the only way I can really think about this system.
- 00:10:58And Tim's gonna help me here in a minute.
- 00:11:01But if you think about this as a piece of DNA--
- 00:11:04and it's a cartoon, obviously, here.
- 00:11:06But if you think of these as kind of genes
- 00:11:08and these little segments where you can see there's purple
- 00:11:11and a color and purple and a color and purple.
- 00:11:14And in science, you know that we look for patterns, right?
- 00:11:17And so, back in 1987, it was identified
- 00:11:21that this pattern was here.
- 00:11:23But then, it took 20 years to figure out
- 00:11:25that it is actually part of an adaptive immune system, okay?
- 00:11:29The adaptive immune system of these bacteria.
- 00:11:33And so, we'll get into how this actually happens here.
- 00:11:37But when you think of CRISPR, I never--
- 00:11:39I was a LASER chemist
- 00:11:41and I always forgot what "LASER" stood for.
- 00:11:44You know, it was "Light Amplification
- 00:11:45"of Stimulated Emission of Radiation."
- 00:11:47You could never-- I never remembered that.
- 00:11:49I never remember what CRISPR stands for.
- 00:11:51But the words "Clustered," right?
- 00:11:54Close together.
- 00:11:55"Regularly" means they have a specific size
- 00:11:59associated with them.
- 00:12:00"Interspaced, Short--" not long, and that's relative.
- 00:12:05I'll show you that.
- 00:12:06And then, a "Palindrome" sequence in biology
- 00:12:10and chemistry matters.
- 00:12:12So it's the same forwards and backwards.
- 00:12:14And what that does is it allows DNA or RNA
- 00:12:17to have a specific sequence.
- 00:12:19They'll pair with themselves
- 00:12:21and make hairpin structures because of it.
- 00:12:23And I'll show you a few of those.
- 00:12:24And then, "Repeats," over and over and over again.
- 00:12:27And I hope someone at the end asks me
- 00:12:30how many times does it repeat over and over again,
- 00:12:32because I'm ready for that one.
- 00:12:34So we're gonna chat a little bit about what these are.
- 00:12:38So that's what CRISPR stands for.
- 00:12:40That basically is recognizing this pattern down here,
- 00:12:44this repeated "repeat spacer, repeat spacer" sequence.
- 00:12:49Now, when we talk about Cas genes--
- 00:12:52so this is kind of a hybrid,
- 00:12:54this system that I'm gonna talk about is a system hybrid
- 00:12:58between proteins and nucleic acids,
- 00:13:01so DNA, RNA, and proteins.
- 00:13:05So something has to play the role of these genes,
- 00:13:09the proteins, everything when they interact
- 00:13:11with viral DNA or the DNA within the bacteria,
- 00:13:16it's usually a protein with it.
- 00:13:17So I'm gonna play that role as the protein.
- 00:13:20I actually specifically wore "Cas" here
- 00:13:23so that you can see this, the Cas protein.
- 00:13:25I thought to myself this morning
- 00:13:27that I ruined a perfectly good t-shirt,
- 00:13:29unless someone goes-- 'cause I'll wear it,
- 00:13:31and someone will go, "They added a C and forgot an S,"
- 00:13:34you know, when-- (audience laughing)
- 00:13:35so, but I'm going to-- I'll be--
- 00:13:38whenever we're talking about proteins,
- 00:13:39I'm gonna play that role.
- 00:13:41I'm gonna be that amino acid chain.
- 00:13:44And these Cas proteins do lots of different things.
- 00:13:47So they are nucleases, which means they cut up DNA.
- 00:13:51They separate, because if you're gonna deal
- 00:13:53with viral DNA that's coming in,
- 00:13:55you have to be able to separate it apart.
- 00:13:57And then, they do other things,
- 00:13:59like identify unique sequences, as well.
- 00:14:03So whenever I'm holding the DNA, remember, I'm the protein, okay?
- 00:14:08So let's get into what this means.
- 00:14:10So I'm a bacteria.
- 00:14:13Let's say the stage is the bacteria up here.
- 00:14:15And I'm gonna be invaded by a particular virus.
- 00:14:18And Tim's gonna be that virus.
- 00:14:21He's gonna be carrying the DNA in here.
- 00:14:23And there are basically three fundamental stages
- 00:14:27of this bacterial adaptive immune system.
- 00:14:30So they wanna get ready so that when a virus attacks them,
- 00:14:35they know what they're going to do.
- 00:14:36They'd like to destroy that viral DNA
- 00:14:38before it actually takes over and destroys that bacteria.
- 00:14:44So the first stage of this adaptive immune system
- 00:14:49is actually taking a piece of this DNA
- 00:14:53out of this virus that's coming up.
- 00:14:56So Tim, if you'd come up?
- 00:14:58What happens is when he brings-- oh, he already did it.
- 00:15:02Yeah. (chuckling)
- 00:15:03So-- yeah, and it happens-- there's a mechanism--
- 00:15:08that's all you have to do-- I appreciate it.
- 00:15:10I'm gonna call you back up for more.
- 00:15:11(audience laughing)
- 00:15:12You did your job.
- 00:15:13So I, as a Cas protein inside of this bacteria,
- 00:15:19I am-- like Cas1 and 2,
- 00:15:21I'm gonna take this, when it gets inserted
- 00:15:23into the bacteria through the cell membrane.
- 00:15:26And I'm gonna look for the specific spot on this.
- 00:15:30And you'll notice that I have this black line here.
- 00:15:32I'll explain what it is.
- 00:15:33When I recognize that, I'm actually gonna clip out
- 00:15:36a little piece of DNA from that viral DNA, okay?
- 00:15:40And then, that obviously gets cut up and it's gone.
- 00:15:44And I'm gonna insert it on the end of my CRISPR array.
- 00:15:48So remember, this is the normal bacterial genes
- 00:15:51that code for, like, me, the Cas gene,
- 00:15:54the things that are involved in this system.
- 00:15:56And then, you'll notice it's been exposed
- 00:15:57to a couple viruses.
- 00:15:59And if you don't mind holding those up.
- 00:16:01Like, those might be DNA from other viruses,
- 00:16:03like a red piece, a little turquoise-y piece,
- 00:16:07and now this yellow piece that I'm gonna add to this, okay?
- 00:16:11So I've taken a piece of DNA from a virus
- 00:16:14and incorporated it into my own DNA.
- 00:16:17I'm a bacteria, right?
- 00:16:19So now, I have this CRISPR system that has--
- 00:16:22I've just added a new repeat to it.
- 00:16:24So it's got this repeated pattern, a spacer...
- 00:16:28that's what type of DNA now?
- 00:16:32>> (indistinct). >> Viral DNA.
- 00:16:34These different viral DNA.
- 00:16:35I've actually incorporated it into my own DNA.
- 00:16:39So it matches the sequence of other viruses, right?
- 00:16:44So this yellow, if I am exposed
- 00:16:46to another yellow piece of DNA, I have a matching sequence.
- 00:16:51So I have these genes and these repeated sequences.
- 00:16:55They're not very long.
- 00:16:57And this actually is kind of a key to how this system works.
- 00:17:00You notice they're about 20 nucleotides long.
- 00:17:03And that's gonna come into play.
- 00:17:05I'm gonna talk about that here again later,
- 00:17:08because it has to do with statistics.
- 00:17:11The longer the piece you come in,
- 00:17:13the more specific it would be,
- 00:17:14because, you know, if everything has an A,
- 00:17:19then an A and a T, there's less likely,
- 00:17:22and then A, T, C, statistically it becomes less likely
- 00:17:26to come across a longer pattern.
- 00:17:30So they incorporate this 20--
- 00:17:31about 20 nucleotides, and then, this other little piece of DNA
- 00:17:35that they use over and over again,
- 00:17:37that black piece, that's about 30 nucleotides.
- 00:17:40So a total of 50 in this CRISPR array, okay?
- 00:17:46You'll notice it says Cas1 and 2 there.
- 00:17:50This is the Cas1 and 2 system.
- 00:17:53So bacteria have this gene,
- 00:17:57like those Cas genes make this particular protein.
- 00:18:00And it's pretty complex.
- 00:18:01It's got, like, lots of amino acids in it.
- 00:18:05It's a pretty big protein.
- 00:18:07But the distance between it actually determines--
- 00:18:10that's what I think is kinda elegant,
- 00:18:11it keeps cutting the exact same size
- 00:18:14of piece of DNA because of its length,
- 00:18:18the protein length of it.
- 00:18:19So it binds to viral DNA.
- 00:18:22This would be the virus.
- 00:18:23And it clips that little piece of DNA
- 00:18:26and adds it to its CRISPR sequence, okay?
- 00:18:30So DNA, according to our central dogma,
- 00:18:35becomes RNA, right?
- 00:18:37So DNA codes for RNA.
- 00:18:39So what the bacteria does is it turns this sequence now
- 00:18:43into little pieces of RNA.
- 00:18:45And this is called "pre-CRISPR RNA."
- 00:18:48And you'll notice it has different colors,
- 00:18:50and it has that little hairpin sequence, as well, okay?
- 00:18:55So what it does is it takes this off,
- 00:18:58an enzyme would come along and make this piece of RNA, okay?
- 00:19:05And then, it would break it up into little pieces
- 00:19:09like this, so it expresses these.
- 00:19:11And then, there'd need to be more of me.
- 00:19:14But I would hold these in my hand.
- 00:19:16So I am ready for these viruses to come in-- into the--
- 00:19:19so I'm gonna ask Tim to come up with a new one here.
- 00:19:24So if you think of this system now,
- 00:19:26I have this-- I'm a protein with this one,
- 00:19:31I'm a protein with this one, or I'm a protein with this one.
- 00:19:33It looks like he's coming in with some red here.
- 00:19:36So what I'm gonna do with this Cas9 system
- 00:19:41is I'm gonna come up and I'm gonna go,
- 00:19:43"All right, this matches, right?"
- 00:19:46I'm gonna look for that black line.
- 00:19:48It matches.
- 00:19:49And I'm gonna cut it.
- 00:19:52What happens to the viral DNA when it's cut?
- 00:19:56It doesn't work anymore!
- 00:19:57So now, that virus is no good anymore.
- 00:20:00So I'm gonna bring the other one up.
- 00:20:02I am this Cas9 system with this piece of DNA.
- 00:20:06I come up, I look for this sequence,
- 00:20:08I match it up, and then I cut it.
- 00:20:11And now, that virus is no good anymore.
- 00:20:13So I am just, like, a virus-destroying machine,
- 00:20:17as long as I've seen it already, right?
- 00:20:20So if I've seen it, I've incorporated it into my DNA,
- 00:20:24I make the RNA from it, and then I have this protein
- 00:20:28that, when this virus inserts a piece of DNA,
- 00:20:33this is the Cas9 system.
- 00:20:35It recognizes it.
- 00:20:37This PAM sequence is that little mark
- 00:20:39that I'm gonna talk about.
- 00:20:40And I bind to it, I make sure that it matches,
- 00:20:43and then I cut it.
- 00:20:45And when you cut viral DNA,
- 00:20:46you make it so that it can't use the machinery
- 00:20:49in the bacteria to make more of itself anymore.
- 00:20:53So that's all the CRISPR system is doing.
- 00:20:55It's taking, incorporating a short piece of DNA
- 00:20:58from a virus into its own genome,
- 00:21:01it's turning it into RNA, and turning it into a system
- 00:21:05that recognizes DNA in foreign, invading bodies, okay?
- 00:21:11So I keep talking-- and you'll notice--
- 00:21:15this is actually an important thing.
- 00:21:17So when you leave and if you ever wanna read about this
- 00:21:19before, you'll notice there's some limitations
- 00:21:22to this system, is there always has to be
- 00:21:25this little black mark.
- 00:21:27And this is usually a three-nucleotide sequence
- 00:21:30that me, as a Cas enzyme, has to recognize before I'll cut.
- 00:21:36Now, this is actually pretty important,
- 00:21:38because if you'll notice--
- 00:21:40and it doesn't matter the order of this.
- 00:21:46This worked so well in my mind. (laughing)
- 00:21:49So if you look at this sequence here...
- 00:21:54Let's put that one on.
- 00:21:55Oh, that's the problem.
- 00:21:56Hang on.
- 00:21:58We can edit this out.
- 00:22:00If you think of this sequence here,
- 00:22:03the difference between it is this piece of viral DNA
- 00:22:10has that black line on it.
- 00:22:12My DNA inside the bacteria
- 00:22:15does not have that black line.
- 00:22:17And so, you've heard of autoimmune diseases
- 00:22:20where your own immune system attacks, right,
- 00:22:23your own cells.
- 00:22:24What this little sequence--
- 00:22:25it's called the "protospacer adjacent motif"--
- 00:22:29and it's three nucleotides that the Cas gene-- me--
- 00:22:33looks for before I'll cut.
- 00:22:36So I would go along my own DNA as a bacteria,
- 00:22:39and I'd go, "Oh, my gosh, that sequence looks like
- 00:22:41"what I wanna cut."
- 00:22:42But it won't, because it doesn't have
- 00:22:44that little "PAM sequence," they call it,
- 00:22:47the "Protospacer Adjacent Motif."
- 00:22:49So you will see this if you read about the CRISPR system.
- 00:22:54That's kind of a unique thing,
- 00:22:56and it ends up being a limitation,
- 00:22:58because if you wanna cut DNA later,
- 00:23:01you can only cut when you have a unique sequence,
- 00:23:03like any random DNA, okay?
- 00:23:06So it's really a self-recognition tool
- 00:23:09for this system.
- 00:23:11By the way, finding pool noodles in February
- 00:23:15in Michigan... (chuckling)
- 00:23:19it's probably like trying to buy a sled in July.
- 00:23:21I think they probably are in the same warehouse...
- 00:23:25especially when you want the same colors, too.
- 00:23:29So they have to recognize that PAM sequence
- 00:23:32before they'll cut, okay?
- 00:23:35So back to-- so that's virally,
- 00:23:38and from a bacterial perspective, what happens.
- 00:23:41Bacteria clip out a little piece of DNA, save it.
- 00:23:45When they see something just like it, they cut it, okay?
- 00:23:49Where this system starts to get interesting
- 00:23:51is in order for this Cas9 system,
- 00:23:56this protein to function,
- 00:23:57it needs CRISPR RNA.
- 00:23:59So it needs this.
- 00:24:04It needs a sequence that matches a virus, or anything,
- 00:24:09this kind of random spacer that forms that loop,
- 00:24:13and then it also needs another piece of RNA
- 00:24:16that they don't really know exactly what it does,
- 00:24:19but they know that it helps prop up the protein,
- 00:24:22like, it's a structural thing.
- 00:24:24And I'm gonna show you an image of it here.
- 00:24:26This is an image I found from that Doudna lab
- 00:24:29where it's this Cas9 system.
- 00:24:32And what Berkeley is famous for
- 00:24:35is they took and made this into one piece of RNA.
- 00:24:39So instead of needing this and another piece of RNA
- 00:24:43for this system to work, they linked them together.
- 00:24:47And they made what's called a "guide RNA."
- 00:24:49So when you think of it from an application of,
- 00:24:52"How are we gonna modify some DNA,"
- 00:24:53they call it a "single guide" or "sgRNA."
- 00:24:56And it includes the piece that goes
- 00:24:59and recognizes the virus,
- 00:25:00and then this other piece that's a scaffold
- 00:25:03or a structural piece of RNA
- 00:25:04that seems to need to be there, okay?
- 00:25:07'Cause if you take it out, it won't work.
- 00:25:09So what scientists did at Berkeley
- 00:25:12was they made this one piece of DNA.
- 00:25:14And they have a patent on that mechanism, okay?
- 00:25:19So I wanted to show you-- the protein database
- 00:25:22is kind of a neat thing if you've ever done
- 00:25:25any DNA or RNA or protein research.
- 00:25:29I found this on their website.
- 00:25:32And I just wanna show it to you,
- 00:25:33'cause it gets this protein three-dimensionally.
- 00:25:37And I was sort of amazed they had put some music to it,
- 00:25:40which I thought was--
- 00:25:41I don't know, I thought it was kinda interesting.
- 00:25:43So just enjoy looking at the Cas9.
- 00:25:46This is the Cas9 system, which CRISPR,
- 00:25:49which we know is the array, and the Cas9 protein.
- 00:25:52This is the system that goes and finds and cuts DNA.
- 00:25:57So...
- 00:25:59(tranquil piano music)
- 00:27:08This goes on for 30 more minutes, is that okay?
- 00:27:10(audience laughing)
- 00:27:12But you can see, it's sort of an elegant system.
- 00:27:15It's got this protein, again,
- 00:27:17and you can see the different components to it.
- 00:27:19It's a pretty complex protein that binds to DNA.
- 00:27:22You saw the pieces of DNA coming in.
- 00:27:25It cuts it, okay?
- 00:27:26That's what renders the viruses inactive.
- 00:27:29And that's a big deal, because if you think about this, um...
- 00:27:37Oh, let me go to "So What?"
- 00:27:40You have a device in a bacteria, but you could pull it out,
- 00:27:44and you could say, "Well, I have this tool
- 00:27:47"that can recognize sequences of DNA.
- 00:27:49"20 base pairs is pretty unique, okay?
- 00:27:53"And it's a snipping tool
- 00:27:55"so it can recognize and cut DNA."
- 00:27:58So when people say the CRISPR-Cas9 system,
- 00:28:00that's what they're talking about,
- 00:28:02a piece of-- well, a bacterial protein
- 00:28:06that can recognize, with a piece of RNA in it,
- 00:28:09that can recognize and cut other DNA.
- 00:28:13So that's what we're talking about.
- 00:28:14And I like that from, like, Word 2000.
- 00:28:20So what happens when you cut DNA?
- 00:28:22So why do we care about this?
- 00:28:25So when you cut DNA, a couple things can happen
- 00:28:27in eukaryotic cells.
- 00:28:30If you just cut it, it sorta scrambles.
- 00:28:33If there's nothing that it can match off of,
- 00:28:36what happens is it will-- they call them "indels,"
- 00:28:39where they have insertions and deletions into the DNA.
- 00:28:43So if you have a gene that, let's say,
- 00:28:45it is coding for a protein that you don't want it
- 00:28:47to code for anymore.
- 00:28:49If you go in with a CRISPR-Cas9 system and cut it,
- 00:28:53it's gonna screw up all those bases in that DNA.
- 00:28:57And it's gonna make it so the protein doesn't exist anymore,
- 00:28:59the protein doesn't work anymore.
- 00:29:02But even more interesting is if you put in this Cas9 system
- 00:29:07to cut a piece of DNA
- 00:29:08and you have a piece of DNA that's correct,
- 00:29:12that has a difference in it,
- 00:29:14what it will do is it'll go through
- 00:29:16homologous directed repair
- 00:29:18and actually make a new piece of DNA that's right or correct.
- 00:29:22So it's a way of correcting problems in the DNA, okay?
- 00:29:27And I'm gonna give you a couple examples of this.
- 00:29:30If you've taken a biology class or you've learned
- 00:29:33about sickle cell anemia, okay?
- 00:29:36Sickle cell anemia, if you look over here--
- 00:29:38and that was why I started with RNA to DNA.
- 00:29:41This is a normal gene for DNA
- 00:29:45for someone without sickle cell anemia.
- 00:29:47And if you notice, it says G-A-G.
- 00:29:51If you have sickle cell, you don't have G-A-G.
- 00:29:54You have G-T-G, okay?
- 00:29:56It's a one base pair difference.
- 00:29:59So if I could design a CRISPR system
- 00:30:02that recognized an area around here and cut it,
- 00:30:06then I had a template that I put in with it,
- 00:30:09it would do exactly what this does.
- 00:30:13So it would cut it, it would find a new piece of DNA
- 00:30:16with the corrected base, and it would fix it.
- 00:30:21Now, I put in this slide, one of the things
- 00:30:23they've tried to do is--
- 00:30:24"heterozygous" means you have one correct pair
- 00:30:29and one incorrect pair.
- 00:30:30So they have shown that in certain cells,
- 00:30:34they can cut it, and it will use the other correct allele--
- 00:30:38or excuse me, the correct piece of DNA.
- 00:30:40So we have two copies of DNA, right, humans do.
- 00:30:43It cuts the bad one,
- 00:30:45and it will use the corrected one to make it--
- 00:30:49to fix it, in a sense.
- 00:30:50So it'll switch that T back to an A.
- 00:30:53And then, hopefully, the central dogma
- 00:30:55is DNA becomes RNA becomes protein.
- 00:30:58Hopefully now that protein
- 00:31:00doesn't have that weird amino acid.
- 00:31:02And it's not weird,
- 00:31:03it just doesn't have the same charge on it.
- 00:31:05And so, you get those sickle cells.
- 00:31:07And it's a horrible disease.
- 00:31:12So modifying DNA in a eukaryotic cell
- 00:31:16would be a big thing.
- 00:31:17If you can cut it, it would repair itself.
- 00:31:20Another example-- and this has actually been done
- 00:31:22in what's called an "organoid."
- 00:31:25Tim and I have worked a little with a researcher
- 00:31:28over at MSU.
- 00:31:29He does some CRISPR research.
- 00:31:32And I visited his lab to see how he was doing this work.
- 00:31:36And they build-- they take cells
- 00:31:40and they turn them into stem cells
- 00:31:42and grow little organs in a Petri dish, okay?
- 00:31:45And that's really neat.
- 00:31:48But what they can do is, if you have cystic fibrosis,
- 00:31:52you will often-- one of the most common ways
- 00:31:54you have cystic fibrosis
- 00:31:55is you have a three base pair deletion in your DNA.
- 00:31:59So you're missing-- I don't remember what it is--
- 00:32:02A-A-A, I think it is.
- 00:32:05But if you're missing that, you could go in
- 00:32:06and cut that region, have a corrected piece,
- 00:32:10and it would fix that.
- 00:32:12And it's just a teeny little deletion,
- 00:32:15but it makes a huge difference.
- 00:32:16If you know anybody that has CF,
- 00:32:19it's based on this membrane protein
- 00:32:23that helps regulate water and chloride ions
- 00:32:26in and out of the cell.
- 00:32:28And they get thicker mucus and it clogs those pores.
- 00:32:33And a devastating disease that could--
- 00:32:36if you could get a CRISPR system in
- 00:32:38to cut that DNA with the correct template,
- 00:32:41you could fix that.
- 00:32:44This is another example of non-human,
- 00:32:48but where they would have-- they have done this, actually.
- 00:32:52They haven't released these, I'm sure--
- 00:32:54can you imagine doing bug research?
- 00:32:56Like flying bug research?
- 00:32:59You know they're out, right? (laughing)
- 00:33:02It would be-- I just think that would be
- 00:33:06an interesting lab to visit,
- 00:33:07how they contain all the mosquitoes.
- 00:33:10But what they do is they do gene modifications
- 00:33:12to make the females have more male characteristics.
- 00:33:16And so, their sexual organs are deformed,
- 00:33:18and their mouths are deformed.
- 00:33:20And these are specific mosquitoes that carry malaria.
- 00:33:25And so, if they release these out into the wild, right--
- 00:33:29I like this-- I just like this image of mosquitoes
- 00:33:32deciding they're gonna pass their genes along.
- 00:33:35And they call it a "gene drive,"
- 00:33:39where they have baby mosquitoes,
- 00:33:43and those baby mosquitoes all have these deformed components.
- 00:33:47And so, they don't pass malaria.
- 00:33:49And that might not be a big deal to us,
- 00:33:51because we don't live with that many mosquito-borne illnesses.
- 00:33:57But in a country where there's a lot of malaria,
- 00:34:00this would matter, right?
- 00:34:04There are two other types of systems
- 00:34:06that could potentially be used here.
- 00:34:08It's called "CRISPR interference."
- 00:34:10So what they do is they take this Cas9 protein,
- 00:34:14and remember, it recognizes pieces of DNA.
- 00:34:18And they can take this, and they can lay it on the DNA
- 00:34:22and then just have it adhere there.
- 00:34:24So they turn off the part of it that cuts the DNA.
- 00:34:27So all they do is use it as a recognition tool.
- 00:34:30And you can change the structure of it
- 00:34:32to make it bind more tightly.
- 00:34:34And it can go and it can interfere,
- 00:34:36and basically stop genes from being expressed.
- 00:34:40So you don't go from DNA to RNA anymore,
- 00:34:42'cause there's this stinking Cas9 protein bonded to it.
- 00:34:49So you can up-- you can upreg-- you can downregulate genes.
- 00:34:53And then, they can also upregulate genes,
- 00:34:56where they use the same CRISPR system,
- 00:34:57they shut off the ability for it to cut,
- 00:35:00but they go and they bind to a specific region
- 00:35:02of DNA with other components on it.
- 00:35:05So they can modify the Cas to attract things
- 00:35:08that will make the gene upregulate,
- 00:35:10so make more genes be created.
- 00:35:14And they've done this.
- 00:35:15They've done this on some organisms,
- 00:35:18and they've done this on mice to increase
- 00:35:20the muscle mass.
- 00:35:21So they turn on the genes that make them build
- 00:35:23more and more muscle.
- 00:35:24So from a food distribution perspective,
- 00:35:27that might be beneficial, right?
- 00:35:29Your organisms create more meat,
- 00:35:31if that's the type of thing you're into,
- 00:35:33and you could feed more people.
- 00:35:39So why aren't we seeing this, like, everywhere?
- 00:35:43I think that the main component--
- 00:35:45and I've read a lot about this, to how you get this into cells.
- 00:35:50So think about what you have to deliver.
- 00:35:52Me, a Cas protein, you have to deliver me.
- 00:35:55You wouldn't wanna deliver a Cas piece of DNA,
- 00:35:58'cause you don't want a bunch of me.
- 00:36:00I'll keep cutting DNA.
- 00:36:02So you don't want me in there.
- 00:36:04So you wanna deliver a protein
- 00:36:06and then that single guide piece of RNA, right?
- 00:36:10So those are the two things you need
- 00:36:11to recognize and cut DNA, and possibly a template, right?
- 00:36:15The correct version.
- 00:36:17So if I'm homozygous, I have a correct version,
- 00:36:21but if I'm not, I need to deliver
- 00:36:23all these things to cells to make this work.
- 00:36:27So they've thought about using viruses,
- 00:36:29human viruses, to deliver this.
- 00:36:31But those typically deliver DNA or RNA.
- 00:36:35But there is sort of some promising work
- 00:36:37around these exosomes.
- 00:36:39And they're basically lipid protein--
- 00:36:42or excuse me, lipid membranes that,
- 00:36:45in this little packet in the middle,
- 00:36:47they could put a protein.
- 00:36:49They could put a piece of RNA in there.
- 00:36:52And then, it would kind of assemble
- 00:36:53when it made it to the cell.
- 00:36:56Easier said than done, though,
- 00:36:57because what happens?
- 00:37:00Our body mounts immune responses to these things.
- 00:37:03So it's tricky.
- 00:37:06When I think of this happening, like,
- 00:37:09"Oh, this is gonna solve cystic fibrosis
- 00:37:11"and sickle cell anemia and all the other genetic diseases,"
- 00:37:14the hardest thing is getting it to the cell, okay?
- 00:37:18I have read a couple promising things.
- 00:37:19If you could remove the cells
- 00:37:21and then put them back in, like, that has some real promise,
- 00:37:25because if you can take the cells
- 00:37:27out of a human, and modify them,
- 00:37:29and put them back in, that's a little easier.
- 00:37:32But again, you don't want Cas9 in there constantly.
- 00:37:37It's just gonna continue to cut DNA over and over again.
- 00:37:42So I opened with that slide on that Chinese scientist
- 00:37:46that modified embryos.
- 00:37:49That's pretty controversial, right?
- 00:37:51Like, to modify a undeveloped organism...
- 00:37:59we probably all could have an argument about that,
- 00:38:01whether or not that should be done,
- 00:38:03because we might say, "Well, all we're gonna use this for
- 00:38:06"is to get rid of CF and sickle cell anemia."
- 00:38:09But you might say, "Well, I want my offspring
- 00:38:12"to have big arms or strong arms or whatever,
- 00:38:17"whatever, blue eyes."
- 00:38:19You might-- that might get a little more complex.
- 00:38:23But you get that that's the best place to do it, right?
- 00:38:26Because you've got one cell you have to modify
- 00:38:29instead of-- I mean, I've read--
- 00:38:32they use the analogy in this book, like,
- 00:38:35"When do you edit the paper?"
- 00:38:37Before it goes to print, right?
- 00:38:39You edit the paper before it goes to print
- 00:38:41because once you, if you modify one cell,
- 00:38:45that's fantastic.
- 00:38:46But once it has produced a baby,
- 00:38:49it is millions and billions of cells.
- 00:38:52So it's a little more difficult to do.
- 00:38:54So the differences between germline cells,
- 00:38:58egg and sperm, or somatic cells-- skin, organs.
- 00:39:02It's a little less controversial
- 00:39:03because you don't have to--
- 00:39:07you know, you're not gonna pass that on to offspring,
- 00:39:09but it's way more difficult.
- 00:39:13There also is, if you're reading about this
- 00:39:17a little bit more, DNA repair can be pretty unpredictable.
- 00:39:22So it's beautiful that I showed those two slides,
- 00:39:25like you get insertions and deletions,
- 00:39:27and you get a correction if you have a correct template.
- 00:39:30But it doesn't always work that way.
- 00:39:34That Chinese scientist, what he did was...
- 00:39:39there is a protein that HIV will bind to on the cells,
- 00:39:44our immune cells.
- 00:39:45And you know, there's a certain amount of people
- 00:39:49in our population that are immune to HIV.
- 00:39:51You can be exposed to it, and they have a mutation
- 00:39:54on that protein in their membranes
- 00:39:58so the HIV virus can't bind to it.
- 00:40:00So what he did was he knocked out that P,
- 00:40:04he modified that gene so that they have a modified protein.
- 00:40:08Now, that's problematic because that mutation happened
- 00:40:12probably millions of years ago.
- 00:40:14And we have other genes-- we don't know a lot
- 00:40:17about that gene that HIV connects to.
- 00:40:20So if it modified just through the natural process of evolution,
- 00:40:26if other genes took its place,
- 00:40:29it if was important,
- 00:40:30other genes actually compensate for it being mutated.
- 00:40:34And so, when you just go in and blindly modify one protein
- 00:40:38and you don't know a lot about it,
- 00:40:40there could be other consequences for those children
- 00:40:44that were born that we don't know about, okay?
- 00:40:47So it is pretty controversial for a reason, right?
- 00:40:52So kind of in conclusion,
- 00:40:55this is an adaptive bacterial immune system.
- 00:40:59Bacteria are exposed to viruses,
- 00:41:00they clip out little pieces of DNA,
- 00:41:03and then they create a protein-RNA system
- 00:41:07that can recognize and cut DNA.
- 00:41:11We know that DNA can repair itself
- 00:41:14if there's a template.
- 00:41:15So cutting it, there's a chance
- 00:41:17that it could fix little mutations.
- 00:41:20I think a lot of the interesting research
- 00:41:22around binding without cutting is really important,
- 00:41:26because we can upregulate genes and downregulate genes.
- 00:41:30But right now, the biggest issue, I think,
- 00:41:33is delivering this to cells.
- 00:41:35And so, that's why egg and sperm cells,
- 00:41:40pretty easy to access.
- 00:41:41But if we wanted to go in and modify my lung cells
- 00:41:45because I had CF, that might be a little trickier to do.
- 00:41:48So that is-- I will give you a little recommendation.
- 00:41:53If you wanna read a pretty good book,
- 00:41:55Jennifer Doudna, again, at Berkeley,
- 00:41:57RNA chemist, biologist, chemist...
- 00:42:01we're all on the same team, right?
- 00:42:04They, uh-- she has a--
- 00:42:06it kind of takes this really good perspective on this,
- 00:42:09because she looks at the power of this
- 00:42:12and worries about it from an ethics standpoint.
- 00:42:15And I think she's trying to get in front of it,
- 00:42:19as a community, right?
- 00:42:21And just because if we were to pass laws
- 00:42:24or make regulations on this,
- 00:42:26it's a big deal if we do it in our country.
- 00:42:28Other countries could do it, right?
- 00:42:30And so, science isn't limited,
- 00:42:32we don't limit science based on our laws
- 00:42:35in one country.
- 00:42:36But she just wants to open the conversation.
- 00:42:39I think she does a nice job kind of outlining this process
- 00:42:43and then talking about what it could become.
- 00:42:48Tim mentioned-- well, actually, Taylor mentioned
- 00:42:52that sometimes we think about this
- 00:42:55in terms of, like, if we were to make a designer baby
- 00:42:59or something like that,
- 00:43:00only people with money would be able to do something like that.
- 00:43:04Where, in turn, she makes the argument
- 00:43:06in her book that we maybe can't afford NOT to do this,
- 00:43:12because if you could cure a disease
- 00:43:15or fix something before it becomes a problem,
- 00:43:17that might be cheaper in the long run.
- 00:43:19And so, there are a lot of ethics around it.
- 00:43:21But it's kind of a fascinating topic,
- 00:43:23and I appreciate Tim for letting me come and talk about it.
- 00:43:26And I'll take any questions you have.
- 00:43:29So...
- 00:43:30(applause)
- 00:43:32I think I got done-- yeah, it's good, good timing.
- 00:43:37>> I have a microphone. >> All right!
- 00:43:44When I interviewed for my job 20 years ago,
- 00:43:47Tom asked a pretty mean question,
- 00:43:50I'm not gonna lie. (laughing)
- 00:43:51>> Now, I'm gonna show my ignorance here.
- 00:43:53So when a bacteria reproduces, replicates,
- 00:43:56I don't know how bacteria do this,
- 00:43:58does it pass on its DNA
- 00:44:03that it's been changing all along here?
- 00:44:06>> Yeah. >> So isn't that getting, like,
- 00:44:08ungainly large after it keeps getting--
- 00:44:11>> Ah, that's a good question-- it's a good way to ask this.
- 00:44:12So interestingly, this is all over the place.
- 00:44:15There are, like, dozens and dozens of CRISPR systems.
- 00:44:20Like, there's type 1, type 2, type 3.
- 00:44:22Some of them recognize RNA.
- 00:44:25A typical bacteria only has--
- 00:44:28that's a pretty dynamic thing.
- 00:44:30So they might only have three to five CRISPR arrays.
- 00:44:34I mean, they might not have many incorporated viral DNA
- 00:44:38in their DNA.
- 00:44:40So they pass on what they have
- 00:44:42when they replicate their own DNA.
- 00:44:44But I have also read that other organisms
- 00:44:46can have hundreds of spacers in there, yeah.
- 00:44:50So yeah, but there are limits.
- 00:44:52So if you look at the rate--
- 00:44:54it depends on what they're being exposed to, as well.
- 00:44:57So it actually runs the other way.
- 00:45:00You have the Cas genes, and they add in the middle...
- 00:45:03and the things that get further down,
- 00:45:05they sooner or later get clipped off
- 00:45:07because they're not being used as much.
- 00:45:09So it can turn it over.
- 00:45:11It's not like once it's in the CRISPR array,
- 00:45:13it's always there.
- 00:45:14So they do clip them out after a while.
- 00:45:17So, that's a good question.
- 00:45:20I like that one-- I knew the answer.
- 00:45:21You redeemed yourself after 20 years. (laughing)
- 00:45:25>> Any other questions?
- 00:45:36>> Could I ask you to comment a little further
- 00:45:38on some of the ethical issues
- 00:45:41that Jennifer Doudna brings up in the book?
- 00:45:47I can give a specific prompt, if you like.
- 00:45:50>> Oh, go ahead. >> Yeah, yeah.
- 00:45:51I was curious if there's any talk
- 00:45:56about who should have the right to control gene editing.
- 00:46:00Of course, 'cause you'd ask,
- 00:46:01do you wanna hand it off to the government?
- 00:46:03Do you want patented gene sequences
- 00:46:05or gene editing tools, like--
- 00:46:09what is-- does she have any commentary on this?
- 00:46:13>> She does.
- 00:46:14Primarily what-- she does talk a lot about access to it.
- 00:46:19And again, from-- it is more that--
- 00:46:23so initially, she was a little horrified by it
- 00:46:27because she thought of what could potentially come about
- 00:46:30from this technique.
- 00:46:32But then, she got to this place where she thought,
- 00:46:35"If we can do this, why don't we?"
- 00:46:37Because it is sort of about...
- 00:46:42easing human suffering.
- 00:46:43And so, she comments mostly on that.
- 00:46:48She doesn't get-- obviously, there's economic
- 00:46:51and different components to it.
- 00:46:52And she talks about that, too.
- 00:46:54But it's primarily on basically costs.
- 00:46:58And she-- I mean, I think she's trying to get people
- 00:47:01to talk about this from the scientific community,
- 00:47:04because it is tricky.
- 00:47:05Who does run it?
- 00:47:06Once people have patents on this,
- 00:47:11they have a patent, and so... (chuckling)
- 00:47:14and I think that that's why she's kinda having the discussion.
- 00:47:17'Cause right now, there are private companies
- 00:47:18that own these patents.
- 00:47:21I don't know if I answered your question.
- 00:47:23It's pretty big.
- 00:47:25>> (indistinct). >> Okay, yeah.
- 00:47:30>> (indistinct). >> Yeah?
- 00:47:31>> I have a question pertaining to cancer.
- 00:47:34Did you-- in your readings, did you come across
- 00:47:37any researchers who were trying to insert
- 00:47:40the sequence that will allow cancer cells
- 00:47:43to remember that they need to go into apoptosis?
- 00:47:48>> Yeah, they have a lot of hopes with cancer cells.
- 00:47:53In fact, over at Michigan State,
- 00:47:56that's one of the interesting things,
- 00:47:58is there's a common mutation in cancer cells.
- 00:48:01It's a tumor suppressor gene that gets mutated.
- 00:48:06And apparently, the cell type
- 00:48:08that you can do CRISPR in
- 00:48:11matters whether it's a cancer or non-cancer cell.
- 00:48:14It's easier to do it when they're cancer cells
- 00:48:17or when they have a particular mutation,
- 00:48:20which makes some sense.
- 00:48:21But absolutely, those are the things that,
- 00:48:23if you can sequence it and find out where the errors are,
- 00:48:27those are absolutely techniques that they could use.
- 00:48:30Like, turn on that process again,
- 00:48:33because something has been mutated
- 00:48:35that it's not getting that signal to destroy itself.
- 00:48:38Yeah, for sure.
- 00:48:45>> So I know you brought up autoimmune diseases
- 00:48:48at the beginning of the talk,
- 00:48:50but I just wanted to ask you to expand on that a little bit.
- 00:48:53What are the hope-- what's the hope
- 00:48:56with CRISPR technology in the treatment
- 00:48:59of autoimmune diseases,
- 00:49:00and is there actually any scientific evidence
- 00:49:03that that could come about?
- 00:49:05>> Yeah, that I actually don't know.
- 00:49:06I will tell you, I was making the analogy
- 00:49:09that the reason they have this little--
- 00:49:15like, the Cas proteins actually recognize
- 00:49:17this little piece right here
- 00:49:19so that they don't go and cut their own DNA up.
- 00:49:22So they don't-- the bacteria don't really have,
- 00:49:25in a sense, an autoimmune disease
- 00:49:26where they'll cut, 'cause the bacteria
- 00:49:28has no interest in cutting itself up.
- 00:49:31So it has a mechanism where the piece
- 00:49:34it nicks out of a virus,
- 00:49:36it has to be next to a specific sequence.
- 00:49:39And the most common one is N,
- 00:49:41which just means any amino acid--
- 00:49:43or excuse me, any nucleic acid, G-G.
- 00:49:46And so, it'll search along here, see A-G-G,
- 00:49:50and then clip out this piece to incorporate into its DNA.
- 00:49:53But it doesn't put N-G-G into its DNA,
- 00:49:56because it would go and cut itself then.
- 00:49:59And so, it was more of a-- I haven't read much
- 00:50:03about autoimmune diseases in CRISPR, though.
- 00:50:07I mean, autoimmune diseases are such--
- 00:50:09are typically where you have a component
- 00:50:14that's self-recognizing.
- 00:50:15So I guess, could you go and cleave out
- 00:50:18that section in your immune system?
- 00:50:21Boy, potentially.
- 00:50:23But I'm sorry, I don't know that much about it.
- 00:50:27Sounds like you have a project now. (chuckling)
- 00:50:31Other questions?
- 00:50:35Oh.
- 00:50:39>> I was wondering-- it's kind of a two-parter--
- 00:50:41is CRISPR interference
- 00:50:43preferred in any way over using an siRNA or microRNAs,
- 00:50:48or is that like a quality check step
- 00:50:52before proceeding on, like seeing a downregulation
- 00:50:55in the protein before actually trying to modify it?
- 00:50:58>> Yeah, I think, that's pretty specific.
- 00:51:02I know RNA interference is--
- 00:51:06I would think that this could have a higher affinity
- 00:51:08for a piece of DNA, 'cause you know that any bacteria--
- 00:51:13or excuse me, any protein,
- 00:51:14you can do kinetic studies on it
- 00:51:16where you modify it and see how strongly
- 00:51:19it bonds to a segment of DNA.
- 00:51:21So I would guess that CRISPR would give you kind of a control
- 00:51:25that just throwing another piece of RNA in it
- 00:51:27to interfere wouldn't provide, right?
- 00:51:30So I would think that this would be a preferred mechanism.
- 00:51:33But I know there are definitely therapeutic treatments
- 00:51:38where they just are putting RNA to interfere with proteins
- 00:51:42being created, so I would think this would be preferred.
- 00:51:47Does that answer your question?
- 00:51:48Was there another part of it?
- 00:51:54>> Any other questions? >> Oh, Taylor.
- 00:51:59>> Do you know if there's been any research in using CRISPR
- 00:52:01to develop vaccines or anything like that,
- 00:52:03as far as altering the immune system to be preventative
- 00:52:06in seeking out certain viruses that we can't right now?
- 00:52:10>> (forceful exhale) I don't.
- 00:52:11I will say that I did read a few articles
- 00:52:15where viruses will put latent bacteria in our bodies, right?
- 00:52:20They will insert-- and what they have done is,
- 00:52:25with CRISPR, you can identify really low concentrations
- 00:52:28of things.
- 00:52:29So I know from a diagnostic standpoint,
- 00:52:31that's where I think a lot of this future is,
- 00:52:34is in diagnostics.
- 00:52:35So like, if you had a virus still in your system
- 00:52:40but you weren't showing any symptoms,
- 00:52:43could you actually go and clip that out
- 00:52:45or identify that it's even still there?
- 00:52:47But in terms-- the immune system's pretty complex.
- 00:52:51(chuckling) I'm not an immunologist, so...
- 00:52:55nor do I wanna give a talk on it next year, Tim.
- 00:52:58(all laughing)
- 00:53:01Anything else?
- 00:53:08>> So Bill, there's a lot of controversy
- 00:53:10about where this should or shouldn't be used.
- 00:53:12Where do you think, or where do scientists in general think,
- 00:53:16are the least controversial uses for CRISPR?
- 00:53:19Where will we see this come along first?
- 00:53:22>> Yeah, so some of that work that I read on--
- 00:53:27with exosomes is I do think that--
- 00:53:31so ex-- so cells apparently put out--
- 00:53:35they communicate with these components
- 00:53:38that will have proteins and DNA in them.
- 00:53:43I would think that they could target specific organs
- 00:53:45or disease using this system, as opposed to like--
- 00:53:49which wouldn't be that controversial, right?
- 00:53:52I think-- what I will tell you,
- 00:53:55the more I read about this,
- 00:53:56the more I see it as a diagnostic tool
- 00:53:59as opposed to a tool that's gonna go in
- 00:54:01and modify people's DNA,
- 00:54:03unless it's on germline cells, truthfully.
- 00:54:07And it's because it's pretty unpredictable
- 00:54:10where this Cas protein will, one,
- 00:54:13how long it'll stay in a system,
- 00:54:15and when as long as it's there,
- 00:54:16it's cutting DNA.
- 00:54:18And they get off-site cuts.
- 00:54:21It's not as specific as it's being touted as.
- 00:54:24So... I think that.
- 00:54:28I mean, if you had-- it's like any drug.
- 00:54:32I think that if you were desperate,
- 00:54:35you would try it, right? (chuckling)
- 00:54:37So I mean-- but I think that where you do see issues
- 00:54:43and people don't like to see are germline modifications
- 00:54:46that result in specific traits.
- 00:54:48But using it for disease,
- 00:54:50I think those are the types of things you'll see.
- 00:54:59All right? >> Maybe one more question,
- 00:55:00if there is any?
- 00:55:04>> There might be cookies left.
- 00:55:05Oh. (all laughing)
- 00:55:08Yeah?
- 00:55:10>> So because CRISPR keeps on cutting DNA,
- 00:55:13as you've said, because it's not exactly well-regulated
- 00:55:17at the moment, if it keeps on cutting DNA
- 00:55:20in areas that you don't want it to,
- 00:55:22couldn't that be a limitation of it,
- 00:55:24where it would cause its own kind of diseases?
- 00:55:27>> Absolutely.
- 00:55:29So one of the things that they're doing, though,
- 00:55:32is that beautiful video with it kinda looping around,
- 00:55:38is there are some of those domains
- 00:55:40in the Cas protein, they're modifying,
- 00:55:43so they don't recognize the DNA as well.
- 00:55:47So they can lower the affinity
- 00:55:48that that Cas9 system has for a particular segment of DNA.
- 00:55:54So it'll periodically find its target and cut.
- 00:56:00But if they lower the affinity,
- 00:56:02the off-site cuts don't--
- 00:56:04it's sort of a give and take, right?
- 00:56:06You lower the affinity for the cutting.
- 00:56:08You don't cut as often.
- 00:56:10But you don't hit your target as often, either.
- 00:56:12And so, I think a lot of the research
- 00:56:14is going to be around modifying that so it doesn't hit as much,
- 00:56:18because what you don't want is to fix one problem
- 00:56:20and create another problem.
- 00:56:23But that's real.
- 00:56:28Oh.
- 00:56:31>> I lied. >> Yeah. (chuckling)
- 00:56:37>> Can Cas9 bind regions of DNA
- 00:56:40that are methylated more so than regions that are not?
- 00:56:45>> Oh, I don't know about that.
- 00:56:47I know where you're going with that, but I'm not sure.
- 00:56:51I think-- I have read that they will cut out
- 00:56:55areas of methylation
- 00:56:56so that they don't have the effects of what that might do,
- 00:57:01like turning a gene on or turning a gene off.
- 00:57:03But you can get Cas systems that recognize
- 00:57:07specific methylated areas, though.
- 00:57:10So they're working on that.
- 00:57:11I just don't know that much about it.
- 00:57:16All right. >> I had a quick question.
- 00:57:18When they do-- you were saying that it's easier
- 00:57:21to use probably when you take the cells
- 00:57:23out of the patient and modify them.
- 00:57:25Is that what they're currently doing with immunotherapy?
- 00:57:28Are they using the Cas9 to do that, and how come?
- 00:57:33Why would that be easier to get that in those cells?
- 00:57:37>> Well, I think it's because they don't
- 00:57:38have to deliver it through your system,
- 00:57:41like inject it into your blood or--
- 00:57:43so they have it in a particular container
- 00:57:46that they can-- 'cause you can change the solvents
- 00:57:48around cells and make them take things up easier,
- 00:57:53'cause you can put more extreme conditions on a cell
- 00:57:55in a test tube than you can in your body,
- 00:57:58because you have to live.
- 00:58:00And so... (laughing)
- 00:58:01so you don't wanna do too many extreme things
- 00:58:04in a biological system.
- 00:58:05But if they can pull the cells out
- 00:58:07and then put them back in, like bone marrow
- 00:58:10and things like that,
- 00:58:11I have seen that they're doing some success.
- 00:58:14But I don't know if they're doing it in humans yet.
- 00:58:17But you see mouse models and things like that
- 00:58:19where they are, so, yeah.
- 00:58:23>> All right, well, we wanna respect--
- 00:58:25>> Thanks for coming. >> Everybody's time.
- 00:58:26And let's give Professor Faber
- 00:58:29another round of applause here.
- 00:58:31(applause)
- CRISPR
- gene editing
- Cas9
- genetics
- biotechnology
- DNA
- RNA
- ethical issues
- biochemistry
- medical applications