CRISPR

May 11, 2020

Information

May 10, 2020

Yale Cancer Center

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00:00Support for Yale Cancer Answers comes from AstraZeneca, working to change how cancer is treated with personalized medicine.
00:10Learn more at
00:11astrazeneca-us.com. Welcome
00:13to Yale Cancer Answers. With doctor Anees Chagpar.
00:18Yale Cancer Answers features the latest information on cancer care by welcoming oncologists and specialists who are on the forefront of the battle to fight cancer. This week,
00:27it's a conversation about how CRISPR is transforming cancer research with Dr. Jun Lu.
00:32Doctor Lu is an associate professor of genetics at the Yale School of Medicine
00:42Dr. Lu, maybe you can start by telling us a little bit about your research and some of the new technologies
00:48that you're using. It's a very interesting question.
00:51Basically we are very interested in cancer in general and we have two major interests.
00:58One is to understand leukemia,
01:00which is a special cancer that's originating from the lymph system.
01:05We are also interested in immune responses.
01:08against normal types of cancers,
01:11what you normally hear about,
01:13what wel call solid cancers like breast cancer,
01:16prostate cancer, colon cancer, etc.
01:18And we have been working with melanoma
01:21as well as colon cancer ourselves.
01:23It sounds like you've been doing a lot of work.
01:27Tell us a little bit more about some of the unique aspects of your
01:31cancer research.
01:37We have been very interested in several types of questions, and we are particularly interested in understanding how cancers work, and one thing that we're trying to understand is how does a normal cell go weird and become bad
01:46and become cancer cells. Number two is, we're trying to understand the wiring, the molecular wiring within cancer cells and the molecular wiring
01:51we are particularly interested in
01:53are what we call non coding regions of the genome.
01:57You may have heard, the human genome consists of important pieces of DNA that we call the coding piece of DNA that encode so-called protein genes and these
02:08account for roughly 2% or less than 2%
02:10of the genome, and the rest of the 98%
02:13of the genome is so called non coding parts of the genome.
02:16They are on the DNA and initially we didn't recognize much out of it.
02:21We think they are less important.
02:23It turns out that they are there for a reason.
02:26They're not just junk, and so we have been particularly interested in the non coding parts of genome and how they control
02:34the coding parts of the genome.
02:36So tell us a little bit more about that because intuitively one would think that the coding parts of the genome are the ones that make the proteins
02:46and the proteins are the things that make functions,
02:49but the non coding parts, they control
02:51the coding parts. Tell us more
02:53about that.
02:55Absolutely right, so the noncoding parts of the genome,
02:57at least through what we currently understand,
02:59one part of their function is to control the protein coding genes themselves,
03:03and they can have many different ways to do that.
03:06For example, one of the types that we work with are so called non coding RNA.
03:11So these are RNAs that are produced in the cells and these are ones that
03:16control how much proteins are made.
03:19So this is one way they can show that,
03:22but there are many other ways non coding parts of genome can control non coding protein genes,
03:27so that's one way the non coding parts of genome can be important.
03:30Another part
03:33is that they can control themselves.
03:36There are so-called non coding genes themselves that can be controlled by non coding parts of genome.
03:42So it's sort of layer by layer that can have very sophisticated control of the human genome.
03:47And you mentioned that another part of your research is to figure out what makes a normal cell go rogue.
03:53What makes a normal cell mutate into a cancer cell?
03:56Do the non coding parts of the genome have
03:59a role to play in doing that?
04:01That's a very,
04:03very good question. Currently our understanding in human cancer perception has been more heavily focused on the printing parts of genome.
04:10We know that when the cancers initially go around,
04:14for example, in the case of leukemia,
04:16it's occurs initially in the stem cells of normal stem cells,
04:20and these normal stem cells that normally give rise to the blood cells in the blood producing system.
04:26And when the protein coding genes are mutated they will allow themselves to
04:31become bad in some sense and eventually become,
04:33for example, leukemia. And there are now more and more research in the non coding parts of genome because many times we cannot completely explain the phenomena of how does
04:44a normal cell go from a normal cell to become a cancer cell and they have to rely potentially on the non coding parts of genome.
04:54And as a matter of fact the new sequencing technologies have been helping science,
04:59especially biomedical science.
05:02Mutations in the negative parts of genome and some of them do seem to contribute to the initiation of cancer.
05:08Let's talk a little bit more about new technologies because certainly one would think that after the explosion with the human genome project,
05:18when that was finally revealed,
05:19everyone thought that this would be the great discovery that would help us to find the cures to all cancers.
05:28How has the Human Genome Project and understanding the genome really helped us and
05:33where do we still have to go in terms of finding those cures?
05:37Because a lot of people thought once the human genome was decoded,
05:40we would have all of the answers and then we would be able to find the cure for cancer and everything
05:47else. That's again a very interesting question.
05:49Actually, I still remember very early on,
05:51actually the government had declared that we're going to have a cancer cure quite a number of years ago and apparently up
06:01to now we still have some success against cancer,
06:04but there's still other things that we don't have success with.
06:07But from the understanding of how cancer works,
06:12the human genome project has to play this very,
06:15very important, and I would say it's a complete prolific role.
06:19And remember that time when the cancer genome of the human genome was initially revealed roughly around year 2000,
06:27I was a student at the time,
06:29and I remember there was a sort of guessing game among scientists saying,
06:34how many genes there are in the human genome and the guesses ranged widely from probably 100,000 genes to,
06:42maybe millions of genes,
06:44but it turns out that after the human genome has been sequenced,
06:48we start to realize that there are much fewer genes in the genome.
06:52According to protein coding we recognize there are somewhere around 20,000 protein coding gene's in the genome.
06:59But now of course we understand that again,
07:02it's a very initial understanding of the problem,
07:04because now we know there are many non coding parts of genome.
07:08They actually play a very important role to control the protein coding parts of genome
07:12which is only 2%, so it's has dramatically enhanced our understanding on a global scale of how things work,
07:19and some of these things are starting to bear fruits,
07:23and we are now seeing many,
07:25many new findings in the cancer field.
07:27For example, now we have a much better catalog of what genes can contribute to cancers.
07:33Some genes can be mutated.
07:35They are called oncogenes.
07:37Some genes are not mutated, called tumor suppressors.
07:40One is to enhance cancer
07:42and one is to block cancer.
07:44If you gain extra copies or extra activity of so called oncogenes,
07:49then you can have a chance for a normal cell to go to a cancer cell or you can lose the function of tumor suppressor gene and they can be reduced and
07:59this has contributed a lot to our ability now to map things back to the human genome and see the cause of
08:07which genes are mutated and we have a better understanding of the cancer genome now in terms of
08:14which genes got mutated compared to 20 years ago.
08:18And it seems like although we've learned a lot and we've gained our knowledge and we now know about oncogenes and tumor suppressor genes,
08:26we also know that they are far more complex than what we initially thought in terms of how these genes are regulated,
08:33how they are packaged, and so on.
08:35That's absolutely right, yeah.
08:45Tell us a little bit more about the technology that we're now using to look at genes and how they control cancer. If we know that gaining an oncogene increases your risk of cancer, and losing a tumor suppressor gene increases your risk of cancer,
08:53what are we doing about that?
08:55Or do we have technology that can actually help us in terms of correcting the problem?
09:00There are several things being done,
09:04and one thing, of course, we need to understand and have a catalog where you can say,
09:13look at this gene, it is doing this and this kind of tissue
09:18can potentially contribute to this kind of cancer,
09:21and that's basically creeping down by sequencing the genomes of the cancer specimens that we can collect.
09:28There you can sequence to see which changed and then you can compare that to the human genome and say Ok,
09:36these are genes that potentially got mutated,
09:38so once you have a catalog like this then the question is, is it important or not?
09:45So these require specific experiments to start to manipulate and change those genes.
09:50We can increase activity or decrease activity
09:54and the technology is called CRISPR,
09:57to basically allow us as a tool to change things around and start to see whether these genes in the catalog,
10:05are they important or are some more important than the others.
10:09And once we have that then we can move on to potential therapies and say,
10:14OK, this looks very important as a
10:15gene and the cancer seems to be dependent on it and if we can find either a small molecule like normal drugs you normally hear about or other ways
10:25of using immune therapies to attack tumors so that allowed us to pave the ground to go from research side
10:34to bedside.
10:38Tell us more about this CRISPR technology because it seems to me that this is a technology that people may have heard about,
10:44but nobody really understands exactly how it works.
10:47Can you tell us a little bit more about how it was developed,
10:53how it works, and how it's being used in
10:56research?
10:59The initial discovery of CRISPR technology was actually from some research in bacteria,
11:05so we think that we are very sophisticated as humans and we have two
11:14immune molecular systems that control immune responses and the bacteria.
11:19We thought they were very primitive
11:23but it turns out that these have all their own immune system as well,
11:29so CRISPR was discovered initially as the immune system of bacteria.
11:33One bacteria got intruded by other bacteria or viruses that's attacking the bacteria.
11:39The bacteria has a very intelligent way,
11:42which is using CRISPR to document their invaders.
11:45They say, OK, these guys invaded me,
11:47so next time I see it, I will destroy it.
11:51CRISPR is basically a way to do that.
11:54And the way it works is they take the intruders DNA as pieces and putt in their own genome.
12:02And next time they see the same piece of DNA start,
12:06they destroy it.
12:08So this is initially discovered as sort of immune response by bacteria to help them to survive against the invaders.
12:15Then roughly around 2012-2013 scientist start to say,
12:18OK, maybe we can utilize this as a way to help us to change cells,
12:26including human cells. Cancer cells,
12:28for example, where we can explicitly design things so we can manipulate and change specific sequences within the human genome,
12:36and this has dramatically allowed us to expand our tool set to change genes.
12:41For example, increasing gene activity or decreasing activity through this kind of approach.
12:47Tell me more. So I get the whole idea of CRISPR being like a bacteria's immune system.
12:54They recognize something and they say I'm going to
12:58understand what this is, incorporate that DNA so that the next time they see it they can kill it
13:06because they know that it's foreign.
13:09Very much like the human immune system.
13:11But how does that help scientists then to increase the number of genes or decrease?
13:19Or change the genes in a particular cell?
13:22How exactly do you translate that bacterial immune system into gene editing?
13:29That is through an engineering process that has been done on the molecular front.
13:34So
13:36let's take the intruders DNA and put some pieces into our genome,
13:40which is probably going to be dangerous to do.
13:43We actually shortcut that step so we just say,
13:46we know that bacteria use their pieces of DNA storing their genome to attack foreign DNA,
13:52but the same machinery can work on whatever piece of DNA as well.
13:57So basically what you can do is you can
14:00take for example, any piece of the human genome you want to change,
14:07and you can design a sequence using CRISPR.
14:10I will go in there and particularly change a sequence within this part of the human genome.
14:15This is basically how CRISPR is used in human
14:19cells.
14:20We're going to have to learn more about how CRISPR works and how this has changed cancer research right after we take a short break for medical minute.
14:30Please stay tuned. For more information with my
14:33guest doctor Jun Lu. Support for Yale Cancer Answers comes from AstraZeneca dedicated to advancing options and providing hope for people living with cancer. More information is available at astrazeneca-us.com.
14:46This is a medical minute about
14:48head and neck cancers, although the percentage of oral and head and neck cancer patients in the United States is only about 5%
14:57of all diagnosed cancers, there are challenging side effects associated with these types of cancer and their treatment.
15:04Clinical trials are currently under way to test innovative new treatments for head and neck cancers,
15:10and in many cases less radical surgeries are able to preserve nerves,
15:14arteries and muscles in the neck
15:17enabling patients to move, speak,
15:19breathe, and eat normally after surgery.
15:22More information is available at yalecancercenter.org.
15:25You're listening to Connecticut Public Radio.
15:30Welcome back to Yale Cancer Answers.
15:32This is Anees Chagpar and I'm joined tonight by my guest doctor,
15:39Jun Lu. We're talking about CRISPR and
15:42how this new technology really is transforming cancer research and essentially doctor Lu,
15:48you were telling us that this is a way of editing genes using bacterial technology that these bacteria have essentially evolved to try to understand foreign invaders into
16:01their own genome. Is that right?
16:04That's right, and so using this technology you can take any gene that you want and you can either amplify it,
16:12make more copies, or mutate it,
16:15or do various things. Tell us how you use that in terms of cancer research?
16:21Yeah, so there are
16:23two different ways that we can change genes.
16:27One way is actually just use directly as you mentioned about in
16:34bacteria what they do is they can use a piece of DNA as the guidance sequence so we can use that guidance sequence and
16:45destroy anything that looks exactly like the guidance sequence.
16:48So this is a way how they destroy the intruder DNA.
16:52So what we can do is utilize this same thing with cancer cells that we can artificially create a piece of DNA that's exactly the same as
17:02the DNA we want to destroy inside the genome.
17:05And then you can put this with the protein machinery,
17:12and this will actually make a cut in the DNA and this cut leads to a short deletion.
17:19Basically you get rid of a few
17:22pieces of sequences within the human genome.
17:27This allows us to do
17:29gene knockouts. Basically
17:33we want to specifically inactivate a particular gene in the genome.
17:36So this is one way we can use it. For the 2nd way we can use it for
17:42we don't make cuts, but we use the same machinery,
17:45but we don't make cuts in the genome,
17:48so the genome is still intact,
17:49but we can modify around the place where the sequence binds to
17:54and say,
17:55we can make a change in the regulatory parts of genome so that once this sequence redesigned guides approaching to that particular place in the genome,
18:06you will lead to increased production.
18:09So then you can basically control copy numbers for whatever you can make proteins for.
18:15There are basically two different ways,
18:17at least two different ways you can use it.
18:21So by doing so you can
18:24increase the gene of interest or decrease changing activity.
18:28So
18:28scientists have worked out how to either cut DNA or amplify DNA in this artificial kind of matrix.
18:34And then what do you do then?
18:36You take this and you put it into a mouse and you see what happens if you amplify a gene or if you knockout a gene.
18:44Yeah, exactly so you can do this in a mouse or you can do this in a dish.
18:49So basically what we talked about many times is
18:54this sequence got mutated in the human cancers.
18:56Does this piece of sequence,
18:58which could be a protein coding gene sequence,
19:00play an important role in the process?
19:02Maybe is it just happened to be mutated and doing nothing?
19:05So first thing we have to tell the difference between
19:10is this a truly so-called functional gene or functional mutation or not and so we have to do experiments in dishes by changing the piece of
19:19DNA and say, OK, does it make a difference or not?
19:22For example, we may see cells proliferate faster or you may see cells die,
19:28or you can see cells migrate better so they can
19:32move from one place to another,
19:35and so there are many different behaviors we can start to see.
19:39Of course you can also do the same thing once you put cancer cells into the mouse to see whether or not you can see differences
19:48in tumor genes, the way by which the tumor is formed.
19:53So there are many different results we can do once we
19:56can manipulate these genes. So if you manipulate
19:59genes in a Petri dish or you can manipulate genes in a mouse,
20:05is there a role for this gene editing in people?
20:09Like if you know thanks to the human genome project and thanks to previous work that's gone on that,
20:18a particular mutation is involved in tumorigenesis of a particular cancer,
20:23is it possible to edit that gene so that it's not mutated anymore and then
20:30reduce people's risk of developing cancer?
20:33That's a great question,
20:35and actually, there are some clinical trials,
20:38so that's ongoing now, not necessarily against cancer,
20:41but in other diseases that have been using CRISPR as a technology, as a potential curative therapy.
20:48And there are a few clinical trials using CRISPR now in the cancer setting,
20:52but the majority of active research currently is in genetic disease,
20:58and one of the prime examples
21:00is sickle cell anemia, you may have heard of sickle cell anemia which is a disease that's caused by a particular mutation in a gene that's producing a protein, that's
21:11very important red blood cells.
21:14And because of this mutation the red blood cells will have some
21:19not normal behaviors, so called sickling behaviors and that causes many different symptoms in humans and we have known this for quite a few decades now,
21:29which genes cause disease and there's a potential strategy to deal with it.
21:34So the gene that's being mutated is a gene called a hemoglobin,
21:39which is probably the most abundant protein
21:42present in red blood cells,
21:44and this protein has several different forms.
21:47There is a form called embryonic form of gene.
21:50And as well as adult form of gene.
21:53So when we are a baby actually still a fetus,
21:57we express the embryonic form of the gene,
22:01and then once we become born and become adults,
22:05we change to a very similar gene, the
22:08adult form of the gene.
22:10The reason for that is because in the uterus as an embryo versus once you're out of mother,
22:16there are different exposures to oxygen.
22:19And as the concentration is very different,
22:23we have to adjust based on that.
22:26However, we know that the embryonic version of the hemoglobin,
22:29although it's not as good as adult form in terms of functions,
22:33is still very good. And if we can change the gene expression within the red blood cells in the sickle cell patients to convert to the embryonic one,
22:42you can actually cure many of the symptoms of the patients.
22:46So this is one area where CRISPR is actively being explored
22:51in research setting as well as a clinical trial setting and this may actually become a
22:58cure for the disease, so that sounds really promising.
23:02My only question though, is given the fact that hemoglobin is so abundant and in all of your red blood cells and you have thousands of red blood cells,
23:13how do you change the genes in every single one of those?
23:21It turns out that you don't have to change every single cell of hemoglobin.
23:26You only need to change a subset of the cells that carry this mutation.
23:30As long as you correct some of them,
23:32you don't have to correct 100%,
23:34so that's really the reason why this is first using diseases where you only need to restore the function of some of those,
23:41but not all cells. This is slightly tougher for cancer.
23:44Of course, if you have cancer,
23:46you have to create almost every single cell and that becomes an issue,
23:50potentially using the same technology against cancer.
23:52However, there is one way
23:54to potentially, using cancer therapies, change the immune system that's basically fighting cancers.
24:00For that you don't have to change every single cell within the immune system.
24:04You only need to change some of the cells within immune system and then we have a better outcome for cancer patients,
24:11and that's being tried right now,
24:13so there are several clinical trials
24:15in the United States, and a few outside of the United States using CRISPR as a technology to change T cells.
24:22T cells are one of the immune cells we have in the body
24:26to help fight against cancer using the T cell therapy.
24:30How exactly does that work?
24:33I don't know if you have heard, but
24:37currently there's one kind of immune therapy called CAR T cell therapy.
24:42Basically we take normal T cells and then we engineer the T cell so that you will have a sort of fighting ability.
24:54Have a recognition. We call a receptor, specifically against a certain type of cancer,
25:00and so we can engineer that to have this special ability,
25:04and then we can put them back into the patients.
25:08And this has shown very good success against a few different kinds of
25:12cancers such as chronic leukemia,
25:14and so it's currently being tested in many other different settings.
25:18But of course one of the things that's happening with the T cells is once you put the so called manipulation of the T cells
25:27called CAR T cells, they can be active against cancer,
25:31but then they get exhausted.
25:33So the question is, can we somehow change it using CRISPR to inactivate
25:38the exhausting capacity or the blocking capacity for T cell to be further useful against cancer?
25:44So this can further enhance the therapeutic outcome and the effectiveness of the cancer.
25:49So the current services using the clinical trials using CRISPR is trying to engineer the T cells so that can have better potency
25:58against cancer.
26:01And how can CRISPR help it not get exhausted?
26:04So if you think about the immune system,
26:07one of the functions carried out by T cells is to recognize specific intruding stuff.
26:14Initially we think that's how it works,
26:16but you don't want this to be active too much.
26:20If you activate T cells too much,
26:22then you can have potential toxicity against yourself,
26:26your own cells.
26:30So you have to control the activity so nature has designed the system in a way that once it's activated,
26:37it will have to be stopped.
26:38And so this kind of exhausting process is one way the system is controlling itself so that once activated,
26:46we don't want to press the gas pedal too much, once you press the gas pedal,
26:50there's naturally something on the back that breaks it down,
26:53so this is basically the natural ability of the T cells.
26:57And basically what CRISPR is currently trying to do is
27:01adjust this feedback control system so that you will have more mileage out of the same gallon of gas.
27:10Are they using CRISPR technology also to kind of edit the genes that the T cells will recognize,
27:20like the bacteria recognizing foreign intruders like you were saying.
27:25Currently talking
27:26about potentially using CRISPR to change the genome of the cancer cells themselves,
27:33In part changing the genome of the cancer cells themselves.
27:42How bacteria use CRISPR to recognize foreign invaders and then attack them like an immune system,
27:51but is there a thought to using that same technology to introduce those genes of cancer cells to the T cells so that the T cells recognize that and fight
28:05just like a bacteria immune
28:08system would?
28:10To my knowledge this hasn't been actively explored at the moment.
28:13I wouldn't say it will never be a possibility because there are many different insights.
28:18We have to open our imagination and there are lots of things that may seem very,
28:23very far from clinics, but turns out that could be very close,
28:27so that's why we have to support many different kinds of cancer research.
28:31The slight difference between the bacterial system and the cancer cell system is that the bacteria have the invading DNA into their own cells.
28:40We want to destroy them.
28:42Whereas in the case of T cells, targeting cancer cells is between the cells,
28:47so you don't have DNA crossing between the two cell types,
28:52as long as the cancer cells have some other protein fragments that T cells can recognize,
28:58that will be allowed to attack some.
29:02Doctor Jun Lu is an Associate Professor of Genetics at Yale School of Medicine.
29:07If you have questions, the address is canceranswers@yale.edu and past editions of the program are available in audio and written form at Yalecancercenter.org.
29:16We hope you'll join us next week to learn more about the fight against cancer here on Connecticut public radio.