Identifying How Genes Function to Better Understand Cancer with Mazhar Adli, PhD

Erin Spain, MS [00:00:10] This is Breakthroughs. A podcast from Northwestern University, Feinberg School of Medicine. I'm Erin Spain, host of the show. Today's guest is part of a large, NIH-funded project that aims to find the function of every gene in the human body. Dr. Mazhar Adli associate professor of obstetrics and Gynecology at Feinberg and a member of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University joins me today to talk about this project and how it relates to his work in cancer research. Thank you so much for joining me today.  

Mazhar Adli, PhD [00:00:48] Thank you. It's a pleasure.  

Erin Spain, MS [00:00:50] The work you're doing in your lab focuses on identifying and targeting key genomic and epigenomic drivers in cancer. Explain this work to me.  

Mazhar Adli, PhD [00:01:00] So, cancer is this disease where there is uncontrolled cell proliferation. To achieve this, cancer cells may have aberrant regulation in their genetic information, but there is also an aberrant regulation in the epigenetic information, which is this second layer of information on top of genetic information. So it is a combination of these different layers that drives a cellular state or cellular identity. We try to understand what is dysregulation in normal cells and how is it aberrantly regulated in cancer cells. And we are using this genomic tools to understand the entire genome in these settings. By genomic, we mean that with single experiment or with this with this within the same experiment, we can look at the entire genes that are aberrantly regulated. Our genome calls for around 20,000 genes. And today, we have technologies that allows us to measure all these different genes and see how they are aberrantly regulated in cancer.  

Erin Spain, MS [00:02:03] Tell me about your background and what led you down this path.  

Mazhar Adli, PhD [00:02:07] So, my background is in cancer biology. I did my PhD at University of North Carolina, with Al Baldwin, where we were studying cancer cells signaling basically how the cancer cells have different signaling mechanism compared to normal cells. But one of the things towards the end of my PhD that I started thinking more and more about it is that, you know, by focusing on one gene, one protein, we cannot really get this systematic understanding of cancers. So, I wanted to do a more entire genome kind of approach or more systematic approach to to reveal all genes in cancer settings. That's why I wanted to do my postdoc in cancer genome or cancer epigenome. So, I joined Broad Institutes where the Human Genome Project was being sequenced. And our goal in my during my postdoc was to reveal this epigenetic information at the at the entire genomic space, basically. And I was part of the Human Epigenome Mapping Consortium. We were mapping all this epigenetic information during this project. One of the things we were you know, we were revealing this epigenetic information. But within the lab and with other folks and colleagues, we were discussing whether there will be one day will be possible to alter this epigenetic information, basically to remove these marks and deposit new ones and and study whether they are causal or not. But back then, we thought, you know, we will you know, who knows, maybe the next generation of scientists will be able to do this. But when I set up my lab at the University of Virginia, it was within the first few months of when I set up my lab, The CRISPR papers came. And we knew that now we have this amazing and very versatile technology. We can target any gene and we can delete that basically which causes mutation that that leads to frame shift and the gene is no longer functional. But there was one particular data in that first paper that you can make a specific mutation it no longer cuts DNA. And that was the idea that that I was discussing with my postdoc back then that, oh, we can maybe use this we call it catalytic aversion, which is nonfunctional. It doesn't cut DNA and we can fuse different epigenetic enzymes to this, that version of this and use it as a shuttle to send these enzymes to different parts of the genome to alter this epigenetic information. That's how we we entered the field of CRISPR technology, basically. And since then we have been further developing different CRISPR technologies to use for gene editing, epigenetic editing, and we could add fluorescent proteins, for example, take movies and track the fate of individual genes, how they move inside the nuclear space. And then nowadays we use how we heavily use this CRISPR technology for large scale screenings.   

Erin Spain, MS [00:05:01] Your team is one of just five teams in the country to be awarded an NIH grant for a program whose goal is to really find the function of every gene. Tell me about this program and the award that you were given.  

Mazhar Adli, PhD [00:05:15] Yeah, it has been a pleasure to be part of this this new consortium. Whose function is to understand the function of every human gene and to reveal these these functions. I can take a step back. Briefly describe what we initially talk about, this human genome organization where the goal was to understand the sequence of all this information. With the Human Genome Project, we revealed that one. With Human Epigenome Project, we revealed the different modification that regulates the genome, this epigenetic information. With the the nucleus project, we understood the for the organization three the organization how this organization changes over time. But one thing that we we still didn't know is what do all these genes do inside of cells? We could get this to meet a long molecule. We could get its organization all the sequences. But we know that this two meter long 6 billion letters code for it is 20,000 genes that are coding for proteins. And each of these genes work together with with all the other group of genes to give a cellular identity. And this new consortium wants to characterize each of these genes. When we look at the the human genome and when we say how many genes are well-characterized and we know tons of information about it for about 10 percent of them, we we characterize them pretty well. And those are, as we discuss, are involved in cancer animal immunology. But for about 90 percent of human genes, we still don't know much about their functions. And that's why NIH started this project. They wanted, you know, all the scientists in nation to come up with an ideas, how can we characterize all these different genes? And we want to basically target all these 20,000 genes. But it is a challenging project. That's why the first phase of this project was for the next five years. The goal is to characterize thousand genes, but during this first phase, we also are going to develop technologies so that we can scale up this effort for the next phase, which can hopefully target entire genome. Now my project is targeting essential genes, so we know that, you know, one way to characterize and a function of of a gene, actually, the probably the ultimate way is to remove that gene to see what happens to the cells. But there are a group of genes called we call them essential genes. When when we remove them, then cells die. So they are so important. But now we know that the cells die, but we don't know why it's dying. Why? What is the function of this gene that makes this so vital for cell survival? We don't know this information. So we are developing a technology and utilizing a technology where we can actually remove this protein. And for, you know, within 20 minutes, within half an hour, we can remove this protein where the cell is still going, its normal functions are going on. And we can monitor different we can perform different assays for the next 40, 48 hours and see what this normal function of this protein is. So that's the project that I am involved. So we are going to achieve this again. We are coming and using CRISPR technology because CRISPR technology allows us to delete genes. But for these essential genes we cannot use CRISPR, normal CRISPR. What we are doing is we are re-engineering human genome in a way we are adding this degree on at the end of all essential genes, and now it allows us to very rapidly deplete this protein of interest within minutes. And then studies function. And the cool thing about this is that we can then remove this, this molecule from the media, from the cells, and the protein comes back so we don't have to kill cells. Basically, we remove this protein, study its function for a while, and then we can just change the media and the protein comes back. So there is this acute inducible depletion of protein and the whole process is reversible. So that's what we are going to create. Basically, the program is called MorPhiC Consortium. The name stands for the Molecular Phenotypes of Nulls Alleles in Cells. There are four data production teams in the nation. My group and with the team at Northwestern University is one of those teams we are working together with Paul Burridge, whose expertise is in stem cell biology and with Feng Yu, whose expertise is in data analysis and large scale data coordination and integration. And my lab, our expertise is CRISPR technologies. So it's one of the nice thing about Northwestern actually to have this world leaders and right around us to be able to form these teams and go for this large scale consortium projects.  

Erin Spain, MS [00:10:14] And tell me about this investment. What does it mean to have the NIH pursuing this activity? What do you think this means for the future of understanding the human genome and understanding cancer better?  

Mazhar Adli, PhD [00:10:27] Targeting all human genes and finding their functions in a multicellular systems is a big task, is a big challenge. And the phase one is NIH wants to develop technologies to do this one and also scale up technologies to see whether we can actually target entire 20,000 genes. That's why the first phase is targeting 1,000 genes. But in the next five years, we hope to, you know, find all this the characterize thousand genes, but more importantly, scale up these tools that we are developing so that in the next phase we can go after the entire 20,000 genes.  

Erin Spain, MS [00:11:05] Back when you first established your lab, as you said, you had no idea that in this generation what we would be able to accomplish. But now, like this project that you're working on with the NIH and how far technology has come, what do you see could be next in the next ten or 20 years using CRISPR technology?  

Mazhar Adli, PhD [00:11:23] So we will definitely have a much better understanding of human genome and how this genome is being able to regulate the different settings, but most critically, how we can actually manipulate this genetic information. And this will open the door for a lot of therapeutic applications. CRISPR already generated huge excitement about, you know, we have 6,000 genetic diseases that, you know, we know that there is a single gene that causes those diseases. I think in the next decade we will figure out how to target those genetic diseases, how to correct those mutations and hopefully cure a lot of these genetic diseases.  

Erin Spain, MS [00:12:05] Your research projects have included focusing on different types of cancer, ovarian cancer, but most recently, pancreatic cancer has been a focus of a couple of papers that you publish using this CRISPR technology. Tell me about these two recent publications involving pancreatic cancer and what did you find?  

Mazhar Adli, PhD [00:12:24] So in one of those studies, we found this gene called ISL2. So the gene has was extremely ill characterized or it was wasn't characterized at all. There was only five publication about this gene in PubMed. So, it was surprising to us that we are in year 2020 and there is only five publications about this particular gene. So, it was novel to us and we wanted to characterize this. What we found is that this is a normally a gene called transcription factor. So it normally it goes and binds to DNA and regulates the expression of many other genes. In pancreatic cancer, our data suggests that this is a tumor suppressor, which means that the normally pancreatic cancer needs to silence or delete this gene. Because with many cancer, we know that cancer deals with tumor suppressor in two ways, either at the genetic level, they delete this gene or make mutations so that the gene is no longer produced, a protein is no longer produced, or at the epigenetic level, they just turn the transcription of this gene off with some epigenetic modification. In for ISL2, we didn't see any genetic alterations in pancreatic cancer, but at the epigenetic level we found that pancreatic cancer, about 60% of pancreatic cancers, are epigenetically silencing this particular gene. Of course, then we have to understand the mechanism, what happens downstream of this silencing. And it turns out that this this ISL2 is regulating the expression of metabolic genes. So when when it is being silenced, pancreatic cancer cells, they reprogram their metabolism. Now, instead of relying on glucose as their main nutrient, they rely on lipids and fatty acids. And that's how they become more aggressive in the pancreatic cancer microenvironment.  

Erin Spain, MS [00:14:11] With this finding, how does this open up the door for folks who do study pancreatic cancer and they're looking for new therapeutic pathways?   

Mazhar Adli, PhD [00:14:21] So pancreatic cancer, as you know, is one of these extremely lethal in our cancer. We know quite a lot about the genomic alterations in this cancer, but still we know that there has been that there are some epigenetic alterations that we are still characterizing about this. One of the the main thing that we know that pancreatic cancer cells do is they alter their metabolism because pancreatic cancer is becoming this fibrotic, very dense tissue. And in the center of this this tumors is very nutrient deprived cells that they don't have easy access to blood vessels, for example. So they are becoming more dependent on the microenvironment to survive. What we think is going on is that in the center of this tumor, the cells they silenced ourselves to and they becoming dependent on lipids, which is coming from the other cells dying around them. So when cells die, their membranes contain a lot of lipid. And this lipid from the membrane of this cells that are dying is becoming a food for the cells in this this nutrient deprived location in the pancreatic cancer. Now, how can we utilize this information now to target pancreatic cancer? We know that that's one exciting field about cancer metabolism, is that if cells becoming selectively more dependent on certain pathways, we can actually use specific inhibitors to target those pathways. And in the case of ISL2 silence pancreatic cancer cells, they are becoming more dependent, dependent on mitochondrial respiration and lipid, fatty acid metabolism. And we have very good inhibitors that targets mitochondrial respiration, for example. And we show that both in vitro on cells and also in vivo in using mice as a model system, we can use those inhibitors. And when we use these inhibitors, the pancreatic cancer cells, which were normally more aggressive when I a cell to be silenced. But now they are becoming very sensitive to this. So, these inhibitors of this mitochondrial respiration. So that's, I guess showing how we can use this unbiased technologies, CRISPR, like high throughput screenings to find this normal tumor suppressors. But once we found the mechanism of this tumor suppressor, we can also find alternative targeting pathways for this this reprogram metabolism. We also used this high throughput screening in another settings where our goal was to find combinatorial drug targets. So, it's a it's the same kind of logic of high throughput screening. But in ISL2 story, we wanted to find which genes when we silence them or when we delete them or deplete them, will make the cells more aggressive. That means it will be a tumor suppressed. But we also use this. We've said in pancreatic cancer, they're being treated with with certain chemotherapy. And gemcitabine is one of the main chemotherapy that is being used currently for all pancreatic cancers. But obviously it's not working very effectively because, you know, it's it's by itself, if you use at a very high dose, it becomes toxic. And at the very low doses, then it's not killing cancer cells selectively. Our goal was that can we find some other genes when we inhibit them by it, by themselves, invade, inhibit them. They are still cancer cells don't care too much, but if inhibit those genes and then add chemotherapy, then it will become what we call synthetic, lethal combination. So this synthetic lethality concept is is one of those concept that the scientists discovered from yeast genetic studies when they were deleting one gene. The yeast is viable, deleting another gene, the yeast is viable. But when they delete both of them together, then the yeast is dead. So we can find similar concepts. We can do similar things in cancer, but we cannot delete genes in cancer because that's not a viable approach. But we can use different drugs. You know, we add drug A, the yeast, the cells, the cancer cells are kind of viable. Drugs be still viable. But when we combine these two drugs, then it the combination becomes synergistic or synthetic lethal. There are a couple of, of course, critical points here that, you know, it's easy to kill cells, but we have to find a combination that will only kill cancer cells and will save the normal cells. That's, I think, the most critical part of this whole this kind of approaches. So we found in our setting, we treat a group of mice with gemcitabine. So there being a group of controls and we found this gene, this called PRMT5, it's a epigenetic enzyme that when we normally inhibit this gene to cancer cells, didn't care too much about it. But when we inhibit this gene and add the chemotherapy, then the cells were dying, you know, synergistically the concept of this combinatorial or synthetic lethality is that the effect of both of this drugs should be more than the total effect of individual effects. That's how we define being synergistic with each other or being synthetic lethal with each other. So we found this gene PRMT5 and there is a good inhibitor of this this gene as well that is being now tested in clinical trials. And we we showed that both in vitro and in mice, the combination will results in in tumor shrinkage and also the blocks of tumor growth in vivo.  

Erin Spain, MS [00:20:05] How rewarding is a discovery like this for you?  

Mazhar Adli, PhD [00:20:08] Our goal is to to understand cancer. And then as a basic scientists, we rarely have the opportunity to actually discover something and take it to the clinic. And this has been one of those rare and amazing findings that and we immediately get in get in touch with the companies who are making the inhibitors of this drug and this this protein. And now we are still in discussions that hopefully we want to start a clinical trial here. And this is an amazing feeling that we didn't know anything about this gene two years ago, and now we have the opportunity to take it to the clinic. And this is all because of this unbiased approaches of high throughput genome screening with this CRISPR technology. We also work on ovarian cancer, where the main problem is chemo resistance in ovarian cancer, you know, in in a lot of cancers, you know, we have certain chemotherapy we can treat cancers. And in ovarian cancer, we have very good chemotherapy early on, we can get rid of cancer cells, but within a period of six months, the tumor disappears. But after six months, it comes back and this new tumor is now chemo resistant. So if you give the same chemo, it no longer cares much about it. And we try to understand what happens during this, you know, process that the cells are now have a different phenotype, basically. And one of the hypotheses that we are now actively working on it and we we got a recent grant about it is that to reveal which genes are being turned on and what are the key drivers of this new state? And can we target these new genes to to better understand this chemo resistant process and block this process so that the cells will not be able to become chemo resistant? And we think that this systematic approach will be highly useful for us to understand this process and also target this process, hopefully.  

Erin Spain, MS [00:22:09] Well, Dr. Adli, thank you so much for coming on the podcast and giving us a big picture of what's happening in your lab and with CRISPR technology in general. It was really a fascinating conversation. Thank you.  

Mazhar Adli, PhD [00:22:21] Thank you, Erin. It has been a pleasure to talk to you.   

Erin Spain, MS [00:22:30] And thanks for listening. And be sure to subscribe to this show on Apple Podcasts or wherever you listen to podcasts and rate and reviews. Also for medical professionals, this episode of Breakthroughs is available for CMT Credit. Go to our website feinberg.northwestern.edu and search CME.