New Era of Highly Targeted Drugs Originating from the Dark Genome: Dr. Samir Ounzain, HAYA Therapeutics

Dr. Samir Ounzain, HAYA Therapeutics: 0:00

We have a full stack approach to discover, curate, identify and target next generation dark genome RNA targets.

Alex Jani, X-Health.show: 0:14

Hi, I'm Alex and welcome to the X-Health show, where I talk to visionaries behind the latest innovations in healthcare. For the eXtra health of the future. We at Biopole, Lausanne, in a conference room surrounded by biotech labs, where researchers work on reprogramming cell states. Dr. Samir Ounzain is the CEO of HAYA therapeutics. A molecular biologists who has researched dark genome and its roles in diseases for over 15 years. He discovered hundreds of long non-coding RNAs – he will beautifully explain what they are. HAYA Therapeutics is a Swiss startup that works on one of these RNAs, called Wisper, to develop highly targeted drug to address cardiovascular disease. That's for starters. There is fibrosis and cancer in the pipeline, and possibly many more. Buckle up as we'll dive into the richness of the regulatory genome, previously called junk genome, tackling disease at its source, and RNA therapies. Samir, how much more do we know now about dark genome? In 2003, that was 98% that we didn't know. How did that change?

Dr. Samir Ounzain, HAYA Therapeutics: 1:26

It's changed a lot. The Draft Human Genome was published in 2001. And then the full, you know, full manuscript, let's say was published 2003. But around that period, we didn't know a lot. We had a lot of clues, because of the work of the previous 20-30 years, around what is the non-coding portion of the genome doing but we had a very limited understanding, because we didn't have the toolset. So genomics, the tools that we all hear about today, using sequencing technologies, data science capabilities, computational biology, they were very nascent. That was really the beginning of the field when we started to think about using data science to assess biology. So in 2000, and 01, 02, 03, we were really at the beginning. We were at this moment, which was somewhat of a shock to the system. It was actually, in a bizarre kind of way, when the draft got published in 2001, the media at the time, so if you'd have looked at any newspapers, then that's it. We've sequenced the human genome, all diseases are going to be cured.

Alex Jani, X-Health.show: 2:29

With it 2% that we actually recognize? I mean the scientists.

Dr. Samir Ounzain, HAYA Therapeutics: 2:33

Well, we thought that having the full draft, the full book of life, would allow us to cure all disease. But when we realized that 98% of it was not coding for protein, which were really the biological units of life and disease. Everybody thought of proteins, which were coded by genes, to underpin all of biology and all of disease. And when we all of a sudden had this realization that most of your DNA, your book of life, is not coding for protein, it kind of created a somewhat of a nihilistic fears of what does all this mean? And how are we going to figure out what our genome is telling us about our origins, our development, disease, how we respond to the environment. So if I compare that to today, so approximately 20 years later, we've had this acceleration of understanding and tools, mainly driven by technology, actually. So the cost of sequencing has been exponentially decreasing. It cost billions of dollars to sequence the human genome in 2001. Today, you could get a pretty decent sequence of your genome for between 500 to$1,000, probably. Actually, even cheaper now. And that's all because of technology. So there was a huge convergence of tools and technologies, and software, and data science capabilities, that over the last 20 years has really, I would say, transformed our understanding of the genome.

Alex Jani, X-Health.show: 4:02

Are you able to assess out of this 98%, how much did that drop?

Dr. Samir Ounzain, HAYA Therapeutics: 4:10

In terms of how much do we know about today?

Alex Jani, X-Health.show: 4:12

Right.

Dr. Samir Ounzain, HAYA Therapeutics: 4:13

Unfortunately, still not a lot. It's very hard to give a number. I mean, there's been some major kind of consortium, an equivalent of the Human Genome Project, called the ENCODE Consortium, which was an extension, essentially, of the Human Genome Project, which stands for Encyclopedia of DNA elements. Some of their pioneering work suggested that maybe 80% of the genome is doing something important, is potentially functional. So we have signals, and we have, you know, signatures and clues that a significant amount of the genome might be important. But if I was to say it, how much of that 98% do we really have a good understanding about today? I would say maybe 5%.

Alex Jani, X-Health.show: 4:58

Wow.

Dr. Samir Ounzain, HAYA Therapeutics: 4:59

So we probably still have about 90% of the genome, which really needs a lot more understanding interpretation. I think one of the interesting things, and maybe we'll get to that is, when you start studying the dark genome, we came from a zeitgeist of thinking about biology in a mechanical way, about proteins, which is the less than 2% of your genome. And as we started to explore the dark genome, or the non-coding genome, we like to call it the regulatory genome in HAYA because we don't believe it's dark anymore.

Alex Jani, X-Health.show: 5:29

I love that name because it's like, there's this 98% of something we don't know, let's call it dark. Just leave it there, right? We don't know about that. That's

Dr. Samir Ounzain, HAYA Therapeutics: 5:39

I agree. I mean, now we believe useless. that the scientific community and ourselves as well, we think we're understanding what it's doing. But what's very interesting about it is, conceptually, how the 98% of your genome works. It's really like software, telling the genes, the proteins, what to do, where to go. And a lot of the insights that have been developed over the last 10 years in particular, are very counterintuitive to how you think about biology from the perspective of protein-centric world. And we're making this transition from a protein centric view of biology and mechanical view, to an information-based view of biology. And there's a lot of surprises. I would argue we're very much still scratching the surface. I think, the more you learn about the dark genome, the more you realize how little you know. And the more you realize how, conceptually, you think about understanding its activity, it does require a slightly different mindset and a perspective on how biology is hardwired and how biology manifests, especially in disease.

Alex Jani, X-Health.show: 6:43

So let's maybe cover first definitions so that we have everyone on board. And I still feel like it's kind of new, even though it's 20 years into discovering our genome and calling it the dark genom – part of it. But let's first say what is the dark genome, and then epigenetics, and what's actually the difference with the coding and non-coding.

Dr. Samir Ounzain, HAYA Therapeutics: 7:11

Sure. The correct definition of the dark genome would actually be the non-coding genome. So it's essentially the regions of your DNA that do not encode the genetic information to produce a protein. So approximately 1.8%, so less than 2% of your genome, encodes a specific code of DNA that allows that DNA to be converted into messenger RNA, which then gets translated into protein. Now, the remaining 98% does not encode that message. So the remaining 98% doesn't have the sequence of DNA letters to allow the RNA to be converted into protein. So the strict definition would be the non-coding genome. It doesn't code for protein synthesis. But what it does do, it's the information processing portion of the genome. So the code embedded within the DNA of the dark genome is fundamental for regulating epigenetics, for example. So when you think about epigenetics, I'm sure yourself and your audience as well, based on some of your previous guests, have a good understanding.

Alex Jani, X-Health.show: 8:20

But it won't hurt if you actually define that too. We had Semira Gonseth Nussle...

Dr. Samir Ounzain, HAYA Therapeutics: 8:24

How you define epigenetics itself is a very big discussion. That would probably be a six hour podcast. But at a very high level, it is how your DNA expresses itself, how it is expressed, independent of the underlying sequence. So you have modifications to both your DNA and the architecture associated with the structure of the DNA that influences how your genome speaks.

Alex Jani, X-Health.show: 8:51

Right, you don't change the DNA itself but you can silence some of the genes...

Dr. Samir Ounzain, HAYA Therapeutics: 8:56

You can silence, you can activate, you can do all kinds of beautiful things to your DNA. And you know, DNA – people think of it is a linear code but actually in the context of how it expresses itself, it's a very complex structure with complex topology that is changing dynamically in response to the environment. And these environmental signals manifest that on the level of DNA, in term of how it's active through these non-DNA modifications. When I say non-DNA, I mean, you're not actually changing the letters of the DNA, you're not creating genetic variation, but you're creating epigenetic variation, which is how that DNA and the structure manifests to activate genes, to repress genes, to silence genes. And really, it's the orchestra. It's the conductor of an orchestra. And that's what dictates actually how all the information in your genome manifests to control biology.

Alex Jani, X-Health.show: 9:54

How was that discovered?

Dr. Samir Ounzain, HAYA Therapeutics: 9:56

Oh, epigenetics has been understood at various levels for over 50 years. We've had lots of clues. There were different breakthroughs. I think the first obvious thing was, we understood very early that all of the cells have the same DNA. So all of your cells have the same DNA yet cells are very different – a cell in the heart, a cell in the liver. They have the same underlying code, yet, they have very different features and characteristics. That immediately created this concept that there's something regulating how the code in the DNA is manifested, how it's expressed. And then over 50 years, we've understood that there can be changes to the DNA that do not change the information but change how it's modified. And then we started to discover in more detail how DNA is structured in your cell. So it forms very complex three-dimensional structures and architecture within the concept of your chromosomes. It's packaged into chromosomes. These chromosomes can have very dynamic and complex 3D structures. And that involves proteins complex with the DNA. And when those proteins get modified, it changes the structure of the DNA, which then changes its activity. And so these are the processes that underlie epigenetics. And there's another, let's say, biomolecule that is central to epigenetics and it's actually what we work on at HAYA Therapeutics, which is there's the DNA component, obviously, there's the proteins that control the DNA structure and how epigenetics can happen. But there's a molecule that interacts with both and in a way synchronizes and conducts their activity, which is RNA.

Alex Jani, X-Health.show: 11:37

Awesome. How did you get involved? We'll come back to RNA. Yes. How did you get involved in this dark genome?

Dr. Samir Ounzain, HAYA Therapeutics: 11:47

I started my bachelor's degree, my undergraduate bachelor's degree, in biochemistry and molecular biology in 2001.

Alex Jani, X-Health.show: 11:54

That's the year.

Dr. Samir Ounzain, HAYA Therapeutics: 11:56

Exactly. So I'd actually always been interested in molecular biology from a very young age. So I decided to go to university to study biochemistry and molecular biology, which is essentially the study in the understanding of how does your DNA manifest at the molecular level to control biology, to control evolution, to control development. And when I started, my bachelor's degree was this seismic moment in the history of molecular biology and biology, which is the community published the draft of the human genome sequence. And that was the big shock at the time. Wow, 98% is not coding for protein. At the time, they call it junk DNA. So when I was starting my bachelor's degree, the whole world was trying to comprehend this concept that 98% of your genetic information is junk, is less

Alex Jani, X-Health.show: 12:46

Useless.

Dr. Samir Ounzain, HAYA Therapeutics: 12:46

Useless, exactly.

Alex Jani, X-Health.show: 12:47

Was there any discussion at the university?

Dr. Samir Ounzain, HAYA Therapeutics: 12:51

So to be really fair, there was already before the draft of the human genome sequence was published, there were clues. So the scientific community realized we had a lot of non-coding DNA. We didn't know exactly how much.

Alex Jani, X-Health.show: 13:05

But do you remember it when you were a student? Was it actually you know, a thing? Like, people thinking what's in there.

Dr. Samir Ounzain, HAYA Therapeutics: 13:12

Sure, it was a huge shock because we realized that 2% was coding for genes. Obviously, at the same time, between 2001 and 2003, we also had the full book of life of the mouse, of a fly and of all these other animals in the animal kingdom. And so we could compare. And we realized, at a gene level, we basically have the same number and complement of genes, proteins as a fly, sounds a worm. So you heard this expression that we have the same genes as worms and flies and we're identical. At the level of proteins, yes, we use the same proteins, they have the same functions, they're highly conserved. But then that raises the question, why is a human different to a worm, or to a fly? One of the first clues with comparative genomics was, as you looked at more complex organisms, in terms of organisms with more cell types, more complexity, more cognition, more able to adapt in very complex ways to the environment, the number of genes proteins did not scale with complexity. But what appeared to scale was the amount of the non-coding DNA. The dark gene. So if you look at the animal kingdom, some of the animals with the highest proportion of the dark genome are animals like humans. And as you go to and I hate to use the word more simple organisms, but if you go to, say, organisms with the less variety or number of cell types and tissues, the amount of the dark genome decreases significantly. So there's a ratio of protein-coding genome and dark genome.

Alex Jani, X-Health.show: 14:55

What would be the percentage for a fly or a mouse?

Dr. Samir Ounzain, HAYA Therapeutics: 14:58

Mouse is still pretty high. But if you go down to a bacterium, then you don't have hardly any dark genome. So if you look across the spectrum of all living organisms, the proportion of an organism's DNA that is associated with the dark genome increases and correlates with biological complexity. So that was a clue for everybody.

Alex Jani, X-Health.show: 15:22

So you wanted to work on that dark thing that we don't know anything about.

Dr. Samir Ounzain, HAYA Therapeutics: 15:29

Yeah, I mean, look, the dark genome term only really, I would say, came into kind of vogue the last five to 10 years, maybe. For most of my career, it was called junk DNA. It was like it's not conserved. It's not coding for proteins. It's just evolutionary trash that is accumulated over time, right?

Alex Jani, X-Health.show: 15:48

What attracted you then to the junk?[Mid-roll begins] We'll be right back. This episode is brought to you by the X-Health.show. And me, Alex. If you still haven't, please hit Follow at the top. That'll help me bring more of these visionaries to you. Thanks a lot. Stay awesome. Now, back to the episode. [Mid-roll ends]

Dr. Samir Ounzain, HAYA Therapeutics: 16:32

I was really interested in, at that time, what makes humans unique. Or what makes any animal unique. But in particular, I was always pretty blown away by the complexity, sophistication and traits of our species. I just thought it's incredible. Like, why are we so different from a dog or a cat? It's very human-centric, thinking we're so special and different. But there's definitely things that we've been able to do on this planet, just look around what we build or we've created. That always fascinated me. For me that a junk DNA was a potential explanation for how do you evolve and how do you program very complex biological processes like consciousness and all of these types of things. I was always a little bit obsessed with the concept of human consciousness. Where is that encoded? How is that programmed? Because I am a reductionist in the sense that I believe that consciousness is a product of the human brain, which is a product of the cells in the brain, which is a product of the information encoded within our genome. So I've always been a strong believer that we can uncover the secrets of our species and our relationship with all the other species around us. I can assume that's still work progresses, is it? So that's a long way away[laughter]. But when you're a bachelor student, you can have these bigger ideas. That in a way pushed me to the non-coding genome. And then I would say, I got a bit more settled in reality and a bit more pragmatic when I started understanding and learning more about the junk DNA or the dark genome, and came back to Earth and I realized: but this is also fundamental for human development, and also human disease. And you asked a question about epigenetics. Most of the, say, common and chronic diseases that plague society, of course, has a genetic component. And we can maybe go back to that because a lot of the genetic variation linked to common diseases found in the dark genome, we understand that now.

Alex Jani, X-Health.show: 18:34

They have a genetic mutation.

Dr. Samir Ounzain, HAYA Therapeutics: 18:36

Yeah, most of the genetic mutations for all these big common and chronic diseases are found in the dark genome. 98%, actually. It's funny, 98% keeps popping up. 98% of genetic variation linked to these common and chronic diseases is noncoding variation, send the dark genome. But also epigenetics. And I think when you look at these common and chronic diseases, we're all aware, most of them are caused by our lifestyle, our environment, what do we consume, what are we exposed to, what are the stresses, you know, psychological stresses, environmental stresses. That's what's driving obesity, heart failure, diabetes, hypertension, cancer. Pick your plagues of society that are having the biggest impact on society. It's these common and chronic diseases that are driven primarily by your environment.

Alex Jani, X-Health.show: 19:25

So it's basically that it's a response of the organism to the environment by switching on or off some of the genes. And here comes RNA. But this is just

Dr. Samir Ounzain, HAYA Therapeutics: 19:34

Exactly, and those switches that you you point to, are all non-coding. This is the core function of the dark genome, or the regulatory genome, as we like to call it. It's the orchestra. It's all of these very complex, sophisticated and holistic switches within the dark genome that are interpreting the environmental signals. So the information processing interface between your genome and the environment – it's the dark genome. So if you understand that, you now have a root cause mechanism that could potentially allow you to start reprogramming that epigene, reprogramming disease. That became then my obsession, how do these fundamental scientific insights into the regulatory genome provide a whole new generation of biological targets and a biological therapeutic paradigm for creating therapeutics for these big common and chronic diseases that plague society. one kind of RNA, right? So if you could first define, okay, so here's genes, then RNA. So DNA, RNA. And then the kinds of RNA and then the one that you picked. Absolutely. RNA is a very beautiful intermediate messenger of life. RNA can very dynamically, in a very sophisticated way, transfer the information from your DNA to other processes. And the most obvious well known understanding is messenger RNA. So this is derived from the 2% of your genome. And this is an intermediate message that serves as a template for protein synthesis. So the code is in your DNA. It gets transcribed into a messenger RNA. That messenger RNA serves as a template to be read by actually other types of RNAs, for example, transfer RNAs and allows the amino acids to be stitched together based on that code in the messenger RNA. And boom, you've got a beautiful protein. So messenger RNAs are translated for protein synthesis. And that's less than 2% of your genome. Now, what we realized with all these accelerating technologies around genomics, was, we reached the point where we couldn't just sequence DNA, we could sequence all of the RNA from a cell. And that was, I would say, the second shock to the system.

Alex Jani, X-Health.show: 22:07

What do they do? When was that?

Dr. Samir Ounzain, HAYA Therapeutics: 22:08

That was 2009-10. So 2000 and 01, 02, 03, we sequenced the DNA and we saw that 98% didn't have the correct code to make protein. So it was non-coding. And then between 2001 to 2010 sequencing technologies had exponentially accelerated and decreased exponentially in price, which allowed us to not just sequence the DNA of the cell, but to sequence every RNA. And we had the shock, which is most of the RNA isn't messenger RNA. Most of the RNA that your cell produces it's RNA from the dark genome. And the technical term for these RNAs are non-coding RNAs. So messenger RNA codes for protein, non-coding RNAs do not get translated into protein. They have an RNA-dependent function, they function themselves as RNA molecules. There's still a lot to learn and a lot to understand. But what we've discovered over the last 10 years as a community, is they can do two or three different things, they can act as guides, or scaffolds for proteins. Many of the proteins that we have, the 20,000 proteins, they're not intrinsically very specific in their activity. And what RNAs do is they can confer by acting as guides to these proteins or to scaffold the formation of protein complexes, they can confer specificity on the activity of proteins. You have an interest in epigenetics – many of the proteins that control epigenetic modifications, there's proteins called histone-modifying proteins... Histones are these proteins in your DNA that get modified by different types of proteins called histone-modifying proteins. Most of those histone-modifying proteins do not intrinsically have the ability to find the region in the DNA to bind. They don't have any specificity. Once they're in a certain location, they can modify histones. But how do those proteins get recruited and guided to the right place in the genome at the right time? A major function of these non-coding RNAs is to guide and recruit the activity of the proteins that control epigenetics. And the RNAs are exquisitely specific. So you can imagine these epigenetic proteins, the same protein is present in every cell in the body. How do you get different epigenetic states in a brain cell versus a heart cell, when the protein that actually lays down the marks is present in both? How you do that is you have very specific RNAs, dark genome RNAs produced in the brain, produced in the heart – only in those locations that then interact with those proteins and orchestrate their behavior, guide them and recruit them in the right place in the genome to silence or activate.

Alex Jani, X-Health.show: 25:13

How many of them do we have?

Dr. Samir Ounzain, HAYA Therapeutics: 25:15

These RNAs? Uh! I think the best quality public curations right now, which are very limited, by the way, would probably put a number in between 30 to 50,000 of these molecules.

Alex Jani, X-Health.show: 25:33

That's amazing.

Dr. Samir Ounzain, HAYA Therapeutics: 25:34

So that's just what's in the, let's say, high curation public domain, which is already double your genetic mRNAs. So it's your genes. We have about 21,000 genes. We already have very conservative estimate – probably 50,000 of these RNAs. However, one of the key features of these RNAs is they're incredibly specific and precise, which means that in order to discover them, you have to go very deep in a very specific cell in a very specific tissue in a very specific moment in time or in disease. And that's what we do at HAYA.

Alex Jani, X-Health.show: 26:11

Exactly that's what I wanted to ask now. How did you actually discover CARMEN and WISPER? How out of these more than 30,000, you discovered these two?

Dr. Samir Ounzain, HAYA Therapeutics: 26:26

I can tell you how we did that but just before I should say that, when you got very deep, looking in a specific cell in a specific disease in a specific tissue, you will discover 100,000 of these and 60 to 70% of them will be unique to that cell or that tissue. So if you do the maths, I would speculate there is hundreds of thousands of these RNAs. Hundreds of thousands – potentially even more. And once we've profiled and mapped, and uncovered the dark genome in every cell in every tissue, you're going to have orders of magnitude more of these RNAs than your proteins, your messenger RNAs. So how did we discover these molecules? Well, once you have an atlas and a map, and you've identified all of the RNAs in a given disease in a given tissue, then you need

to ask the question: 27:15

but which of these thousands is really important for a specific process?

Alex Jani, X-Health.show: 27:21

What tissue may be first? Because did you choose...

Dr. Samir Ounzain, HAYA Therapeutics: 27:24

We started in the heart. [This conversation continues on the podcast]