S3, E07: (Re)programming Stem Cells for Drug Development

Mark Kotter (00:01):
What's unique about bit.bio is not really the use of these pluripotent stem cells. It's the way that we turn these stem cells into the cells that we want to use, for example, drug discovery purposes or therapeutics purposes. So for example, if you want to study neuroscience disease or brain disease, then ideally you want to use the cells that actually exist in the human brain, and the conversion of the stem cell to these brain cells has been really quite tricky. And that's one of the things that bit.bio is solving.

Gina Mullane (00:49):
The average time to develop a therapeutic today is 14 years. Historically for most of the drug development process from discovery through toxicity testing, and up until clinical trials, there has been a missing piece, the ability to test compounds on a full range of disease relevant human cells, including those that can be challenging to harvest, that is until now. Scientists have discovered that pluripotent stem cells can be used to create brain cells, skin cells, and other cell types to help us better understand how a drug interacts with the body before it ever reaches the clinic.

If we can reliably obtain human cells for use in preclinical research, what insights might we gain and could these insights help us bring drugs to market faster? I'm Gina Mullane, and in this episode of Vital Science, Chris Garcia speaks with Dr. Mark Kotter, founder and CEO of bit.bio. We'll discuss bit.bio's game changing technology for reprogramming stem cells consistently, how the company aims to accelerate pharmaceutical research and what this paradigm shift could mean for the future of drug development and therapeutics at large.

Chris Garcia (02:05):
Welcome to Vital Science Mark. Thanks for joining us. Can you tell us a little bit about yourself and how you came into the field of neuroscience?

Mark Kotter (02:13):
Yeah. Thanks Chris. Thanks for having me on your podcast. So my background, I'm a medic with an interest in neuroscience and stem cells. I ventured into research after my medical degree, was very interested in brain repair, did a PhD at the university of Cambridge, and then combined my career as an academic and a junior doctor until a point where we spun out bit.bio.

Chris Garcia (02:44):
Can you tell us more about bit.bio and your role there?

Mark Kotter (02:48):
So I'm the scientific founder of bit.bio. We try to overcome some of the challenges of pluripotent stem cells and their use for research, but also in the context of therapies and struck lucky by finding a way of generating homogeneous and pure cell types. And this led to a patent application and ultimately then to the generation of two companies.

Chris Garcia (03:18):
Mark, can you explain to our audience the difference between stem cells, IPSCs and bit.bio's reprogrammable technology.

Mark Kotter (03:26):
So stem cells or pluripotent stem cells are the origin of all cells in the human body. They used to be taken from embryos. So these are embryonic stem cells, but in 2006, 2007, Shinya Yamanaka came up with a protocol using transcription factors that allows you to induce stem cells from skin cells. And these are so called induced pluripotent stem cells. So in a way, the IPSCs and the ESCs are very similar in terms of the use case. Biologically, they're very close as well. And what you can do with these cells in tissue culture is to create the cells that we have in our body. Because of course, we very quickly move on from being a lump of stem cells, to creating an organism during development.

What's unique about bit.bio is not really the use of these pluripotent stem cells. It's the way that we turn these stem cells into the cells that we want to use for example, drug discovery purposes or therapeutics purposes. So for example, if you want to study neuroscience disease or brain disease, then ideally you want to use the cells that actually exist in the human brain, and the conversion of the stem cell to these brain cells has been really quite tricky, and that's one of the things that bit.bio is solving.

Chris Garcia (05:02):
And how are these reprogrammable cells applied to drug development?

Mark Kotter (05:06):
The big difference between cells that have been differentiated from stem cells and cells that we program from stem cells is the consistency and the scalability at which we can achieve those. So for example, take a neuron, it takes 60 days, maybe sometimes 80 days to create a neuron from a stem cell using conventional traditional direct differentiation. If we program this cell, this happens within a few days and not only the speed is different, but also the consistency and the reproducibility is very different. Differentiation entails a lot of different steps with chance events called sulfate choices and this causes inconsistencies. However, if you reprogram a pluripotent stem cell using our technology, you get a very homogenous culture, it's very reproducible. And what this allows you to do is you can now use these cells for large scale screening applications. And this is really important because so far, most of the drug discovery has been done on animal cells.

And what we've learned over the last decades is that there seems to be a difference between an animal cell and a human cell in many cases. And some of the diseases that we want to treat are uniquely human as well. So in order to actually create drugs, we had to engineer animals to create so-called animal models of the disease that we want to treat. And often, these disease models weren't a hundred percent the same as the diseases that we'd like to treat in the clinical setting and this mismatch in terms of species and in terms of the disease has contributed to some of the difficulties to create new medicines.

Gina Mullane (07:19):
As mark mentioned, stem cells can dramatically improve drug developer's ability to screen new drugs for side effects much earlier in the development process, significantly lowering costs and potentially shortening the time to market. Right now, new therapeutics go through extensive animal trials before they are ever administered to humans. This is both time consuming and expensive. And even if a drug appears safe in animals, there is no guarantee that the same will be true for humans. bit.bio's technology allows us to test new compounds on human cells before entering clinical trials. For example, a drug developer may wish to test a drug on liver, kidney, and heart cells, where the most common side effects can occur. Let's hear more on how these different types of cells are generated.

Chris Garcia (08:11):
So how does bit.bio software inspired approach facilitate reprogramming cells into various human cell types?

Mark Kotter (08:18):
So the unique thing about bit.bio is that we use a completely different paradigm in biology. Traditionally, if you wanted to take a stem cell into say, brain cell or a liver cell, you try and recapitulate what happens during development. You essentially expose cells with chemical cues that push them down various lineages, and that is very difficult and very difficult to reproduce. Now, reprogramming is a totally different paradigm. It's built on the understanding that cells are defined by the programs that are active. So if you think about a cell, the nucleus contains all the different genes. We've got 20,000 of them in a human cell in any particular moment in time, there's about 10,000 genes active, and these genes dictate the function and the identity of a cell, and these 10,000 genes are again controlled by a class of proteins called transcription factors.

So these are the regulators, they determine which genes are on or off. Based on that paradigm, which sounds much more like a software paradigm than a traditional biological paradigm, scientists such as Yamanaka were able to show that it's sufficient to activate transcription factors to create a new cell type. So what Yamanaka managed to do is, he found a transcription factor combination that can turn a cell into a stem cell. And then others in the field like Marius Wernig show that there are transcription factors that turn cells into brain cells. So bit.bio uses this synthetic biology approach, this reprogramming approach, and applies it to stem cells. And what this allows us to do is to create very defined, very precise cells at scale and with speed.

Chris Garcia (10:29):
And how does this reprogrammed approach create consistent batches of human cells?

Mark Kotter (10:34):
So every cell type has a particular transcription factor combination that defines its identity, and the key here is to activate this transcription factor combination with position and consistency. So what bit.bio has, is essentially a method that allows you to control these transcription factors in a very precise manner, and this then allows you to create these consistency that you require. For example, the context of high throughput screening.

Gina Mullane (11:12):
A key technology in drug discovery is high throughput screening, where compound libraries are used to find drugs that can modulate biological aspects relevant to disease. These libraries can contain millions of compounds. And when repeating high scale experimentation with millions of compounds, the cells being used must be consistent in order to yield reliable results. The value bit.bio's technology brings to throughput screening is not only scalability by helping drug developers reach the cell numbers that are required, but also consistency by providing a product that is consistent batch to batch.

Chris Garcia (11:52):
Past research has shown that it's very difficult to create large numbers of consistent cells from IPSCs which has caused real problems in high throughput drug screening. What benefit is it to use bit bios reprogrammed cells?

Mark Kotter (12:05):
So the past paradigm cell differentiation really consisted of nudging cells down with chemicals from one intermediary cell type to the next until you reach, for example, a brain cell, a neuron or a muscle cell, and on the way these cells encounter much of a branch points at which they have to decide which cell they become, and this is called self fake choices. The problem with these self fake choices is that they're based on chance event, probabilistic events. And so traditional protocols were accumulating these chance events and as a result were quite inconsistent. And if you then use inconsistent batches to screen for drugs, the reproducibility is a struggle. And that means it's very difficult to tease out the drugs that can actually have an impact on the disease process that you're studying. Now with reprogrammed cells, you can create batches of cells that are extremely consistent, batch to batch but also inter-batch, essentially. And it's also very scalable. And I think these are the two sort of major advantages of using reprogrammed cells.

Chris Garcia (13:42):
Mark, how many cells are used for each of these screens that we're talking about?

Mark Kotter (13:46):
I think Charles, our partners, Charles River know a lot more about how many cells they require. It will depend on the assays, but we're talking in the right of billions of cells.

Chris Garcia (13:56):
And can you produce the billions of cells needed for HTS?

Mark Kotter (14:02):
Absolutely, yes. That's really one of the key advantages.

Chris Garcia (14:07):
It sounds like this technology could open a lot of doors for drug developers. Can you tell us how bit.bio's mission of coding cells for cures might translate to a new generation of cell and gene therapies?

Mark Kotter (14:18):
So cell therapies rely on the concept that the cell actually becomes the medicine. And the amazing thing about cells is that they can not only replace lost cells, but they can also interact with the environment and therefore become much more potent medicines. And we've seen this in the context of the first cell therapies that are now used in clinic, so called CAR T cell therapies. These are engineered immune cells that were able or are able to cure cancers that weren't curable before. So it's very powerful medicine. The problem with cell therapies at this point in time is that they're extremely expensive. And this is because for a CAR T-cell, your own cells are being sample and used, then engineered and then put back into the patient. So you can imagine that this is a very complex and very expensive process. In fact, at this point in time, these therapies cost many hundred thousand dollars.

What stem cell derived cells promise is that you can bring the costs down, because you can now engineer them and produce them in house, so to speak. But traditional stem cell differentiation faces the same limits that we've discussed before, which is issues with scalability and consistency. And of course, for a medicine you want even higher consistency than you need in the context of drug screening. So we feel at bit.bio that our technology can solve these basic bottlenecks are of translatability that we can actually create cells with consistency at scale that are robust enough for medicine.

Chris Garcia (16:21):
And ultimately are these reprogrammed cells intended to replace donor cells?

Mark Kotter (16:26):
Absolutely. We just discussed how difficult the processing of donor cells is, and if you had an in-house manufacturer of human cells, that you can transplant, you get much more consistency and scalability. And of course, that would make these cell therapies available to a much greater patient population. At the moment, you could call them very expensive experimental medicine paradigms, but my definition of a medicine is that everyone can benefit from it. And I think that's really what motivates us to create cells for therapeutic use.

Chris Garcia (17:14):
So besides the various cell types, I understand you've also had success reprogramming these cells to be more disease relevant, that you're reprogramming cells to mimic diseases such as Huntington's, ALS, Alzheimer's and Duchenne muscular dystrophy or DMD. How will these disease relevant cells help to develop better assays?

Mark Kotter (17:33):
So disease relevant means that these cells actually display a phenotype that is relevant for the condition. So as you know, DMD is a genetic disease that's based on a mutation in dystrophin and this brings along a very tragic condition which affects mainly young male patients. And so if you wanted to create a drug to address this condition, the best starting point would obviously be a human muscle cell that is affected by this condition. And so what you can do with reprogrammed cells, you can create isogenic models. You can actually introduce these genetic mutations into the cells that you produce. And that allows you then to contrast this with a wild type muscle cell and study what's wrong in the context of this disease. And that, of course, is the case for the other conditions that you have mentioned ALS, Alzheimer's, Huntington's disease.

Chris Garcia (18:56):
And what impact will these disease relevant cells have on accelerating drug development?

Mark Kotter (19:01):
The key issue, again, in this context is that we can use reprogramming to create disease models that are scalable and reproducible. Ultimately, when it comes to drug discovery, you really need the consistency in the scale in order to run your high throughput screening campaigns or your high content imaging campaigns, and doing so allows you to very systematically study what's wrong, but also discover the compounds that may make a difference.

Chris Garcia (19:44):
What about the impact of accelerating or improving successful translation in the clinic?

Mark Kotter (19:49):
Yeah, I think, the major impact is that you can actually now use human cells in the context of these screening campaigns, because what we've had so far is mainly animal cells and cell lines being used in this context, which in some instances fundamentally different from the cells that we want to treat in a patient in terms of species, but also in terms of actual disease. So for example, taking Alzheimer, it's not been possible to create sufficiently consistent large batches of brain cells that are affect by Alzheimer's. And so what scientists have done is they've created mouse models that look like Alzheimer, but using these mouse models, we've not been really very good at developing Alzheimer drugs. I don't think there is an approved... Well, there's one approved therapy now, but there's been a lot more that failed. By actually using cells that are affected in our human bodies, I think we can improve the odds of translation and ultimately bring down the costs of drug development.

Chris Garcia (21:19):
And how can bit.bio's technology support rare disease research.

Mark Kotter (21:24):
I think again, because rare diseases are often based on genetic mutations, these reprogrammed cell models are really extremely applicable. For example, think about Duchenne's or you think about Huntington's, you can literally study the cells that are affected in these conditions in your labs or in your drug discovery processes.

Chris Garcia (21:57):
As an industry, we are still finding our way in the field of cell and gene therapy. However, moving from concept to clinic is not always straightforward. What sets the work that bit.bio's doing apart from the others?

Mark Kotter (22:10):
You're right, this is extremely difficult and complex and we are experiencing this as we are on this journey. I guess what sets us apart is that we don't struggle with the scalability or the consistency of our protocols from the onset onwards. But that doesn't mean that translation is easy. We still need to make sure that the protocols are GMP. We need to make sure that the cells reach the functionality that they require, that the consistency is reached and demonstrated using qualified assays, that the cells actually do what they're meant to do in a preclinical setting. And that our ID fighting is successful.

Chris Garcia (23:05):
Mark, in what ways can contract research organizations help programs such as yours?

Mark Kotter (23:11):
Getting a cell therapy into the clinic requires a lot of heavy lifting. And of course, CROs like Charles River have a lot of experience doing that. So there's many aspects where I think we could collaborate. This includes, GMP development, the manufacturing of cell products, the qualification of assays, maybe even the distribution of product all the way to the clinical trials, the design of clinical trials, the execution of clinical trials.

Gina Mullane (23:56):
But bit.bio's role in therapeutics doesn't end there, for most of human history our approach to treating disease has been clinical to address symptoms in order to alleviate pain. The relatively new field of regenerative medicine allows us to go a level deeper to directly treat the tissues or organs that have been damaged by disease or trauma. To date, tremendous progress has been made in the field of cellular therapy, which involves the transplantation of human cells to replace or repair damaged tissues in cells. But we're just seeing the tip of the iceberg when it comes to what is possible in this promising field. There are still several challenges that stand between drug developers and a reliable, consistent, and scalable platform for sourcing human cells. Let's hear from Mark on what he sees on the horizon for cell therapies. And the part bit.bio could play in getting us there.

Chris Garcia (24:53):
And tell us what's next for the future of cell and gene therapy development?

Mark Kotter (24:57):
So I think the most exciting point for me is that we are seeing the field going beyond the initial use of cell therapies in the very narrow context of oncology. So just before Christmas, last year, we heard how Vertex reported the first diabetic patient being cured with a cell therapy derived from a pluripotent stem cell. And that's a huge game changer because we are moving into what has been promised now for decades, which is the field of regenerative medicine. So at this point in time, we're still struggling with technical difficulties in terms of manufacturing these cell types, and I think technologies like reprogramming can make a huge difference here, because it allows you to create cells with consistency at a scale. And that is the major bottleneck at this point in time.

And it also allows you to create new therapies that are going to be much less expensive than the cell therapies that we are currently having in our clinic, but also the manufacturability, in terms of price, needs to come down so that we can treat conditions where perhaps the treatments can't be as expensive. Think, for example, autoimmune diseases, infectious diseases in comparison to cancer. So we need to make these cells much more affordable and available. And then the approach here is to enable in-house production of cells. So ideally off the shelf or matched in some paradigm. And I think if all these pieces come together, we will see a third wave of medicines, which is based on cells as medicines.

Chris Garcia (27:19):
Well, I think that's the perfect note for us to end on. Mark, thanks so much for your time today. I really learned a lot and I'm sure our audience did as well.

Mark Kotter (27:27):
Thanks Chris. It was a pleasure to be with you.

Gina Mullane (27:30):
Dr. Mark Kotter is founder and CEO of bit.bio. In our next episode of Vital Science, we'll talk with Aled Edwards of M4K Pharma about how the company is using open science to advance new cures for childhood diseases. Until then, thanks for listening.