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Delivering neoantigen peptides with nanoparticles

First Author Conversations Podcast

Episode 7: Delivering neoantigen peptides with nanoparticles,
Geoffrey M. Lynn, Ph.D., Avidea Technologies

Posted: Feb 11th, 2020

In this episode, Dr. Geoffrey Lynn talks about the development of a polymer-based antigen delivery technology- SNAP, or self-assembling nanoparticles, displaying a patient’s own neoantigens to induce a CD8 T-cell response and tumor regression in animal models. The work was published on Nature Biotechnology on Jan. 13th 2020, “Peptide–TLR-7/8a conjugate vaccines chemically programmed for nanoparticle self-assembly enhance CD8 T-cell immunity to tumor antigens”.

Geoff first introduced personalized cancer vaccines. He then explained how one class of therapies- checkpoint inhibitors unleashes the immune system to attack cancer.

"Now the reason why precision medicine or personalized therapy is important is because… each cancer is going to have a unique set of mutations…, if we want to leverage the immune system, we may have to target a unique set of cancer antigens or these mutations which are often referred to as neoantigens".

By sequencing DNA and RNAs from a tumor, as well as using bioinformatics methods, one can identify predicted peptide neoantigens, and create a patient specific vaccine.

We discussed the different delivery vehicles for personalized cancer vaccines. "When you have a peptide antigen, that's exactly what you want to display to the immune system. So there's no concern that if you have a DNA, RNA expression system or virus that your antigen won't be expressed in vivo… They [peptide antigens] are a very modular platform."

Geoff further explained how his team was able to stimulate a stronger immune response by combing peptide antigens with specific adjuvants, Toll-like receptor 7/8 agonist.

The final challenge they tackled in this work is the amino acid sequence variability and physical/chemical heterogeneity of peptide neoantigens. This is why SNAP technology is developed and where SNAP comes in handy. SNAP links neoantigens to a polymer that self-assemble into the same particle size, the same amounts of peptide antigen in each particle, and the same overall charge of the particle. Geoff specifically acknowledged GenScript's support in building thousands of peptides for them to evaluate and develop SNAP technology, especially "peptide antigens that are very rare, are the most hydrophobic, the most charged, and the most hydrophilic", Geoff said, "this allowed us to really prove the versatility of the technology; so that was quite critical to really convincing us as well as potential funders, that we've really addressed this issue of allowing for consistent formulations with any peptide antigen."

Dr. Lynn is the CEO of Avidea Technologies. This publication is also highlighted in a BioWorld article, “Standardized delivery of unique neoantigens improves T-cell vaccines”.

Full Transcript »

Tracy:
Hello everyone. It's 2020. We are thrilled to come back. Today, I'm happy to share with you that I have my colleague, Dr. Raymond Miller with me. He's our Global Product Manager for our molecular diagnostics and therapeutics material portfolio.
Tracy:
Welcome Ray.
Raymond:
Thanks for having me, Tracy.
Tracy:
Our guest for today is the CEO of Avidea Technologies, Dr. Geoff Lynn. Geoff, thanks for joining us. You recently published on Nature Biotechnology as the first author. Congratulations again.
Geoffrey Lynn:
Thank you Tracy, and thanks for allowing me to be here.
Tracy:
Before we dive in, can you briefly introduce yourself and Avidea Technologies?
Geoffrey Lynn:
Yeah, hello to Tracy and Raymond, and all of your listeners out there. This is Geoffrey Lynn. I'm the CEO of Avidea Technologies. What Avidea is doing is developing polymer-based immunotherapies that aim to improve the safety and efficacy of treatments for cancer, infectious diseases, as well as, allergy and autoimmunity.
Tracy Yin:
Thanks Geoff. Maybe a little bit more about your background?
Geoffrey Lynn:
Yeah. The way I came to get involved with Avidea is I started as a MD-PhD trainee doing a PhD project between the National Institutes of Health and Oxford University in England. And the goal of that work was to develop a vaccine that induces T cell immunity for treating cancer, as well as, certain infectious diseases, such as HIV, tuberculosis, and malaria. The reason why we were interested in a vaccine that's able to induce T cell immunity is because most of our currently licensed vaccine technologies will work by inducing antibody responses. So many of the childhood vaccine programs are very effective and they work by mediating antibody responses that prevent infection. However, for cancer and certain infectious diseases, where we don't currently have vaccines, we likely need a T cell mediated response to provide protection or treatment of established infection or disease [cancer]. And so, the goal of my work at the Vaccine Research Center was to develop a T-cell based vaccine.
Geoffrey Lynn:
Just as a little bit more background in terms of how this relates to Avidea; I worked very closely with researchers at the Vaccine Research Center; at another Institute in Prague, Czech Republic, that's the Institute of Macromolecular Chemistry; as well as with researchers at Oxford university's Department of Oncology as well as the Jenner Institute. And, what we did is, over several years, developed vaccine candidates that we thought would be effective for inducing T cell immunity. We built different candidates, screened these in animal models at the Vaccine Research Center and did this as part of an iterative process that eventually led to a vaccine technology that we decided to spin out and commercialize as a part of Avidea Technologies. Several of the scientists who were involved at the academic institutions are now either scientists at the company, providing management as well as scientific roles, as well as scientific advisors. And, so, Avidea is the vehicle to move this technology forward, to develop it in hopes that we can advance this technology to the clinic.
Tracy:
I met Geoff like three years ago, I believe back in 2016, so since then GenScript started to support your projects. Five years past, and precision medicine is really taking off, and we are really excited to see your progress in developing your platform in the application of personalized cancer vaccine. To maybe give us a very brief start, what is a personalized cancer vaccine and why from your perspective you think this PCV is more effective?
Geoffrey Lynn:
Yeah, Tracy, great points. And I want to also address as part of this question, how we worked with GenScript. Because I mentioned the work that I did between several institutions before founding Avidea, but I'd also like to highlight and give my thanks to GenScript's role in this work as well. So I'll come back to that.
Geoffrey Lynn:
So the first part I want to address is: what are personalized cancer vaccines? And I want to think about this in two ways. So the first is, I think, for several decades, oncologists and immunologists were aware that due to the inherent genetic instability of cancers, the cancers accumulate mutations. And it was believed that those mutations could lead to mutated proteins, that when viewed by the immune system, may look foreign. As you know, our body's immune system is able to clear an infection, because they differentiate between our self-proteins, those are proteins produced by our own cells, and differentiate those from protein or other components that are part of viruses or other microorganisms.
Geoffrey Lynn:
And so that's the way the immune system differentiates between cells [self] and foreign pathogens. And what was believed is that the immune system could also differentiate between healthy cells and cancerous cells, on the basis of recognizing these mutant peptides or mutant components that might be part of the cancerous cells. And so the challenge in trying to realize some benefit for patients is that, we didn't quite understand how to leverage the immune system to target these mutations in cancers. However, as many of your listeners may be aware, in the last decade there's been tremendous excitement around a class of therapies called checkpoint molecule or checkpoint inhibitors, which are able to unleash the immune system to attack cancer.
Geoffrey Lynn:
And what these treatments are showing us is that many patients actually have preexisting immune responses that recognize their cancer. And so if you come in with a checkpoint inhibitor, you can unleash those preexisting responses and those patients can actually, in some cases, are able to clear even advanced cancers that were otherwise untreatable with conventional cancer treatments such as radiation, chemotherapy and surgery. And so this has led to a lot of excitements in the field of immuno-oncology, by showing that you can leverage a patient's immune system to kill cancer by targeting mutations that are specific to that cancer.
Geoffrey Lynn:
Now the reason why precision medicine or personalized therapy is important is because, as I noted, each cancer is going to have a unique set of mutations. And, so, if we want to leverage the immune system, we may have to target a unique set of cancer antigens or these mutations which are often referred to as neoantigens.
Geoffrey Lynn:
The other important point to make here is that, we don't know what those neoantigens are unless we actually go into the tumor, sequence a patient's tumor and identify those patient's specific antigens that are unique to each tumor type [patient]. And, so, the idea behind a personalized cancer vaccine is driven by the fact that one, we know that patients with T cell responses can have a good benefit from checkpoint molecules, and clear otherwise aggressive tumors. The problem is that many patients lack a preexisting T cell response, and so it's important to induce a T cell response in people who do not already have one. One way to do that is to use a personalized cancer vaccine.
Geoffrey Lynn:
The paradigm for personalized cancer vaccines is to biopsy a patient's tumor, sequence protein-coding DNA and then sequence the RNA to identify which of those mutant DNA sequences are expressed through RNA, which would then lead to a mutant peptide sequence expressed by those cancer cells. Based on the sequencing as well as informatics algorithms, what you can do is identify, what we call predicted neoantigens. These are mutant peptides in a patient's cancer cell that are predicted to be displayed on the cancer cell and recognized by T cells.
Geoffrey Lynn:
So once you identify patient specific neoantigens, you can create a patient specific vaccine. And one way to do that is to produce those neoantigens as peptides, and then combine those in a vaccine to be used to administer to a patient.
Raymond:
Hey Geoff, that's a really great overview in terms of the background behind personalized cancer vaccines and how one would go about invoking an immune response. One of the things that I've been struck in reading literature and then reading your publication, is how many different options there are for delivery vehicles for personalized cancer vaccines. I mean, to your point, not just peptides, but also RNA-base vaccines. Could you kind of expand a little more on why you decided to take a peptide specific approach?
Geoffrey Lynn:
Yeah, it's an excellent question. The way you think about a vaccinologist toolbox is, you really have three different types of vaccine technologies.
Geoffrey Lynn:
There are protein or peptide based vaccines. This is if you take the antigen itself and formulate that with an adjuvant or a particle to try to elicit an immune response directly with the peptide or protein antigen. There's DNA and RNA based vaccines. And for these, you encode the peptide antigen in the DNA or RNA, and this has to be expressed in situ, following administration.
Geoffrey Lynn:
The other kind of technology you have is viral based vaccines, and again similar to DNA and RNA based vaccines, you can actually encode your peptide antigens into a viral vector and then administer this to the patient to increase expression by the virus in the patient to induce an immune response.
Geoffrey Lynn:
Without getting too much into how these differentiate, the reason why we and others have selected peptides, is because, as you know, they can be rapidly manufactured, using entirely synthetic technology, and largely automated technologies. And the other thing is, when you have a peptide antigen, that's exactly what you want to display to the immune system. So there's no concern that if you have a DNA, RNA expression system or virus, that your antigen won't be expressed in vivo. If you already have the peptide, and you can manufacture that through entirely synthetic means, that certainly allows some benefits in terms of cost and scalability, but then it also takes the guesswork out. You don't have to worry about whether or not your protein or peptide antigen is going to be expressed. You're giving exactly what you want the immune response to recognize in the form of that peptide or protein antigen.
Raymond:
So if I understand you correctly, it's really about having a vaccine delivery system that is very specific in terms of targeting only cancer mutations, And not having any sort of off target effect. And that by using this peptide based approach, you're able to avoid any sort of challenges with encoding something that the immune system can't recognize. So going from DNA to RNA, protein, take out all those little pieces and just go right to the delivery of the peptide.
Geoffrey Lynn:
Yeah, exactly, Raymond.
We do think that there's some excellent DNA, RNA and virus technologies out there, but, one of the biggest advantages with peptides actually, is that they're a very modular platform. So peptide antigens alone are weakly immunogenic. However, the benefit of that is that you can combine them with specific adjuvants; these are components added to a vaccine to enhance or modify the immune response to the antigen. And these adjuvants can be added in a way to get the specific type of immune response that you want. So that's actually, I would say, maybe one of the biggest advantages of peptide antigens, is that they're completely modular. It can be mixed and matched with specific adjuvants to get the desired immune response that you need.
Tracy:
So you made a good point, the adjuvants. And I know you've been working on Toll-like receptor seven/eight agonists. Maybe you can also elaborate a little bit here?
Geoffrey Lynn:
Yeah. And so let me tie this together. So, we wanted to have a modular system that focused the immune response against specific neoantigens. And so we selected peptide neoantigen based subunit vaccines. However, as I mentioned, if you just have the peptide antigen without immune stimulation it's not going to generate a T cell response. So you have to combine that peptide antigen with specific adjuvants that induce a T cell response. And the type of adjuvant that we focused on is called a Toll-like receptor 7/8 agonist. And Toll-like receptors 7/8 , naturally recognize single stranded RNA from viruses. And so agonists that bind that receptor induce an antiviral type immune response, which is also the type of immune response that you need to fight cancer.
Geoffrey Lynn:
So what we wanted to do is combine these adjuvants, Toll-like receptor 7/8 agonists, with peptide antigens to induce anticancer T cell immunity.
Geoffrey Lynn:
So the way we thought to go about that was to use Drosophila cells, which have an analogous VHL HIF pathway, just like in humans. And we decided if we knocked out VHL in fly cells and we looked for something synthetic lethal in that setting, and we did the same, knock it out or use these ccRCCs where it's already knocked out, in human cells and we find something that's synthetic lethal there. Anything that overlaps between a Drosophila cell and a human cell, which are so different, that relationship that we might find should be something that is fundamental and really robust. And if it's true in a human, and it's true in a fruit fly, we expect it will hold true across small variabilities between cell lines and between human patients.
Geoffrey Lynn:
Now the reason why we were motivated to develop what we call SNAP technology, is because we understood a major problem for peptide antigens, which is that due to the amino acid sequence variability, unique peptide neoantigens are going to have variable physical and chemical characteristics. And what that means is, that some of those peptide neoantigens are going to be highly positively charged or negatively charged. Some will be neutral, others will be hydrophobic, some will be hydrophilic. And that range of physical and chemical characteristics can be very challenging to induce the same response every time.
Geoffrey Lynn:
And so our motivation for developing SNAP, which is self-assembling nanoparticles based on amphiphilic polymers, was to try to standardize peptide antigen delivery in nanoparticles and try to account for the variability of the peptide characteristics. And so what we did is set out to try to understand how do we take any peptide antigen, irrespective of its underlying characteristics, and have it self-assemble into a nanoparticle of the same size and characteristics each time? The other aspect is, we also want to include in those particles Toll-like receptor 7/8 agonists that are able to act as an adjuvant and induce T cell immunity against the antigen encoded or formulated within those particles. So that was our motivation for developing the SNAP technology, that includes Toll-like receptor 7/8 agonists that can be used as a vaccine for inducing T cell immunity against peptide antigens.
Raymond:
Very awesome. So if I understand correctly, SNAP is a very modular approach where you could start with a different mixture of peptides encoding different neoantigens for specific patients with essentially different tumors. And then what you and your team have done here is, you built a system where you can kind of, in a very modular manner, modify these peptides to have the right properties to make these nanoparticles. Is that correct?
Geoffrey Lynn:
Absolutely. And one of the key points here is, in working at the Vaccine Research Center at NIH as well as with the groups over Oxford and other institutions that we collaborated with, what we understood is that if you take a soluble peptide antigen or a native peptide antigen, it may not be effective for inducing an immune response. However, if you reformulate that peptide antigen into a particle format, with adjuvant, it's much more effective for inducing T-cell immunity. The reason why is our body has, what we call the Lymphatic System, and what this functions to do is concentrate antigen in the lymph nodes that can be sampled by T cells, and those T cells can be activated to recognize the antigen in that lymphatic tissue.
Geoffrey Lynn:
Now what's important to note is that particles are able to concentrate antigen in lymphoid tissue for recognition by T cells. So what we knew going into the development of the SNAP technology is that we wanted to deliver peptide antigens, including neoantigens, in a particle format. Now, as many of your listeners likely know, there are a lot of particle delivery technologies out there. What we alluded to is a key challenge is: how do you get a consistent loading of different peptide antigens, including neoantigens, into a particle each time? What we did is we've linked peptide antigens, to a polymer that induces nanoparticle self-assembly. The beauty of this technology is you can take multiple of these peptide polymer conjugates, we'll call them a peptide neoantigen conjugate, and mix them together in equimolar ratios and you can then simply add water, and this induces that mixture to assemble into a mosaic particle. And what that allows you to do is have a lot of control over the composition of your nanoparticle vaccine.
Geoffrey Lynn:
So, for example, if you have a patient with multiple different peptide antigens, you can simply mix those peptide antigens together and then simply add water to induce particle self-assembly and then you end up with a particle that reflects exactly what you put into that mixture. Now the benefit of this is that you have very consistent formulations, irrespective of the underlying peptide antigen characteristics. And this is, I would say, a major development in particle formulation, because a lot of existing particle formulation technologies are entirely empirical. And what that means is, you would end up with different characteristics each time. And so what the [SNAP] technology allows you to do is have consistent characteristics, irrespective of the underlying antigen composition.
Raymond:
Yeah, that's incredible. I mean, looking at some of the data within your publication, I was struck by how even the size each of these nanoparticles where were, regardless of the peptides that were used, regardless of the tumor that you had assayed and developing a treatment to combat. It's really impressive.
Geoffrey Lynn:
I did want to come back to this point and say that to Raymond's point there about, what was needed to develop this technology was a tremendous R&D effort to try to understand how do we build a peptide antigen linked to a polymer that self-assembles into the same size particle each time with the same overall characteristics? And what I mean by that is: the same particle size, the same amounts of peptide antigen in each of those particles and the same overall charge of that particle.
Geoffrey Lynn:
And I really want to emphasize here that it was a huge collaborative effort with the different groups that I mentioned earlier, as well as a partnership with GenScript. And we worked very closely with GenScript over several years, building a lot of peptide antigens to evaluate, to try to systematically develop this kind of technology. And so it quite literally took us thousands of peptides that we built with GenScript, and evaluated in different, in vitro and in vivo models, to try to establish that, one, we could systematically develop a technology that can allow for consistent self-assembling nanoparticle formulations of peptide antigens each time, and then actually prove that we could do that with even the most challenging peptide antigens. And so I'll say that we selected peptide antigens that are very rare, are the most hydrophobic, the most charged, and the most hydrophilic and asked GenScript to synthesize these with our modifications. And GenScript's peptide chemists worked very hard to synthesize even the most challenging sequences. But this allowed us to really prove the versatility of the technology; so that was quite critical to really convincing us as well as potential funders, that we've really addressed this issue of allowing for consistent formulations with any peptide antigen. So Tracy, I want to thank you and your colleagues over at GenScript for really enabling us to be able to do this work.
Tracy Yin:
Thank you very much for letting us have this opportunity to support. So what's the next step, Geoff? Any plan for clinical application?
Geoffrey Lynn:
Yeah, Tracy, I'm excited to talk about that. So as you can imagine, this is a very competitive field and there's a lot of different technologies out there under development. And I'll say that when we set out to develop this vaccine technology, when we spun Avidea out of NIH in 2016, our goal was to make a peptide based personalized cancer vaccine technology that addresses the main limitations of current peptide based cancer vaccines.
Geoffrey Lynn:
And if you look back, in 2015, 2016, the main limitations were that you have challenges in terms of manufacturing consistency and formulation consistency, depending on the peptide antigen composition and you also have, oftentimes weak and variable immunogenicity. And what I mean by that is, if you take what was published at that time, is if you took say a hundred predicted neoantigens, you may only get responses against about 10% or less of the predicted neoantigens. And what I mean by that is CD8 T cell responses that are needed to mediate tumor clearance. And so we looked at that problem, we said, "Okay, we believe we can systematically address this with the SNAP technology." And it took us about two years to systematically develop the technology and then validate it through pretty extensive animal studies. And based on that, we were able to secure financing to move the technology forward into clinical trials.
Geoffrey Lynn:
And so we haven't made an announcement publicly about a partnership that we've secured with a group that we're very excited to work with, but it's a company with a complementary technology to ours. And what we're doing as part of this cooperation is moving our cancer vaccine to clinical trials by Q2 2020 of this year, so we've started manufacturing a vaccine as well as completing the IND-enabling studies to move this to clinic, and are excited to start to move this technology forward to patients by the end of this year.
Raymond:
That's really impressive progress that you've made just in four short years. And obviously we're extremely excited to have not only partnered with you, but hear that you are moving forward with clinical trials. That's obviously just an amazing accomplishment.
Tracy:
That's great. Yes. So Geoff, I think we've discussed a lot today about the Avidea technologies' SNAP platform, about the personal cancer vaccines and the peptide based delivery. Anything else you want to add?
Geoffrey Lynn:
As mentioned earlier in the discussion, personalized cancer vaccines are trying to address the need for inducing T cell responses in patients who do not have preexisting T cell responses against their cancers. And so those patients do not currently respond to checkpoint inhibitors and may not benefit from adoptive cell therapy. So our goal and our hope of what personalized cancer vaccines can achieve is to induce T cell responses in a greater number of patients to be able to extend the reach of immunotherapies. And there's a lot of great work going on in this field and I'll say that we're only a small part of that. We're really excited about our technology and what it can do and we hope that our findings will really benefit a lot of other researchers out there. But it's part of a much larger effort. And we believe, and I think many others out there believe that there is tremendous promise in getting personalized cancer vaccines to patients to be able to benefit a larger patient population with cancer immunotherapies. I really want to stress that to you, because this is really the driver for everything that we're doing, to try to get these therapies to patients and to further improve the lives of those individuals who are affected by cancer.
Tracy:
Geoff, thank you very much for your time today and we're really happy to have you talk about your publication and technology. And thanks everyone for tuning in.
Geoffrey Lynn:
Thank you, Tracy. Thank you Raymond.