DeciBio Q&A

The Future of Proteomics: Seer’s Origins & the Proteograph’s Commercial Launch Q&A with Omid Farokhzad

April 20, 2022
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We are joined by Omid Farokhzad, the Chair, CEO and Founder of Seer, a publicly traded company that works in nanotechnology-based proteomics research and discovery tools with their complete analysis system, the Proteograph Product Suite. Seer has had an exciting recent couple of months coming off of the official commercial launch of the Proteograph Product Suite and presentations at both JP Morgan Healthcare 2022 and the U.S. Human Proteome Organization (USHUPO).

Omid is known for his diverse and influential background in biotechnology and academia ⁠— a pioneer in the fields of Nanotechnology and Nanomedicine ⁠— with significant therapeutics and research tools and diagnostics expertise as the founder of multiple companies, including PrognomiQ, Selecta Biosciences, and Tarveda Therapeutics. In academia, Omid served as Professor of Anesthesiology at Harvard Medical School and held the past role of Director of the Center for Nanomedicine at Brigham and Women’s Hospital.

Thank you for taking the time to join us, Omid. To get started, could you speak on how your past experiences in biotechnology and academia led to the founding of Seer and how they influence your perspective as CEO for what Seer can become as a company?

Alex, thank you so much. Let me first talk about my background and then move on to Seer.

I’m an academic physician by training. I did my postdoc at MIT with Bob Langer and then joined the Harvard Medical School faculty in Boston. I had done my clinical training there as well. And from the beginning, my focus was largely on science with very little clinical practice. The area that my lab focused on was nanomedicine and biomaterials, which I started in 2004. Back then, not many people knew about this field and some folks in our institution asked the question: "What does this even mean?"

Fast forward a decade later, we started a center called the Center for Nanomedicine in our institution. By that time, there were many such centers across the world, but it was an interdisciplinary lab with biologists, chemists, engineers, and physicians coming together to solve interesting problems. Most of my effort was developing nanoparticle technologies for medical applications, with some of the most amazing students and postdocs who did extremely innovative work. To quantify what that means scientifically, 200 plus patents were filed from the lab and published about 180 or so papers. Those technologies formed the basis for the launch of a number of companies; Seer was the fifth to come.

A lion's share of that work went into understanding how nanoparticles behave in biological systems. You would take a pristine nanoparticle that you had engineered and designed, and you would put it in a biological sample. Very quickly a layer of biological coating would form - we called that “biofouling” at the time, and so we tried to engineer systems to prevent things from binding to the surface of the nanoparticles. Those technologies formed the basis for the launch of several companies over the years. As it turned out, the binding was quite precise, driven by the physico-chemical properties of the nanoparticles – so it wasn’t “fouling”. Depending on the biological sample and the nanoparticle design, a specific biomolecular corona was formed.

The term “protein corona” was coined back in 2007 in a PNAS Publication. What we learned over the years was that, as you change the physical and chemical properties of the particles, the protein corona would change, even when exposed to the same biological sample. So we took a “bug” and turned it into a new “feature,” and that was the idea that sparked the creation of Seer, which was founded in early 2017.

I realized at the time that if this technology could truly work, it would change a lot of things. It would allow us to sample the proteome in ways that were never possible before. So, if I was right, it was just too big an impact for me to sit on the scientific advisory board or board of the company in a consultative role. I needed to lead this. Of course, it was early stage, and I could have been very wrong, but I took the risk. I left HMS by initially taking a sabbatical, then became a first investor in the company myself. Next, together with Philip Ma and Bob Langer, whom I had done my post-doctoral training with, we gathered a great group of investors together, and launched the company.

We had a three-pronged vision for the company at that time: It could become a tools company selling instruments, it could become a diagnostic company developing proteomic tests, or it could become a data company because it would give us access to massive amounts of data and this would span all the way from discovery to clinical. That was the vision of the company. That's how it started. And now fast forward four years and four months into it, it has been one amazing ride. I'm so proud of what we have accomplished – the employees, investors, board, the launch of the Proteograph Product Suite, and what I'm seeing as the future of this field. Sometimes I pinch myself just to make sure that it is real.

First of all, congratulations on the official commercial launch of the Proteograph Product Suite and Seer’s impressive performance in fiscal year 2021. Looking at your revenue guidance, you expect revenues to grow from $6.6 million in 2021 to ~$15 million in 2022. We at DeciBio see a lot of appetite and excitement around proteomics, so we would argue that this forecast is conservative. What do you think are the key drivers and barriers to adoption for the Proteograph Product Suite and how is Seer working to address them?

Thanks so much. We get that question from investors as well: "Why is the guidance conservative?"

Our philosophy is, you've got to walk before you run. The Proteograph Product Suite is designed to enable deep, unbiased proteomic study at scale. And by doing that, we are opening a new gateway to the proteome. The product as we launched it has received amazingly positive feedback from our customers everywhere. From the arrival of the instrument to getting it installed, the ease by which they get trained, and the batch-to-batch reproducibility of data that they get. Overall, we’ve heard that the user experience has been great. And we think that this is going to have a lot of legs.

We just went into broad release after our two early phases of commercialization: The collaboration phase and the limited release phase. Last year, during the limited release phase, 25+ abstracts were published and 17 instruments got shipped, but we're now in broad release and there is an enormous amount of appetite for what Seer offers, but it is still early. As a scientist, I always like to see publications and data presentations, and more and more of those are going to be emerging from our customers as they complete their studies. In fact, I think these studies and the resultant publications will create a network effect, creating even more demand. That said, we want our estimates and forecasts to always be something that we feel we can reach. I feel very good about the revenue estimates for 2022, which I think reflect the strong demand for what the Proteograph offers.

In the last approximately 2 decades, the level of interest in genomics has been extremely high. It seems like the pendulum is starting to swing back with a lot of excitement towards proteomics. Would you agree with this statement, and if so, what recent developments do you think are driving the growing excitement around proteomics?

First of all, I couldn't agree with that statement more. There's a lot of excitement for proteomics, I would say for two reasons. One, genomics made a massive impact. Our world changed so dramatically because of wide scale access to genomic content. Entire markets were created, like liquid biopsy (LBx), personalized medicine, cancer therapy, etc. Genomics is an excellent indicator of an individual’s risk, but true biological and functional status happens at the level of proteins. Previously, the challenge was accessing this functional status at scale, which was very, very difficult. Researchers always wanted to have access to function data to annotate their genomic content, but it just wasn't possible. What we've now seen over the course of the last decade is progressively newer technologies being developed that make it possible to access proteomic content at scale and Seer’s Proteograph is one of them.

When you are talking about deep unbiased proteomics, an area that Seer uniquely enables, the largest published study in plasma was 48 samples before Seer. And by the way, we are defining “deep” here as any study that identifies at least 600 proteins. Fast forward to where we are today, literally 16 months after shipping our first instrument, we now have customers that are seeing thousands of proteins across the dynamic range with studies of 1,000+ samples.

For example, there's a particular customer that's doing a study of a thousand serum samples to look at biomarkers that are clinical endpoints of prostate cancer. There is another customer in the multiomics space that is looking at early detection of cancers and doing a study of 2,000+ samples. Aging is another area where proteomics is very important; we recently signed a project in this area involving 1,500 samples. The incremental increase in what became possible wasn't small, it was a big jump.

Building off the last question, to what extent do you believe that the excitement for Seer and the Proteograph is driven by interest in standalone proteomics versus multiomics? In the multiomics realm, what do you think will be the interplay of genomics and proteomics, and more specifically, next-generation sequencing (NGS) and mass spectroscopy (MS)? How is Seer positioned to address these developments?

In short, it’s all about content.

If you think about what played out in the genomics space, access to the genome at scale enabled massive discovery of new content. This content discovery and its application is what drove entirely new end markets, such as noninvasive prenatal testing (NIPT) and liquid biopsy, for example. What I think is going to happen is, Seer will enable access to novel proteomic content that today we've never seen. The proteome is vastly more complex than the genome. There are 20,000 genes in the human genome. Those genes are the same genes in the different cells of our body, but from those genes come millions of different protein variants that drive function across the body.

And this biology is actually quite efficient; everything has a purpose. Protein variants exist because they're important in health and disease. As we begin to access that proteomic content, which was relatively inaccessible before Seer, we're going to expand what we know about biology. This will extend beyond human health to agriculture, microbiology etc. It will take us closer to understanding function than we have ever been.

There are also applications that genomics has not been able to impact as much, where I predict that proteomics will be quite relevant. Fields such as neurodegenerative disease, where it's not very clear what genomic variants drive the disease, for example, need to get closer to function to unlock disease biology. Changes in proteomic signatures could be a very good indicator of when neurodegenerative diseases are developing and progressing, serving as targets for early detection as well.

Today, genomics and proteomics are relatively distinct fields. In the future, they will be much more connected, as referred to by the term “proteogenomics”. The enablement of unbiased, deep proteomics at scale will enable us to tie genomic content at the nucleotide level to proteomic content at the amino acid level, essentially “functionalizing” genomic variation. This important bridge will enable unbiased proteogenomics studies at scale. My expectation is that we're going to really see a massive amount of impact from proteomics in the coming years, potentially larger in magnitude than what we saw in genomics.

Seer recently had an impressive showing at the U.S. Human Proteome Organization with 8 poster presentations addressing all aspects of the Proteograph, specifically assay, computational method and software in diverse research applications including cancer research and neurodegenerative disease. Are these applications indicative of the major research and discovery areas Seer plans to initially target and are there any other research areas ideally suited for the Proteograph?

We believe there is unmet need for unbiased deep proteomics at scale across a broad range of customer types spanning academia, pharmaceuticals, translational medicine, and diagnostics, and applications ranging from cataloging protein discovery to biomarker discovery, target identification, multi-omics for cancer and complex diseases, and proteogenomics.

For example, we spun off PrognomiQ from Seer in the second half of 2020 before Seer went public. PrognomiQ is a multiomic company in the liquid biopsy space, and of course, core to their technology is access to deep unbiased proteomics. But in addition to that, they also explore other omics like genomics, transcriptomics, lipidomics, metabolomics, etc. That's a good example of a company doing liquid biopsy in the diagnostic space leveraging deep unbiased proteomics.

We're also seeing customers using the technology in research applications using animal models, in plant biology, and now, in aging. Frankly, what's really exciting is thinking about what applications this technology will enable in the hands of our customers that may not even be possible today. I'm very excited to see what entirely new applications get created because of the access to unbiased, deep proteomics at scale that our technology creates.

Seer made an exciting announcement about the recent launch of its Centers of Excellence (COE) program to accelerate global adoption of unbiased, deep proteomics at scale and enable customer access to the Proteograph through commercial and research partners. The announcement was then followed by the establishment of a first-of-its kind Proteogenomics Consortium with SCIEX and Discovery Life Sciences for large-scale studies. For example, enabling up to 100,000 sample capacity per year. Please speak to us about how these developments came about and what Seer hopes to accomplish through their extensive partner network.

At the J.P. Morgan Healthcare Conference, we announced the launch of our Centers of Excellence program or COE program. With this program we essentially partnered with a number of leading centers around the world to increase access to our technology via services using the Proteograph Product Suite. In Europe, it was Evotech, in Asia, it was Soulbrain, in North America, it was Biodesix, Discovery Life Sciences (DLS), and the Sanford Burnham Prebys Medical Discovery Institute.

These COEs bring expertise working with pharma, genomics, and academic customers. These COEs will broadly serve customers that either wouldn't have the resources to run those experiments internally or are not yet in a position to make the capital investment to bring those capabilities in-house.

In addition to that, one of these centers, Discovery Life Sciences, a premier genomic service provider, and one of our commercial partners, SCIEX, partnered with us to form the Proteogenomic Consortium. In this consortium, Seer will make the Proteograph Product Suite available to DLS, SCIEX will make the ZenoTOF 7600 platform available to DLS, and DLS will build the capabilities to process samples, with a capacity that eventually reaches 100,000 samples per year. This will broadly enable proteogenomic studies, providing access to genomics customers and others who seek to perform large studies and who have not been able to do so previously. The Proteogenomic Consortium is expected to become operational in the second half of 2022. I’m very excited about this effort and look forward to providing updates in the upcoming months.

With Seer’s recent key appointment of a seasoned industry veteran in Scott Thomas as Chief Commercial Officer — the past Senior Vice President of Sales and Marketing at Singular Genomics and Vice President of Global Commercial Strategy and Enablement at Illumina for nearly 12 years — how do you believe his addition will help Seer accomplish its commercial goals and what changes will come as a result of his joining?

As we accelerate our commercial efforts following the broad release of our Proteograph Product Suite, I’m thrilled to have Scott lend his extensive commercial knowledge to help us build out our global commercial organization, expand our reach to customers around the world, and continue to empower our customers to achieve exceptional outcomes using our technology.

I’m very proud of the leadership team we are building at Seer and having Scott join us to lead Commercial is very exciting.

Seer is differentiated from competitors due to its deep, unbiased proteomics approach made possible by proprietary multi-nanoparticles (multi-NPs) with alterable physicochemical properties to generate variable, yet specific protein coronas not possible in more targeted approaches and harsher workflows (e.g., high-pH fractionation). Please give us some insight into what Seer’s advantages are and how your approach and underlying technology differs from traditional proteomics methods and those of competitors? (DOI: 10.1073/pnas.2106053119)

There's a lot of enthusiasm for the whole proteomics space today. Technologies are now reaching a point where solutions are becoming more adept in accessing the proteome. We are one of the players in this space, particularly providing deep, unbiased, scalable access to the plasma proteome in a way that was just not possible previously.

Seer’s technology is uniquely enabling – it is the only technology on the market that can provide a comprehensive look at the proteome at the resolution and scale needed to drive studies that reveal novel content and open up a new gateway to what the proteome means in biology and human health. Existing methods of proteomic analysis have major drawbacks, they either require you to know what you’re looking for by using aptamers, or they let you explore broadly, such as in fractionation and depletion protocols, and are tedious and do not scale well. Seer offers the first and only product for proteomic studies that lets you sample across the entire proteome, enabling the discovery of novel protein variants with the reproducibility, and speed needed to do this at scale. Researchers are truly able to see the proteome in a new way.

Images provided by Seer.

Authors
Alex Amram
Analyst
Stephane Budel
Founding Partner
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