Proteomics in Cancer Treatment: Guiding Clinical Decisions

Brian McCloskey and Brad Power July 27, 2022 “Genes don't reliably predict response to treatment, and the gene mutations or expression in cells don't reliably predict the expression of proteins in our cancer cells… If we ever want to achieve precision oncology, we must figure out both on the science side and on the institutional side how to embrace diagnostics of many proteins, coupled with some genes or gene expression, and patient data.” Amanda Paulovich

A panel of experts in proteomics: Karin Rodland, PhD, (Pacific Northwest National Lab and OHSU), Amanda (“Mandy”) Paulovich, MD, PhD, (Fred Hutch), Kristina Beeler, PhD, (Biognosys, which provides proteomics services to biopharma), and Marlon Ruiz and Michael Förster, PhD, (Olink, which offers a proteomics platform to scientists), discussed the role of proteomics in clinical decisions. Where are proteomics as an emerging technology?

Amanda Paulovich: Mass spectrometry has proven to be a reliable measure of proteins, which can be combined with genomics to offer clinical insights through laboratory- developed tests.

The challenges now are (a) clinical translation from a laboratory environment to a regulatory environment meeting FDA approval, such that pharma will begin to adopt it in its late phase trials, potentially leading to companion diagnostics; (b) increased reimbursement for diagnostics in general, and for mass spectrometry specifically, so that laboratories that provide the service can stay afloat; and (c) increased physician uptake.

Kristina Beeler: The applications of our proteomics technology when we started a decade ago were in small scale studies answering basic research questions for our biopharma customers. In the last seven or eight years, we've seen a push for the technology to be adopted much later down the drug discovery pipeline.

We've seen the adoption of the technology in preclinical settings to understand the mechanism of action in drugs to identify novel drug targets. Now, clients are waiting for the data to make decisions on the next cohort enrollment. This is something that we could never have imagined a few years ago. This is still in a clinical trial setting. Taking that to the next step is still quite a way down the road.

Karin Rodland: We're at the stage of developing tools to combine genomic, mRNA, and proteomic data to improve the selection of likely therapeutic drugs that you will respond to. How are proteomics helping guide treatment decisions - what is distinctive? Michael Forster: Proteomics have the ability to monitor proteins and biology and cancer- related changes in real time.

The biomarker information you derive in real time is closer to the therapeutic intervention, enabling you to gear therapies better to specific patients. 3. anel Discussion) Michael Forster: Proteomics have the ability to monitor proteins and biology and cancer- related changes in real time. How should proteomics be integrated with other diagnostic tests to guide clinical decisions?

Karin Rodland: If I was doing an N-of-1 research experiment on Brian, I would take his RNA-seq data and the biological processes that had been implicated, and I would use Mandy's targeted proteomic assays, and I would verify which kinases in that pathway are actually upregulated and driving the abnormal behavior in the pathway. What's next? Kristina Beeler: Complex biological processes are characterized not by just one level of -omics.

They need the multi-omics level and current status. Proteins provide essential functional information to understand the true phenotype. Karin Rodland: Looking at Brian as a research project, how do we make proteomics available to him as a research subject? He has to find a physician and a precision oncology clinical trial to look at all these different molecular measurements and integrate them and get enrolled.

” Amanda Paulovich: You really need partners in large academic centers that are willing to go out on a limb, and centers that are legally adventurous enough and willing to go down that path with you. Unfortunately, it's just hard to do. As Karin said, you're pushing the envelope beyond what standard of care is. We need better diagnostics.

80% of healthcare decisions are based on diagnostic tests, but they account for less than 20% of healthcare costs. Somehow, diagnostics must be valued in the same way that blockbuster drugs are, and they're way way undervalued right now.

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Meeting Notes SUMMARY KEYWORDS proteomics, proteins, technology, cancer, patient, question, mass spec, samples, mass spectrometry, genomics, clinical, diagnostics, clinical trial, liquid biopsies, data, oncology, fred hutch, reproducibility SPEAKERS Karin Rodland, Amanda (Mandy) Paulovich, Kristina Beeler, Saed Sayad, Michael Förster, Marlon Ruiz, Brian McCloskey, Sheeno Thyparambil, Brad Power Brad Power 00:03 This is the Prostate Cancer Lab where we're learning about novel tests that can help personalize cancer treatment decisions.

Today we have a panel, which is the first time we've done this. I want to first introduce Karin Rodland, who introduced me to a number of the panel members, so she's really the network organizer and helped to bring the panel together today. I'll let each of the panelists introduce themselves.

Please provide your personal background, your organization and its role, and the topic you will cover including where you are in the evolution of this emerging technology. Karin, why don't you start, please, and then we'll move to Mandy, Kristina, and then Michael and Marlon. Karin Rodland 01:17 I am a cancer cell biologist who has been studying signal transduction in cancer for close to 50 years.

I use mass spectrometry and mass spec-based proteomics very heavily. I am a joint appointee at Pacific Northwest National Lab, which is a major site of technology development in the field of mass spectrometry. I also have a joint appointment in Oregon Health Sciences University, which is a leader in precision oncology and SMART trials. Also, I do know a lot of people, and I tried to get them involved.

I've been a cancer patient, having been diagnosed with early-stage breast cancer at the age of 40, which I guess technically makes me a cancer survivor. I'm now a cancer researcher and a clinical oncologist. As an oncologist treating patients, I was very struck by the variability that I saw from patient to patient.

I saw patients with what looked like the same tumor would have very different responses to the same therapy, and very different profiles in terms of side effects as well. That led me to yearn for what we now call personalized, or precision oncology, which is what we're trying to achieve. I did a postdoc at one of the major genome centers that completed the human genome sequence.

That was a very critical start on our path to precision oncology, but it's not enough. Since proteins are the targets of therapies, we have to be able to quantify proteins. When I got into this field 19 years ago, and still today, most studies on proteins use conventional technologies that are 50 years old and wholly inadequate to meet the needs of the post genomic community.

In fact, there aren't good assays for measuring most human proteins in a clinical setting. This very critical human proteome, as it's called, remains clinically inaccessible. In 2003, I joined Fred Hutch to set up a translational proteomic lab to try and leverage new technologies to solve this gap based on mass spec.

We've been colleagues in the National Cancer Institute's clinical proteomic consortium called CPTAC. As I mentioned, in 2003 I came to Fred Hutch. A couple of years later, we launched this NCI CPTAC program and spent five years and probably $30 million convincing the world that these conventional technologies that are 50 years old aren't the only way to measure proteins.

We can use newer technology based on mass spec to make reliable measures of proteins. That got us another five years of the program at NCI where we spent five years and another $30+ million proving, in my opinion, common sense, that measuring proteins adds value over just sequencing DNA.

That finally proved beyond a shadow of a doubt, even to the genomics-centric folks at the National Cancer Institute who are now on board, that there's value in combining proteomics and genomics - what we now call proteogenomics. Then we spent the last five years and another $40 million, laying the groundwork for the clinical translation of mass spec-based proteomics.

There's a lot of proteogenomic characterization centers looking at the gamut of human tumors trying to characterize them on a molecular level using mass spec-based technologies. For the first time, we also introduced translational research centers to these technologies whose goals are to try and take them and push them into the clinic. In that phase, we saw the development of laboratory-developed tests.

In fact, my laboratory is now a CLIA-certified environment, and we have successfully translated this new mass spec-based measurement technology into clinical trials where we run patient samples for correlative studies in our CLIA environment. That's where we're really stuck right now. In my opinion, this is where the field needs to go.

We need to achieve clinical translation not just in a CLIA environment, but in a regulatory environment meeting FDA approval, and we need precedent for that before this technology is de-risked enough that pharma will begin to adopt it in its late phase trials, potentially leading to companion diagnostics. Reimbursement for diagnostics in general, and for mass spec specifically, is woefully inadequate.

It's very difficult for laboratories to provide the service and stay afloat. Also new technologies always meet the challenge of physician uptake. These are areas that I'm looking strongly at in the next phase of my career - how can we now usher these things a little bit further forward? Brad, you mentioned commercialization as well.

My lab, under this NCI program, has developed a large catalog of assays that depend on a valuable and expensive-to- make reagent called a monoclonal antibody. We make all of that publicly available through open-source portals that the National Cancer Institute maintains, and that's for non-commercial research use. Expert labs can run any of those assays that they want.

But to fully democratize access to this new technology, we need to make it available also to laboratories and research groups that don't inherently have those technologies in house. It's expensive and complex to use mass spectrometry so we're trying to solve that problem.

We recently announced a partnership with CellCarta, which is a global contract research organization based in Canada that does correlative studies for clinical trials where all our assays will be made publicly available. They've licensed Fred Hutch's rights to all those assays to make them available to the community as well to try and get this out there. We really need to take up these new technologies.

A critical reason is cancer phenotypes and predicting drug response are far more complicated than a single gene mutation or the measurement of a single protein, which is what we typically do now. If we ever want to achieve precision oncology, we must figure out both on the science side and on the institutional side how to embrace multi-analyte diagnostics that have many proteins, may be coupled with some genes or gene expression, and patient data.

This information is going to go into algorithms that are going to output scores that put patients into categories for treatment selection. But our institutions are not set up to deal with any of that. We now have lots of institutional barriers that must be broken down. We need new mass spec technology to enable that part of proteins because the old ones just usually measure one protein at a time.

I have a scientific background, including a PhD in immunology and oncology. I have been fortunate to see the rise in the use of proteomics and its entry into the clinical space of this technology, especially in the last several years. I'll give you a little bit more information about Biognosys as an institution. We have been around for 14 years pioneering the field of mass spectrometry.

We are co-inventors of a technology called DA, data independent acquisition mass spectrometry, which has really revolutionized the field of mass spec proteomics. It has become the method of choice for large scale biomarker studies. We have developed a set of proprietary platforms that serve our partners from early R&D/early discovery to the late clinical trial application. We are active across this research pipeline.

We have more than 100 customers across the globe that trust our services and products. We are headquartered in Zurich, Switzerland and have recently opened an office in Cambridge, Massachusetts, and are expanding our US footprint. Brad Power 12:25 You said most of your customers are biopharma.

How do you see the insights that you're developing - either the identification of biomarkers or maybe predicting drug response/resistance - how do those translate into clinical use and how does that translation work? Kristina Beeler 13:08 If we look at the history of the commercial activity of Biognosys, in the early days, we were mostly working with the early adopters of the technology because DA was a novel technology.

People had their questions about the approach. The early adopters of the technology were technology-savvy people who were excited about our technologies. The application was in an early R&D setting - basic research, small scale studies answering basic research questions. In the last seven or eight years, we've seen a push from the market for the technology to be adopted much later down the drug discovery pipeline.

We've seen the adoption of technology in preclinical settings to understand the mechanism of action in drugs to identify novel drug targets. But also, most recently, we have been applying that technology in clinical trials as pharmacodynamic markers. Now, clients have been waiting for the data to make decisions on the next cohort enrollment.

This is something that we could never have imagined a few years ago that our technology would be used for subsequent decision making. This is still a clinical trial setting. Marlon Ruiz 14:44 I've worked in proteins my entire life. I strongly believe that proteins are where we find a lot of the answers that we're looking for, just like Mandy was saying and the rest of you have said. Olink is a platform provider for proteomics.

It's an immunoassay-based technology that utilizes the power of antibodies but also the power of next gen sequencing. Our antibodies are bound to oligos that are complementary. It's two of them that bind to a protein, and they hybridize, are elongated, and amplified via either qPCR or a next gen sequencing that enables us to do up to 3000 proteins in one sample - a very small amount of sample.

It's something that's been very complementary to a lot of mass spec methods. It's a very exciting spot to be in. " What is the source material? Is it blood? Is it fresh frozen tissue or FFPE? Marlon Ruiz 16:23 Generally speaking, we validated our platform on plasma and serum; however, it has been optimized for many different sample types including tissues, cell lysates, supernatants, CSF, aqueous humor and ocular fluids and urine.

We've had pretty much all sample matrices on our platform. Although they aren't validated entirely, they are optimized and have shown to work really well. Michael Förster 16:56 My scientific background is in proteomics. I did a PhD in protein genomics at Karolinska Institute, working on circulating factors and how genes, or polymorphisms, control cytokines in circulation.

I took the long way round and did a postdoc but thought complex diseases are too much, so I decided to do something simpler like immunodeficiencies. That's how I stumbled upon cancer because I worked on a gene that was also a susceptibility factor for hemato oncology malignancies. After that, I exited the academic world and went into liquid biopsies. I've worked a little bit on liquid biopsies in prostate cancer for prostate cancer diagnosis.

Later, I got involved in genomics diagnosis for all kinds of cancers.