At ASHG, Seer showcased its Proteograph product suite which it claims delivers proteomic insights that complement and strengthen other forms of omics data. Through various sessions at the meeting, the company highlighted applications of the technology in the context of neurodegenerative disease, cancer, and metabolic disease. Seer also announced a co-marketing and sales agreement with Thermo Fisher Scientific to jointly promote Proteograph alongside Thermo Scientific Orbitrap Astral™ mass spectrometers to provide customers of the Orbitral Astral an integrated solution for unbiased proteomic analysis.
The list of presentations at ASHG, which was held in Denver, CO, included one from healthcare company PrognomiQ focused on lung cancer. Philip Ma, PhD, CEO and founder of PrognomiQ, a spin-out from Seer, and his team are exploring a multi-omics biomarker test that uses proteomics, transcriptomics, and metabolomics to detect early-stage lung cancer.
Earlier this year, the company shared results from a study in a medRxiv pre-print that highlighted data generated from a 2,513-subject case-control study using their multi-omics classifier. For that study, they analyzed molecular differences between the peripheral blood plasma of lung cancer subjects and noncancer controls, including those at high risk for lung cancer. The research demonstrated 89% overall sensitivity and 89% specificity in the validation cohort to detect lung cancer, including 80% sensitivity to detect stage one lung cancer.
A separate presentation at ASHG, this time from the Satchidananda Panda Lab at the Salk Institute for Biological Studies, focused on Relative Energy Deficiency in Sport (REDs), a condition associated with insufficient energy intake and excessive energy expenditure that can result in systemic neuroendocrine and metabolic abnormalities in athletes. Mouse studies of the condition have shown wide-ranging effects including significant shrinkage of vital organs like the kidney and reproductive organs, deterioration of bone quality, and negative psychological consequences.
Salk scientists are using Seer’s technology to analyze data from animal models of REDs in order to identify protein signatures of the disease. “A multi-omics approach, including unbiased proteomics, is arguably even more important for a condition like REDs for which little is known about its diagnosis, effects, or potential treatments,” said Satchidananda Panda, PhD, director, Wu-Tsai Human Performance Alliance at Salk Institute. “Seer’s technology allows our team to understand REDs on a cellular and molecular level, which in turn could lead to diagnostic tests and therapies to halt, reverse, or prevent it entirely.”
Pairing deep proteomics with mass spectrometry
Seer’s collaboration with Thermo Fisher builds on an existing relationship between both companies. Under the terms of this new nonexclusive agreement, Thermo Fisher’s global sales force will be able to quote and sell the Proteograph product suite, which includes an automation instrument, proprietary engineered nanoparticles, and software analysis suite. The partners will also conduct joint marketing activities, including conference promotions, seminars, and webinars, to showcase the combined power of their proteomic platforms.
The integration is set to commence in early 2025. When it does, it will further expand the commercial reach of Seer’s platform, Omid Farokhzad, MD, PhD, CEO and chair of Seer told GEN in an interview during the meeting. The companies will work together to improve workflows, creating a seamless sample-to-data experience. Seer and Thermo Fisher also plan to collaborate on research studies that demonstrate the comprehensive capabilities of their combined platforms.
Farokhzad described the Orbirtrap as the gold-standard for mass spectrometry. Pairing it with the Proteograph will help researchers extract even more information. To date, Seer has invested well over $250 million in developing its platform to ensure that scientists get the most from their data. “If you take a plasma sample and digest it and inject it in the Astral, you will see about 750 proteins. But if you take the same plasma sample, and run it on the Proteograph and then run it on the Astral, you would get to about 6,000 proteins,” he said. Now “if you do a study of let’s say 40 or 50 or a hundred or a thousand samples… you may get to 8, 9, or 10,000 proteins across the study. So truly remarkable numbers.”
Seer’s team will be on hand to support Orbitrap customers who purchase Proteograph including providing consumables and other support services. Customers for the combined solutions will likely fall into a few buckets, Farokhzad said. A key demographic is customers who are processing complex samples such as plasma or serum.
Access to the Proteograph suite could also be helpful for customers of the Orbitrap who are working with a large number of single cells. With the Proteograph, these customers could automate their workflows with improved reproducibility. The other is customers focused on single cells. For these customers, “you can get pretty deep on a mass spec without the Proteograph” but “you’ll see more with [it].” He anticipates that as much as half of the Orbitrap customers would benefit from the insights provided by Proteograph.
The solutions from both companies already work together seamlessly, according to Farokhzad. Customers can simply transfer the peptide output from the Proteograph into their Orbitrap. However, the partners plan to work on workflows for specific use cases and applications.
“Both Thermo and Seer are interested in larger studies. When you combine the two, suddenly you have the tools to do population scale, deep proteomic study, something that previously was completely impossible to even imagine,” Farokhzad said. “To be able to exemplify to the customer and to the scientific community the powerful biological insights that can emerge when you do very large scale studies at [a] different speed that was previously not possible … at a cost point that makes it feasible.”
The response to Proteograph from attendees at ASHG was very positive. Serafim Batzoglou, PhD, Seer’s chief data officer, told GEN at the meeting that the company’s conversations with scientists indicated that many were surprised at how quickly proteomics is advancing. For a long time, some scientists’ impressions of proteomics was that while the information was useful, it was a “really difficult” data type to get access to.
“Before our technology, doing mass spectrometry on plasma involved a considerable amount of time [to] first of all process the samples depleted of the common proteins and then mass spectrometry acquisition,” he explained. Advances in mass spectrometry technology as well as the launch of Proteograph have now made it possible to routinely run tens of samples per day using a single instrument at a much lower price point. Moving forward, “I think that things are picking up [and] hopefully it’s going to speed up over the next year or two. And this data type will become more and more ubiquitous.”
Reaching the clinic
So far Proteograph is designated for research use only. However, Seer has secured certifications that allow it to move the instrument towards use in clinical testing. In line with those efforts, Seer spun out PrognomiQ in September 2020. The company’s proprietary approach combines the information provided by the Proteograph product suite with genotype and phenotype data including cell-free DNA, RNA, metabolites, and lipids to identify important biomarkers.
PrognomiQ recently announced a series D financing round in which the company raised $34 million. The round was led by Seer with participation from a new strategic investor in the diagnostics segment as well as from existing investors, including Catalio Capital Management, aMoon, Invus, and Bruker. The company has raised more than $135 million in total since its founding four years ago. Isaac Ro, a partner with Catalio Capital Management, has joined PrognomiQ’s Board as an independent director.
PrognomiQ is using that funding to develop a laboratory-developed test for lung cancer as well as an in vitro diagnostic test for the disease. PrognomiQ was recently granted a Clinical Laboratory Improvement Amendment license to support the development of the LDT product, and it is currently enrolling a prospective 15,000-subject study in lung cancer that was initiated in 2023 to support registration of the IVD product.
