NEW YORK – Having raised $310 million in a recent initial public offering and concurrent private financing, proteomics firm Seer is now looking to get its technology in the hands of early-access users in preparation for a broader commercial launch in 2022.
The Redwood City, California-based company has reached collaboration agreements with two undisclosed research sites where it will be placing its Proteograph platforms and plans to add to up to two additional collaboration sites as part an initial push to move the system into the field.
Following this collaboration phase, which will extend into 2021, the company plans to target six to 10 early-access customers in the academic and pharma space as well as commercial genomics firms, said Omead Ostadan, the company's president and chief operating officer.
"We will be working in a very specific way with customers who operate at scale, who are adept at incorporating novel technology, and who can work and collaborate with us deeply," he said.
Seer's Proteograph system uses nanoparticle-based enrichment of proteins in samples like human plasma to enable deeper proteomic discovery experiments at high throughput. The technology is based on the observation that when incubated in a biological sample, nanoparticles collect proteins, which form a "corona." Given this, nanoparticles can serve as an enrichment tool, allowing researchers to pull proteins out of a sample, which they can then identify and quantify using technologies like mass spec.
From a proteomic profiling perspective, it is notable that nanoparticles appear to collect proteins from across a large portion of the dynamic range present in samples like plasma. This means they could allow researchers to analyze low-abundance proteins without using time-consuming and expensive steps like protein depletion and fractionation that are required for mass spec-based experiments that aim to go deep into the proteome.
In a study published this summer in Nature Communications — the first peer-reviewed publication demonstrating its technology — Seer scientists and affiliated researchers used a version of the platform featuring five nanoparticles to analyze 141 plasma samples from non-small cell lung cancer patients and healthy controls, identifying more than 2,000 proteins, 1,992 of which were quantified in at least 25 percent of the 141 samples. The researchers completed the mass spec analysis in roughly two weeks.
The results were not particularly notable for their throughput. Each nanoparticle was run as a separate mass spec injection for each sample, meaning that in the five-nanoparticle setup used for the study, analysis of each sample required five mass spec runs. The researchers used 30-minute LC gradients, making for a mass spec analysis time of 2.5 hours per sample. In recent years, a number of labs have begun running single-shot mass spec experiments in plasma per-sample run times under an hour or even 30 minutes. These analyses typically top out at around 500 proteins quantified in undepleted plasma, however, compared to the 2,000 proteins measured by the Proteograph system in the Nature Communications study.
Seer believes that by expanding its repertoire of beads, it will continue to extend the system's proteome coverage.
Ostadan said Seer sees a variety of applications for its technology including basic proteome discovery, protein biomarker development both for diagnostics and drug development, and proteogenomics, which is a rapidly growing area within proteomics and could benefit from a platform that provides the depth and throughput that would allow proteomic data to better match genomic data in terms of cohort size and depth of coverage. He said the company envisions moving into assays for other non-protein molecules in the future, as well.
Ostadan said that there are around 16,000 mass specs currently in use for proteomics and that he expects a substantial proportion of this market would be interested in the company's technology. He added that given the product's potential for proteogenomic research it would draw many users from genomics, many of whom might choose to use the Proteograph platform for enrichment of samples and then outsource the subsequent mass spec work. Longer term, Ostadan said Seer anticipates pairing its technology with emerging non-mass spec proteomic technologies such as nanopore- and sequencing-based approaches currently under development.
Thus far, investors have responded enthusiastically to the company's pitch. Launched in 2017, the company raised $162.8 million prior to the $310 million it raised earlier that month. Since its IPO at $19 per share, its stock has roughly quadrupled. On Friday afternoon trading on Nasdaq, it was $78.38 per share.
Oliver Rinner, CEO and founder of Swiss proteomics firm Biognosys, which specializes in mass spec-based proteomics, including plasma proteome analysis, said that he thinks the investor interest reflects a general enthusiasm for proteomic technology broadly as much as it does enthusiasm for Seer's technology specifically.
He said that based on the Nature Communications study and other information about the Proteograph platform that Seer has made public he does not see it as a particularly groundbreaking technology, a view he said is shared by other proteomics researchers and investors he has spoken to. However, he said that if it in fact performs as advertised it could prove a useful new tool for proteomics sample prep, particular for plasma proteomic studies given the dynamic range challenges such efforts face.
"This, of course, is what everyone is eager to understand," he said. "Is it clearly superior [to existing methods]? Is it vastly superior? Or is it just another good protocol that has advantages and disadvantages?"
Rinner noted that one potential issue is the fact that on the current system, each nanoparticle enrichment must be run as a separate mass spec experiment, meaning that, as in the Nature Communications study, an experiment using five different nanoparticles requires five mass spec runs per sample.
"With advanced data analysis you can do many things and stitch data [from different runs] together," he said. "But it is always an advantage if you don't have to. It inevitably becomes more complex, so you would always prefer not to do it. If in the end it proves such a superior reagent that gives you so many more proteins, then of course you would pay that price."
Omid Farokhzad, Seer's CEO and founder, said the company is exploring multiplexing that would allow combining different nanoparticle enrichments in a single mass spec run.
While Ostadan and Farokhzad frequently analogize the company's potential place in proteomics to the dominant position Illumina has established in sequencing, Rinner said that he believed this is unlikely given the wide range of approaches used in proteomics.
Seer and Biognosys are not direct competitors, and, in fact, the Swiss firm could be a future user of Seer's technology if it ends up being adopted by its customers. Rinner said that, in general, demand for larger-scale plasma proteomic experiments is on the rise.
"The interest in large-scale profiling in plasma is clearly increasing," he said, noting that this has been reflected in growing demand for Biognosys' plasma profiling services and for products from companies like Olink that offer the ability to profile plasma with deep coverage and high throughput.
Somalogic, which similarly offers a platform for deep, high-throughput proteomic analysis in plasma and other samples has also seen significant investor interest, closing in November a $121 million Series A funding round. The company, which has raised more than $485 million since it was founded, said that it expects to close on additional funding in the next three months.