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Proteomics Firm Bertis Targeting Cancer Dx, Biomarker Discovery With Launch of US Business


NEW YORK – South Korean proteomics firm Bertis is ramping up its US business with the recent launch of a proteomics services product and the signing of its first US customer.

The company last month began offering its Pan-omics Analysis Solution and Systems (PASS) service through its San Diego-based US subsidiary, Bertis Bioscience, with its first customer, the Salk Institute for Biological Studies.

Bertis also published last month a study in Cell Reports Methods describing its DeepMRM targeted proteomics software, which it has integrated into the widely used Skyline proteomics software package.

Bertis established the San Diego facility, which includes a CLIA laboratory, in the fall of 2021 but has only recently begun offering proteomics services out of it. Sangtae Kim, the company's chief technology officer, said that among the main targets for the PASS service are pharmaceutical companies for which Bertis hopes to do companion diagnostic work.

It also plans to offer its own proprietary proteomic tests out of its CLIA lab, with its lead product being a pancreatic cancer test for screening high-risk patients.

The company's work with the Salk Institute is focused on protein biomarker discovery in cancer, Kim said, noting that in addition to traditional protein biomarker work, the parties are also looking at microproteins — proteins with less than 100 amino acids — as potential cancer biomarkers.

Bertis plans to do this discovery work in plasma, taking advantage of recent developments in plasma proteome enrichment that have allowed researchers to probe samples much more deeply and with higher throughput than was previously possible. The company has a Proteograph Product Suite system from Seer, where Kim was a principal bioinformatics scientist before joining Bertis in 2021. It also plans to use an extracellular vesicle-based approach to plasma proteome enrichment recently developed by University of Washington researchers Michael MacCoss and Christine Wu.

According to data released at the American Society for Mass Spectrometry annual meeting in June, Seer's new Proteograph XT assay kits can measure around 6,000 proteins in plasma at a rate of roughly 30 samples per day when used on Thermo Fisher Scientific's recently launched Orbitrap Astral instrument. The UW researchers, meanwhile, have said that their EV enrichment approach is able to consistently quantify around 4,800 proteins in plasma using a 30-minute LC gradient on an Orbitrap Astral, allowing for throughput of around 40 samples per day. It can measure between 5,000 and 6,000 proteins using a one-hour LC gradient.

Kim said that Bertis has not had a chance yet to compare data generated using the two approaches, but he believes they will largely be complementary.

"It's going to be exciting," he said. "I think the Venn diagram [of the two approaches] will look quite interesting."

For its targeted proteomics work, including clinical assay development, Bertis has developed its DeepMRM software. The software is based on taking extracted chromatograms from mass spec data and converting them to images, which, Kim said, are well suited to machine-learning analysis. In the Cell Reports Methods study, the researchers found the approach outperformed existing targeted proteomics software.

Kim said the method can also be used for analysis of data-independent acquisition (DIA) mass spec data but noted that it relies on spiked peptide standards, which limits the breadth of coverage it can feasibly achieve.

Bertis hopes to use the DeepMRM approach in both its pancreatic cancer test and a next-generation version of its MastoCheck breast cancer test, which the company currently sells in South Korea as a complement to traditional mammogram-based breast cancer screening, particularly in women with dense breasts for whom mammograms may not be as effective.

Bertis received approval in 2019 from the Korean Ministry of Food and Drug Safety to sell MastoCheck, which measures the levels of three proteins in patient blood samples, as an in vitro diagnostic. Since then, the company has sold roughly 100,000 tests, many of them as part of routine health screening packages that Kim said are popular in South Korea. When purchased as an individual test, it costs around $80 to $100.

Despite the relative success of the test in South Korea, Bertis isn't planning a US launch until after it launches its pancreatic cancer test. While the company said last year that it aimed to release the pancreatic product as a laboratory-developed test by the end of 2023, Kim suggested this week that it may take significantly longer.

The company has done the bulk of the assay development work in South Korea and is now in the process of transferring the technology to its US facility. Kim said Bertis is planning in the near term to launch validation studies for the test in cohorts in both South Korea and the US. He added that it is too early in the development and validation process to say when the test will be ready for a US launch.

"It will take a lot of time," he said.

Bertis is also developing what it calls its Broad Target Scanning (BTS) mass spec workflow, which Kim said will allow it to collect discovery proteomic data while also performing targeted analysis of samples.

"It is basically a hybrid method," Kim said. "It takes a sample with spiked-in peptides as an input, and when it detects a spiked-in peptide, it does [a targeted measurement], and when it is not [detecting spiked peptides], it is generating DIA data."

The company has developed a 15-minute workflow using the method, which Kim said it hopes to incorporate in its clinical work as a means of compiling large-scale proteomic datasets. He offered the example of if the company had been able to use the workflow for all of the MastoCheck tests it has run so far.

"If we had proteome profiling data for 100,000 samples, I'd be living in a dream," he said.

The upcoming Human Proteome Organization (HUPO) annual meeting will take place in Busan, South Korea, and Kim said Bertis will have a strong presence there. The company will make oral or poster presentations on its DeepMRM and BTS workflows as well as approaches for microprotein profiling, single-cell spatial proteomic breast cancer analyses, and assays for breast and pancreatic cancer detection.