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RareCyte Moving Into Higher-Plex Spatial Proteomics


NEW YORK – Spatial biology firm RareCyte is looking to make inroads into high-plex spatial proteomics with its Orion imaging platform.

According to RareCyte Chief Commercial Officer Selena Larkin, the system offers a combination of multiplexing, data quality, and throughput that the company believes will make it an attractive option in the increasingly crowded spatial omics space.

Founded more than a decade ago, Seattle-based RareCyte has traditionally focused on its CyteFinder instruments, which allow for fast, whole-slide fluorescent imaging of up to six proteins for circulating tumor cell and rare cell liquid biopsy applications. As spatial biology emerged as an important segment over the past several years, RareCyte retooled the CyteFinder platform to include tissue applications as well as immunofluorescence, immunohistochemistry, and H&E bright field analyses.

Seeing the demand for larger multiplexes, the company developed the Orion, launching it in the middle of 2020. Larkin noted, though, that, due in part to the COVID-19 pandemic, RareCyte didn't launch a serious commercialization effort for the platform until last year. She said that since then the company has been selling the instrument into the North American and European markets and has just begun marketing and sales in the Asia-Pacific region.

Topping out at 20 targets per sample, the Orion doesn't offer the multiplexing capability of spatial proteomic systems like Standard BioTools' Hyperion or Akoya Biosciences' PhenoCycler-Fusion, which can target around 40 and 100 proteins per experiment, respectively. Larkin said RareCyte believes the Orion offers advantages in throughput and data quality that will prove appealing, particularly for applications like biomarker validation where researchers typically run smaller multiplexes across a greater number of samples than in discovery experiments.

A key feature of the platform is that it performs its analyses in a single staining cycle and single scanning workflow, unlike many other fluorescence-based systems, which use multiple staining rounds — with fluorescence stripping performed on samples between each round — to achieve high levels of multiplexing. This enables the instrument's high throughput, Larkin said, noting that it can scan full slides using a 20-marker panel at a pace of 70 minutes per 1 cm2, allowing users to scan multiple samples per day. Performing the analysis in a single pass also improves data quality compared to iterative methods, she said.

Larkin said that RareCyte has found among its customers that they typically "have a scientific or medical thesis they are coming to a study with and very often need 12 to 18 markers."

"We found that the sweet spot was anywhere between 10 and 18 markers, in terms of what people were asking for," she said, "and so we developed the platform to specifically address that need."

Larkin said that RareCyte has seen researchers move to the Orion for validation in larger cohorts of biomarkers discovered using higher-plex spatial proteomics systems.

"We find a lot of people who are using other platforms for very high-plex [analyses] will then come to us with the Orion to run large cohort studies," she said. "The ability to run a large number of samples in a reasonable period of time is critical to obtaining statistical significance from a study. Orion provides the necessary throughput of multiple slides per day."

Larkin said RareCyte has also seen strong demand from researchers in the spatial transcriptomics field who are using the system to validate candidate markers identified via transcriptomic analysis.

Larkin said that, as is the case with spatial biology broadly, one of the main uses of the Orion platform thus far has been in immuno-oncology for looking for spatial signatures linked to cancer, drug response, and patient outcomes.

She said the company has also seen uptake among researchers studying autoimmune conditions as well as neuroscience research groups.

RareCyte also continues to grow its CyteFinder business. Its CyteFinder II HT allows for automated, whole-slide scanning of up to 80 slides per batch at a speed of four minutes per slide.

"You can load up 80 slides and analyze all of those slides in a completely unattended way," Larkin said.

The platform is widely used for identification and isolation of rare cells like circulating tumor cells, both for research purposes and clinically as part of laboratory-developed tests, Larkin said. She said that a number of companies and institutions are using CyteFinder instruments either for LDTs or clinical trial work, including NeoGenomics, Laboratory Corporation of America, CellCarta, Icon, the University of Washington, and Weill Cornell Medicine. RareCyte also offers assays out of its own CLIA lab.

RareCyte technology is also being used in an LDT for better assessing HER2 status in breast cancer patients that was developed at the Yale Cancer Center and launched commercially this fall. As detailed in a study published last year in Laboratory Investigation, the Yale researchers used a combination of quantitative immunofluorescence and mass spec-based standardization to determine the ideal dynamic range for an assay intended to measure HER2 levels in breast cancer patients with low, but clinically meaningful, levels of the protein. They then designed such an assay, which can be used for assessing HER2 status in patients at the lower range of expression, where existing assays are typically not effective.

RareCyte has developed software for use with the Yale assay that allows pathologists to highlight specific areas within a tissue slide they are interested in and quantitatively assess the HER2 expression levels for that section, Larkin said.

"It's a means of being able to better stratify which patients might be good candidates for treatments such as antibody-drug conjugates that can deliver Herceptin in a much more efficient way to those low-level HER2-expressing cells,” she said.

RareCyte’s most recent financing round was a $24 million raise that it closed in September 2021.

Larkin said RareCyte used much of that funding to build out its commercial and lab services teams, adding around 20 employees and bringing its headcount to approximately 70 people. She said the company might consider an additional funding round in the future but said that it currently has a “very good cash position” and noted that if it stays on its current growth trajectory, "we will be sustainable just by our revenues within the next 12 to 18 months."