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Celsee Launches Single-Cell Analysis Platform for Proteogenomics, Sequencing Applications

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NEW YORK (GenomeWeb) – With the commercial launch of its single-cell analysis platform today, Celsee aims to tap into the expanding markets for proteogenomics, immune monitoring, and single-cell genomics.  

Researchers can use a variety of methods to prepare single cells for analysis. Tools like flow cytometry and lasers offer expedited cell isolation and differentiation. However, certain methods may lack the capture efficiency, cell viability, and reproducibility required for widespread and large-scale use in research and clinical settings.

"With current technology, you don't know your viability during the process of isolation," Celsee head of marketing David Coe said. "You can determine that post-sequencing, but there's a lot of cost involved in library prep."

Formerly known as DeNovo Sciences, Celsee changed its name in 2016 to Celsee Diagnostics to reflect its focus on developing commercial tools based on its circulating tumor cell enrichment products. The firm later changed its name again to Celsee as it turned its attention primarily to research applications for its single-cell analysis tech.

Celsee's new Genesis single-cell analysis platform builds on the firm's original Celsee Prep tool to capture and isolate individual target cells.

After preparing a liquid, tissue, or cell suspension sample, researchers use the platform's Celsingle micro-analysis slides — which Celsee said can have the capacity for up to 1 million cell microwells — to isolate individual cells.

By passively capturing the cells through gravity, the Celsingle slide maintains cellular integrity and viability. Microbeads in each well with oligo attachments then capture each cell's transcriptional information. The Genesis system automates cDNA synthesis, pairing each cell with a unique cellular barcode and molecular indice for downstream analysis. According to Coe, the firm uses a patented automated reagent delivery system to perform lysis and reverse transcription directly in the wells.

"Celsingle slides can also be imaged to determine capture efficiencies, sample viability and quality, population analysis, and additional functions," Coe explained. "We want to offer people the flexibility to process samples at [both] a low input or high input level."

Celsee claims that the Genesis tool can sort cells in about 20 minutes and capture at least 70 percent of analyzed cells for downstream analysis. The firm said that the tool can use "any [liquid] sample containing cells and cells from dissociated tissues," including blood, urine and saliva samples. Coe noted that Genesis will allow researchers to process up to 4 ml of fluid at a time using the "appropriate enrichment or preparation slide" and routinely analyze 100,000 single cells in one sample run.

According to Coe, Celsee has been developing the major components of the platform since the firm began 2011. Celsee has integrated previously established workflows and methodologies into the new platform while developing a workflow to isolate single cells for genetic analysis.

The company began offering a version of the platform to early-access users in April. Coe said that these users span the research and translational spaces, and most are under confidentiality agreements.

Some early users from a large non-profit genomics research institute who wished to remain anonymous due to the status of their early-stage research explained that they are using Genesis to profile single cells related to their research. While they have not begun exploring the system's use in detail, they plan to apply it in human tissues, such as muscle, kidney, and gut tissue, as well as splenocytes.

In addition, the early users commented on Genesis' ability to dramatically reduce the per-cell analysis cost, batch effects, and running time, as well its high throughput due to automated processing. They also noted that the platform's open system allows for a wide range of applications.

"In terms of the reaction, it's up to us to select what reagents to use exactly," one user said. "It makes customized uses very easy, which is something to keep in mind for other tissues."

Coe said that Celsee will initially offer Genesis for research use only, and declined to comment further on the firm's plans to commercialize the platform for clinical use. According to Coe, Celsee is targeting downstream proteogenomics as one of the first applications for the platform because the market is expanding as  researchers not focus on expression data, but also protein epitopes and "we offer the ability to do this at scale."

In addition to proteogenomics, Celsee said it plans to market the platform for immune monitoring as an alternative to flow cytometry, as well as for the expansion and scale of next-generation sequencing library preparation.

The single-cell analysis market is rapidly crowding, with several companies offering their own novel tools to examine a variety of cells. Celsee will most likely compete with firms such as Fluidigm, who helped shape the current market with its C1 single-cell genomics system for preparing single-cell templates for mRNA sequencing, DNA sequencing, epigenetics, or miRNA expression. Fluidigm also offers its Hyperion imaging platform, which examines proteins in hundreds of single cells while maintaining their spatial and structural context in a tissue sample.

Researchers can also use flow cytometers sold by companies like Becton Dickinson to flow sort single cells into multi-well plates for phenotypic and genotypic analysis.

Recent market entrant Cell Microsystems sells its AIR system to isolate single cells, integrating fluorescence microscopy to automate the sample prep process. Another entrant, Berkeley Lights, uses a light-based platform for single-cell selection, characterization, culture, and export. However, both firms' tools require exporting the desired cells for analysis into single tubes.

In addition, NanoCellect Biomedical's WOLF cell sorter and N1 single cell dispenser platform use a laser to provide information on both scatter and cell fluorescence, amplifying and converting the signals into data for cell sorting.  

Coe argued that the Genesis platform distinguishes itself from other tools by offering users flexibility and scale. For example, the firm can offer a viable workflow for a flow cytometrist interested in examining 30 to 50 proteins in hundreds of thousands of cells "at an economic cost."

The company disclosed today that the Genesis platform will cost around $70,000, and Coe emphasized that Celsee is aiming to cut down on the per-cell cost by an order of magnitude compared to other technologies.

One of the  early users, however, pointed out that a challenge with using the Genesis system is collecting enough targeted cells to load the machine for analysis. While the platform can identify and analyze several hundred thousand cells in a single run, the researchers also noted that users need a large amount of additional funds to sequence all the resulting cells.

At the same time, Coe highlighted that the Genesis tool will be an open system that can be use with a variety of different sequencing kits from various vendors.

"The Genesis system will offer an open platform on which many applications can be scaled and utilized, making it an appealing system for scientists to understand their samples in greater detail," Coe said.

Despite its focus on the RUO space, Celsee is already exploring clinical applications for its technology. For instance, it partnered with IncellDx in January to commercialize a CTC screening panel following a screening collaboration on a multi-cancer diagnostic study. Noting that the collaboration has been successful in analyzing cell samples, Coe said that Celsee plans to release additional news "very soon." After collaborating with Zomedica in 2017 on a specific canine cancer liquid biopsy assay, the partners are now commercializing a veterinary liquid biopsy tool for cancer.

Since 2011, privately held Celsee has received funding from its original founders and the firm's board of directors. However, Coe declined to comment on the amount of funding the firm's raised so far nor other investors in the company.

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