Scipio Bioscience Bets on Hydrogel Tech to Differentiate New Single-Cell RNA-seq Kit – GenomeWeb

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NEW YORK – Paris-based Scipio Bioscience this week announced the European launch of its Asteria hydrogel-based single-cell RNA-seq kit.
With less reliance on equipment and reagents, the RNA-seq library preparation kit provides researchers with a flexible benchtop protocol for labeling, isolating, and lysing cells, and recovering labeled mRNA.
The Asteria kit comes with access to Cytonaut, Scipio’s cloud-based bioinformatics analysis platform. The company says that this user-friendly platform was designed with non-bioinformaticians in mind and forms part of the company’s strategy to offer clients a complete workflow from library preparation through data analysis.
One of Asteria’s key features is the use of a hydrogel to physically isolate cells labeled with DNA-barcoded beads. Due to physical separation between cells and limited free movement within the hydrogel, cell-specific mRNA binds to the barcoded beads following cell lysis, due to their physical proximity. The beads are then recovered, and the mRNA amplified and sent for sequencing.
“It leaves a lot of flexibility in terms of actually being able to manipulate your cells while the mRNA is kept where it belongs,” Pierre Walrafen, Scipio’s CEO and cofounder, said in an interview.
Bart Deplancke, a professor of systems biology and genetics at the École Polytechnique Fédérale de Lausanne, in Switzerland, and an expert in scRNA-seq, commented that the Asteria technique appears “quite creative and easy to implement,” as well as inexpensive.
“The beads might still be the major weakness, however,” he commented, “as we found through our own work that unpaired beads tend to be “mRNA hungry” and as such are eager to pick up nonspecific RNA, which adds quite a bit of background noise to the data.”
Walrafen admits that despite physically constraining cells, the hydrogel necessarily allows for some diffusion.
“But [the background noise] is very minimal,” he said, “not impacting at any relevant biological scale.”
Walrafen pointed out that Asteria also has potential applications beyond RNA-seq library prep, wherever certain cells or cell-specific gene panels need to be targeted.
“We think the Asteria hydrogel technology in itself has loads of applications which can build on the fact that you can reach the cells within the hydrogel,” he said.
Although the use of hydrogel in library prep appears unique, the overall technique draws parallels to droplet-based protocols such as Illumina’s Drop-Seq and 10x Genomics’ Chromium.
While Walrafen couldn’t provide many technical details, pending the publication of a peer-reviewed study, he commented that Asteria’s transcriptome quality-to-complexity ratio is comparable to the more favorable ratio seen in 10x’s Chromium.
Here again, Walrafen says that the hydrogel plays a key role. In contrast to oil-based droplets, the hydrogel holds individual cells in a semipermeable compartment, effectively diluting the concentration of the inevitable contaminants.
Customers who purchase Asteria also gain access to Scipio’s cloud-based Cytonaut bioinformatics platform.
Cytonaut, says Walrafen, “covers the entire workflow from raw reads to actionable data and publishable figures.”
“We think biologists … should be given a tool to play around with the data sufficiently that they’re comfortable their project is going somewhere,” he said.
This way, he continued, a scientist without, or with minimal bioinformatics know-how, can bring a complete data package, with guidance on what they think needs to be analyzed to a bioinformatician when needed. Walrafen hopes that this strategy results in “more fruitful” interactions between bioinformaticians and scientists working at the bench.
Although Scipio has so far only launched Asteria in Europe, the company is planning further launches in the US and Asia in the near future.
There are roughly a dozen current Asteria users, Walrafen said, and Scipio is waiting to market it more aggressively until the upcoming peer-reviewed paper is published. While an exact date of that publication remains unknown, the company expects it to happen relatively soon.
In the meantime, the company is working to release other Asteria kits, for RNA-seq as well as “other applications,” and is pursuing a variety of industrial partnerships.
“We have exciting discussions with people who want to integrate the kit with [workflows] for preparation of cell suspension or library preparation downstream,” Walrafen said. “So, there’s lots of things we will have our hands full with in the next few years.”
Scipio, which currently has roughly 30 employees, raised $6.5 million in Series A funding in early 2020.
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