NEW YORK – UK startup CS Genetics is working on commercializing an instrument-free, single-cell analysis technology that the company says is simple, flexible, and easily scalable.
Earlier this year, the firm, which is headquartered in Cambridge, UK, and has an office in San Diego, launched a technology access program for early customers. It is slated to release its first single-cell RNA sequencing kit in 2024.
"Our first product will be a single-cell 3’ gene expression product that is called SimpleCell," said CEO Jeremy Preston, who joined CS Genetics in 2022 after spending over a decade working at Illumina. "One of the goals around that name was [to show that we have] the simplest single-cell technology to use, period."
At the core of CS Genetics’ technology lies a single-cell indexing method that is enabled by so-called kinetic confinement, a process to control reaction kinetics within the three-dimensional solution space.
The company’s foundational technology was developed by Lucas Edelman, the firm's founder and chief technology officer, after he received a Ph.D. at the University of Cambridge. CS Genetics is privately owned and has no affiliation with any academic institutions.
Overall, CS Genetics’ kinetic confinement technology leverages two proprietary solutions: an indexing reagent named CPair that delivers index sequences directly to single cells, and the kinetic confinement buffer (KCB), a bifunctional reagent that allows heat-activated cell lysis and kinetically confined indexing.
More specifically, Preston said, the CPair solution contains cell-binding molecules anchored at the end of so-called coding strands (where CS Genetics gets its name from), which are engineered DNA strands attached to beads. The coding strands also contain indexing oligos for barcoding nucleic acids.
As cells are introduced to the CPair reagent, optimized stoichiometry drives the binding between CPair and cells at a one-to-one ratio, Preston said. This is followed by the addition of a proprietary viscous buffer, which is designed to prevent the spatial diffusion of indexing oligos between cell-CPair complexes.
Once the cells bind with the CPair reagent, they can be stored on ice or frozen before further processing, Preston noted.
After cell pairing, the kinetic confinement buffer is added to lyse the cells via heat activation, releasing their nucleic acid content. The increased temperature also releases the indexing oligos from the coding strands, and the barcodes are subsequently hybridized to target nucleic acids by cooling the reaction.
From there, users can proceed with standard molecular biology techniques to prepare sequencing-ready single-cell libraries.
According to Preston, one advantage of the company’s approach is that it requires no physical separation of the cells for single-cell indexing, eliminating the need for special equipment. In addition, he said the protocol, which is solution-based and does not involve combinatorial indexing or an emulsion, is relatively straightforward to execute.
"As long as you have a centrifuge that could spin strip tubes or a plate, and you have pipettes, perfectly multichannel pipettes, and you have a thermal cycler PCR machine, you can do the assay," Preston said. "That's pretty much it."
Moreover, he said he believes the ability to stop the process between cell pairing and heat-activated lysis can be "really valuable."
"Often for single-cell assays, once you start, it is a lot of work," he pointed out. "This really gives you huge flexibility — maybe batch up more samples, maybe do some time points and multiparameter experiments."
So far, the company has tested its technology "extensively" on human and mouse cells, including peripheral blood mononuclear cells (PBMCs), neurons, dissociated cells from mouse brain tissue, and cells from spleen tissue. The firm has not tested its method on formalin-fixed paraffin-embedded (FFPE) tissue samples yet, but "there is no reason why it wouldn't work," Preston said.
As for sensitivity, internal data has shown that the method can routinely capture more than 2,000 genes per cell, although he thinks that metric can still go higher. While the company has yet to finalize its product specifications, he said it targets up to about 5,000 cells per sample. Additionally, it aims to achieve above a 40 percent cell capture rate.
In terms of turnaround time, the workflow of the assay up to sequencing takes about seven hours, and the company is working to condense that further. Moreover, there is "a ton of room" for automation, he said, potentially opening the door for the method’s adoption by "much bigger single-cell studies."
While the company’s initial product will be developed for Illumina sequencing, Preston said the single-cell libraries can be adapted for other platforms using commercially available conversion kits.
The company’s internal studies have shown "identical" data quality when sequencing the same samples using the Element Biosciences versus an Illumina platform, he added.
Furthermore, Preston claimed the company’s method can "naturally get the longest RNA fragments," given that it is "very gentle on the cells" without any microfluidics or shearing components. The firm has also tested the product with PacBio sequencing, which, without any optimization, produced "nice results" and 2 kb read lengths, he said.
As for pricing, Preston asserted that the technology would be "significantly cheaper" than that of the market leader while being "comparable" with other instrument-free single-cell technologies. He declined to disclose the per-sample price, however.
Preston said CS Genetics kicked off a technology access program in June. Due to "resource limitations," the company only took on about a dozen early-access customers, including Cancer Research UK, the Stowers Institute for Medical Research, the University of Zurich, and Newcastle University.
CS Genetics’ first product will be a single-cell analysis kit for 3’ gene expression, which the company is hoping to release in early or mid-2024. "We are just trying to tie up a few loose ends and work on [the product’s] robustness and reproducibility," Preston said.
The assay will have an "incredibly small footprint" with only two boxed components. The first product is designed to accommodate eight samples, but the company plans to release a 16-sample version afterward, he said.
The initial target customers will be core labs, but the firm also has its sights set on pharmaceutical companies that could deploy single-cell analyses across their drug development pipeline.
CS Genetics is not the only company that has developed methods for instrument-free single-cell analysis. Fluent BioSciences, a Watertown, Massachusetts-based firm, for instance, has already commercialized a single-cell RNA-seq reagent product based on a templated emulsification-based technology called particle-templated instant partition (PIP).
Scale Biosciences, a University of Washington spinout, has also launched an instrument-free single-cell transcriptomics assay based on combinatorial indexing technology.
Also, while Preston believes CS Genetics’ technology is relatively simple and cost-effective, it remains to be seen how the method will fare compared to other products in the market, including those from currently dominant players such as 10x Genomics.
So far, CS Genetics has garnered a "small series A investment," the amount of which Preston did not disclose. He noted that the company plans to embark on a Series B financing round in 2024.
As the firm raises more capital, Preston said it will build and expand a transcontinental team in Europe and the US. Currently, the company operates small R&D headquarters in Cambridge, UK, with about 20 employees. In addition, it has five staff members, including Preston, in California focusing on commercial operations.
Beyond transcription analysis, Preston said the company plans to further develop its kinetic confinement technology for additional applications, such as selective capture of single cells using antibodies. The firm has also established proof-of-concept work on proteomics analysis at the single-cell level.
"This is not just 3’ gene expression of single cells; this is a technology platform where we can turn the crank and we can bring out all different flavors, which is really exciting for us," Preston said.