1CellBio, OMI to Validate Single-Cell Analysis Platform for Personalized Medicine Applications

sarahjibrinMedia Coverage, News

Dec 06, 2018  | John Gilmore

NEW YORK (GenomeWeb) – After introducing an early-access version of its InDrop system in April 2017, 1CellBio has released a commercial research-use-only version of the system that it says offers customers maximum flexibility and freedom for their experiments.

The firm has also partnered with the Open Medicine Institute (OMI) to validate the InDrop systems for precision medicine applications, where it will profile thousands of cells to track potential biomarkers for inflammatory and immunological conditions in patients.

“Up until recently the only methods you could use … for single-cell genomics analysis was either a Fluidigm chip (low throughput and expensive) or microplate,” 1CellBio CEO Colin Brenan explained. Now, microdroplet-based systems like 1CellBio’s allow single-cell genomic analysis “pretty efficiently and economically,” Brenan added.

Founded in 2016 at Harvard University, 1CellBio recently moved to Watertown, Massachusetts to set up its own laboratories. Having licensed the InDrop technology from Harvard and put it in the hands of early-access users, the firm is now commercializing an improved version of the system and selling it to CLIA-certified, CAP-accredited laboratories.

“Since we launched our first instrument in April 2017…[we] have made significant improvements to make the cell barcoding and library construction more predictable, reliable, faster, and easier to use,” Brenan explained. “Users are now able to barcode fewer cells in significantly less time.”

The current system consists of two instruments and a consumable kit, integrating single-cell capture with cell sorting technology. The firm’s method use barcoded hydrogel beads with a polyT terminus, which allows researchers to perform whole-transcriptome barcoding.

According to Brenan, one instrument accepts the microfluidic chip, barcoded gel beads, cells in suspension, and the lysis buffer with reverse transcriptase. The instrument loads the reagents into a microfluidic device, where the InDrop method occurs. The second instrument “photo-cleaves with a burst of UV light the barcodes from the gel beads,” Brenan explained.

After lysis finishes, the cell’s RNA transcripts bind to the barcoded DNA primers. Researchers can dissolve the drops, remove the resulting bounded genetic material, and synthesize cDNA sequencing libraries. The OMI is using a method called CEL-Seq2 for cDNA synthesis. Researchers then  take the resulting sequencing data and run it through a third-party bioinformatics pipeline.

Brenan said that researchers can control the droplet size in order to allow for a broad range of cell types, including yeast, pluripotent stem cells, bacteria cells, and large embryos.

“Typically, the cells [range from] 20 microns in size, roughly a third of a gel bead, down to 10 microns,” Brenan explained. “The gel beads themselves are about 65 microns in size.”

According to Brenan, the InDrop process “takes very little time to implement; in a day’s time you can process the sample, run the InDrop method and perform the reverse-transcription step.” Researchers however will need at least two days to generate sequencing libraries using tools such as Cel-Seq2 and sequence the encapsulated RNA samples.

In its partnership with the OMI, announced last month, 1CellBio now seeks to validate the InDrop system for personalized medicine applications. The company eventually hopes the system will eventually be used to run laboratory-developed clinical tests. OMI Founding Director and CEO Andrew Kogelnik said that the group will begin a pilot study that will target undiagnosed immunological and inflammatory conditions in patients.

“We hope that, as we dive in on the immuno-profiling level, we can look at 12,000 profiles of cells from one individual and see how they have changed before and after the patient’s treatment to understand what’s going on,” Kogelnik explained. “Sometimes, these patients do not have any biomarkers that are abnormal, and so we hunt for specific immune biomarkers.”

According to Kogelnik, the OMI and 1Cellbio began initial talks about two to three years ago as they explored potential uses for the InDrop system as it “matured.”

“Since we were set up as a very-well validated tech lab and were already doing tech-based services for other [groups], the conversation flowed pretty naturally,” Kogelnik explained. “But we also wanted the tech for our own research, so we were killing two birds with one stone.”

Kogelnik believes that InDrop will be a useful tool to obtain a wide view of multiple cells at once in a patient’s immune system. Kogelnik’s team aims to dive into populations of cells linked to conditions such as acute myeloid leukemia and T-cell deficiency diseases.

As part of the pilot study, OMI will use its nationwide clinical and research phlebotomy network of patients to collect blood samples. The institute will provide sample isolation and processing equipment before running the cells on InDrop. After collecting data from third-party sequencers, OMI will apply a bioinformatic pipeline developed with 1CellBio and other academic collaborators to interpret the data and generate a tailored report.

Kogelnik acknowledged that interpreting the bioinformatics report will be the hardest part of the study for his team. However, he noted that there are several ways to address the issue and that it’s part of “understanding the signal and understanding what you’re getting out of the test.”

“As we collect more data on more populations, the next step will be to start working with various groups to provide more clinical validation [for InDrop], or simply use it for a given research study,” Kogelnik said.

While OMI will ultimately offer partners’ assays as LDTs within its CLIA-certified lab, Kogelnik noted that “we’re not quite there with 1CellBio”. Kogelnik believes that the team will need at least a year before it can validate InDrop in the clinical setting.

In addition to the OMI, Brenan highlighted that 1CellBio has found interest in its InDrop system globally, working with undisclosed customers in Europe, China, Singapore, and Australia.

Brenan acknowledged that his team has struggled to keep up with the demand for InDrop, as “we’re a small company that’s currently growing.” He noted that part of the issue stems from the manufacturing process, as the firm is trying to “offer the gel components … at a price point that is attractive to customers.” While Brenan declined to comment on the price of InDrop directly, he noted that the tool barcodes cells with higher than 90 percent efficiency and at a cost below $300 per sample. In addition, he said that the kit components are sold separately to give InDrop customers maximum flexibility for their experiments.

1CellBio is entering a very crowded market for single-cell analysis. Several firms, including 10X GenomicsCelsee, and Cellular Research — a Becton Dickinson subsidiary — currently offer their own single-cell analysis platforms.

Last year, 10x Genomics launched immunology kits on its Chromium instrument that enables VDJ analysis of human T and B cells. In addition, Celsee’s Genesis single-cell analysis platform captures and isolates individual target cells using micro-analysis slides.

BD’s Rhapsody, a single-cell multi-omics analysis tool, leverages Cellular Research’s Precise technology and enables digital quantitation of hundreds of expressed genes across several thousands of cells.

“Competing approaches, like 10x Genomics and such … they’re closed systems, and if it fits researchers’ needs, that’s great,” Brenan noted. “But if your application does not fit into that envelope, the InDrop is the preferred alternative because it is an open system, as we allow to change the InDrop process to optimize it toward their experiment’s needs.”

Kogelnik added that “the 10x might be better as a screening tool if you identify the biomarker, but the [InDrop] allows you to hone and customize your application.”

1CellBio aims to improve the technology’s ease of use while maintaining its open nature. While the tool is currently used for barcoding RNA molecules, Brenan believes the barcodes could track other genetic material and proteins. The firm is also working with researchers on a variety of different applications, such as tumor profiling, drug discovery, stem cell research, and cell lineage tracing.

“We are beginning to roll out our targeted barcode and gel beads, which currently have a poly-bead sequence to capture the polyA tail of the transcript,” Brenan explained. “We will soon be offering a semi-customized gel bead for targeted transcriptional analysis on a limited basis, [as] we believe this will be very attractive to clinical researchers who know the genes they want to profile and want to process more samples per sequencing run.”

According to Brenan, 1CellBio will soon release a new barcode version (V3), targeted gel beads, and additional improvements in the Cel-Seq2 workflow to improve overall system performance. Brenan believes that the firm ultimately wants to link the phenotype of the cell based on its function with the genotype of the cells using the InDrop and downstream methods.

Kogelnik added that the platform “is a way of rapidly screening cellular systems to look at a single system, and very quickly [identify] what part of it is breaking down. You can potentially screen [a patient] for a rare immune disease, isolate the molecular pathology of the individual, and potentially find a solution.”