NEW YORK (GenomeWeb) – Becton Dickinson plans to launch its single-cell gene expression analysis platform Resolve this fall and has already installed five systems for early-access users, the company said this week at the Advances in Genome Biology and Technology conference.
The system is based off of technology developed by Cellular Research, a startup founded in 2011 that BD acquired in 2015, and enables users to process up to 10,000 single cells for gene expression analysis via downstream methods such as PCR or next-generation sequencing.
At the AGBT conference in Hollywood Beach, Florida this week, one early access user, Vivek Bhalla, an assistant professor of medicine at Stanford University, discussed using the platform to study kidney cells, while BD researchers described in poster presentations internal work on tumor heterogeneity and comparing gene expression in single blood cells from healthy individuals and those with rheumatoid arthritis.
The Resolve platform can automatically process up to 10,000 single cells. It is based on a method the Cellular Research team published in Science in 2015, which makes use of barcodes to label cells such that every molecule can be traced back to the original cell. The firm received a patent related to its technology, US Patent No. 8,835,358, that covers "Digital counting of individual molecules by stochastic attachment of diverse labels."
A suspension of cells is loaded onto an array of microwells and the cells settle into the wells via gravity. The array consists of 200,000 wells (up from 100,000 wells originally) and the cell mixture is loaded such that there is one cell for every 10 wells. This reduces the chance that multiple cells will land in the same well, according to Christina Fan, a scientist at BD.
After the cells fall into the wells, magnetic beads are added, such that every well gets a bead. Included on those beads are functionalized oligonucleotides. Each oligo contains a barcode that is the same for all the oligos in the bead in order to identify the cell, a barcode that will identify the RNA molecule, a universal PCR primer, and a capture probe. Next, a lysis buffer is added to open up the cells and the mRNA targets bind to the capture probes. Because the molecules all contain their unique barcode as well as a barcode that can trace them back to their cell, the beads can be pooled together in a single tube, where cDNA can be synthesized and the molecules can be amplified.
The Resolve system also includes an automated pipetting system as well as a fluid handling station to manipulate the beads, Fan said.
Stephen Gunstream, vice president of BD Genomics, said that the company expects to run its early-access program through late spring or summer and to roll out a commercial instrument by early fall. The firm has already installed five systems with early users and anticipates installing 10 to 15 total systems for early access and running samples in its own lab for collaborators. Throughout the early-access period, Gunstream said the company will work internally and with collaborators to develop applications for Resolve. For instance, one application it is working on uses Resolve's imaging capabilities to distinguish between live and dead cells.
The company has not yet set a price for the system, but said that reagent costs to prepare a cell for sequencing would be "significantly less than $1 per cell." In addition, turnaround time from loading cells onto a Resolve cartridge to having an NGS library prepared will be less than one day.
The Resolve platform adds to BD's nascent genomics business. In 2015, it made its first entrance into that space with the launch of its FACS cell sorter and Precise kits for whole-transcriptome analysis and targeted gene expression. Also at AGBT this week, BD introduced a whole-genome protocol for its NGS sample prep instrument, CLiC, which can process 24 to 384 samples per run.
Gunstream said that although at first glance a single-cell system may seem like a bit of a jump, it fits in well with its other products, all of which relate to the theme of better ways for analyzing protein and RNA. In addition, he said the firm has many years experience working with individual cells and a natural extension is to move into the NGS space.
He added that the BD Genomics group plans to focus on driving applications for Resolve in key areas of the BD Bioscience business, such as immunology.
Stanford's Bhalla, whose research focuses on kidney diseases, said in a presentation that he used the system to analyze 1,200 cells from a mouse kidney. He is interested in doing single-cell RNA sequencing on kidney cells because, as he described, the "kidney is not anatomically organized for the benefit of scientific discovery."
Bhalla is interested in looking at the effect of diuretics, which cause the body to excrete salt and lower blood pressure, on kidneys. "We know the kidney undergoes remodeling because of this," he said.
Kidneys contain between 1 million and 2 million functional units known as nephrons. Each nephron is divided into 14 different segments, and these segments react differently to diuretics. "We wanted to understand what caused these changes," he said.
The initial work with the Resolve platform was able to identify all known cells from the 14 segments of the nephron, he said. In addition, he said, because of the platform's high throughput, they were able to subsample just the 1,200 cells they wanted to sequence, rather than 10,000 cells, which would have been more expensive, while still evaluating hundreds of cells from each segment. Already, the work has yielded some interesting insights in differential gene expression between different cell populations, he said.
Separately, in a poster BD described comparing blood cells from three healthy individuals with those from three individuals with rheumatoid arthritis. From each person, they analyzed between 8,000 and 14,000 cells, performing a targeted RNA sequencing study of 454 genes. The showed they could identify immune cells based on the expression of cell-type specific markers. In addition, they identified gene expression differences between healthy and rheumatoid arthritis patients, including an activated monocyte population in rheumatoid arthritis patients.
In another poster, they evaluated 8,500 cells from primary tumor and metastatic samples from a patient, identifying gene signatures from divergent cell populations that could shed light on the process by which a primary tumor metastasizes.
The Resolve system will compete with other single-cell technologies on the market, including Fluidigm's C1 system and WaferGen Biosystems' ICELL8 system. Gunstream said BD is looking to set itself apart from those other technologies in part by enabling flexibility of experiments.
While the Resolve platform can be high-throughput and process tens of thousands of cells at once, researchers can easily scale down and choose to examine fewer cells. For instance, he cited Bhalla's use of the technology to select just a 1,200-cell subset for sequencing.
In addition, Gunstream said, the company is focused on driving down the cost by not using microfluidic equipment and is targeting a market that does not necessarily have extensive experience in the single-cell or NGS space. For instance, Bhalla said that his work with the Resolve platform was his first entrance into the NGS space.