Laboratories looking to expand into or improve upon their single cell capabilities have some new products to consider from the two leading public companies in the space.
10x Genomics has launched two new products from its Chromium single-cell analysis line aimed at expanding its customer base by emphasizing reduced costs as well as top-tier performance for both larger- and smaller-scale projects.
At the larger-scale end, 10x has rolled out its GEM-X Flex Gene Expression offering, a next-generation successor to its Chromium Flex single-cell gene expression technology that is designed to lower customer costs per project, per experiment, per sample—and even per cell, where the company is promising to deliver “single cell for a single cent.”
For smaller-scale analyses, 10x has introduced its GEM-X Universal Multiplex product, intended for customers with samples in the thousands of cells that are looking to run more cost-effective single cell studies.
“We’ve heard from a lot of people that single cell is incredibly valuable, but that in order to get this to the next level, they need to be able to scale this up and reduce the cost per cell or cost per sample in different ways, depending on their experiments, so that they can run really large-scale studies,” Michael Schnall-Levin, PhD, 10x’s chief technology officer, founding scientist, told GEN Edge. “We think these products are going to be meaningful steps towards that.”
New CellScape chemistry
Bruker on Tuesday rolled out new technology for its CellScape™ Precise Spatial Proteomics platform for highly multiplexed immunofluorescence (IF).
In what it called “a major technological breakthrough,” Bruker launched new chemistry for CellScape, called EpicIF, short for Enhanced photobleaching in cyclic immunofluorescence. EpicIF is intended to expand the range of compatible commercially available fluorophore conjugated antibodies by nearly 10-fold, as well as simplify assay development, and increase throughput by up to two-fold.
EpicIF enhances photobleaching efficacy by combining a proprietary reagent with visible light to gently erase fluorescence signal from nearly any fluorophore and preserve epitopes while maintaining tissue integrity, the latter also a feature of the earlier version of CellScape.
Bruker is supporting EpicIF through its concurrent release of a new version of its CellScape software. The new version, called CellScape Navigator, introduces what is designed to be a more intuitive user interface and easy experiment setup. EpicIF and CellScape Navigator will both be available as upgrades to current CellScape instruments, according to the company.
“This breakthrough gives scientists an unmatched level of flexibility in their highly multiplexed IF experiments,” Ranga Partha, PhD, Senior Vice President of Product Management and Marketing at Bruker Spatial Biology, said in a statement. “This new advancement builds on the best-in-class performance of the CellScape, which already offers differentiated quantitative performance, reliability, and modularity at any time.”
“Wider selection”
“By enabling the erasure of previously photostable fluorophore signals, researchers can choose a wider selection of antibody conjugates than ever before,” Partha added. “In addition, EpicIF enables compatibility of the CellScape platform with additional fluorescent readouts, such as RNA-ISH. It’s a leap forward in versatility for high-throughput spatial proteomics and we’re thrilled to offer this transformative technology to our customers.”
The CellScape platform was initially developed by Canopy Biosciences, which Bruker acquired in 2020 for an undisclosed price. According to Bruker, CellScape offers best-in-class resolution and high dynamic range (HDR) imaging, while capturing the entire continuum of protein expression in a biological sample—from least to most abundant—while capturing fine morphological details.
CellScape uses directly labeled primary antibodies, which Bruker says enables a robust and modular chemistry that allows researchers to build assays by combining panels and/or individual markers, even after the conclusion of an experimental run.
Bruker said its new Bruker Spatial Biology division, announced earlier this month, will be sharing more about the improved CellScape offerings at the Society for Immunotherapy of Cancer (SITC) 2024 Annual Meeting, set for November 8-10 in Houston.
Bruker Spatial Biology is a division within Bruker Scientific Instruments (BSI) Nano segment, which has topped the five public companies ranked by revenue in GEN’s updated A-List of Top 10 Spatial Biology Companies.
Ranking second among public companies is 10x, which introduced to customers in March its GEM-X technology architecture that powers both the company’s GEM-X Flex and GEM-X Universal Multiplex. 10x unveiled its first two GEM-X products in February at the Advances in Genome Biology and Technology (AGBT) General Meeting in Orlando, FL.
Greater scalability
GEM-X Flex offers greater scalability than its predecessor, namely the ability to profile up to 2.5 million cells per run and 5 million cells per kit, for a cost that can shrink to a penny a cell. With input recommendations starting at 25,000 cells per sample—down from between 100,000 and 300,000 cells per sample—GEM-X Flex delivers what according to 10x is the ability to explore limited samples such as small tissue biopsies and flow-sorted cells, with a four-fold improvement in sample recovery.
“This opens up new samples that previously, if people only had, say, 50,000 cells in their sample, they couldn’t run it on [Chromium] Flex, though they could run it on our other products. Now they can run this on GEM-X,” Schnall-Levin said.
He said GEM-X Flex will eventually supplant Chromium Flex, launched in 2022, though both are continuing to be marketed for now. According to 10x, Flex is the only single cell assay compatible with varied sample types that include fresh, frozen, PFA-fixed tissue, whole blood, and FFPE samples.
Also launched by 10x is GEM-X Universal Multiplex, through which researchers can batch and run four independent samples, up to 5,000 cells per sample, for approximately $560 per sample—a price point the company says will expand single-cell access to a wider range of labs and research projects.
GEM-X Universal Multiplex introduces new on-chip multiplexing capabilities for the company’s flagship GEM-X Universal 3′ and 5′ Gene Expression assays. On-chip multiplexing allows researchers to combine cells from up to four samples directly on the chip and collect the partitioned cells in one recovery well. However, on-chip multiplexing is ideally suited for limited samples such as organoids and stem cells.
According to 10x, on-chip multiplexing simplifies the workflow and reduces hands-on time compared to other sample multiplexing methods, by eliminating the need for upstream sample tagging and enabling high cell recovery with low cell input requirements. Following sequencing, the samples are distinguished through computational demultiplexing to streamline the process.
Schnall-Levin said 10x’s earlier 3′ CellPlex Kit allowed users to multiplex by tagging their sample cells with a physical or chemical tag, then combining them for later disambiguation. The method brought with it challenges such as manipulating cells upfront, which led to loss of cells and additional workflow complexity.
“This universal multiplexing, it’s a really dead simple way of doing sample multiplexing,” Schnall-Levin said. “What does that mean for our customers? Basically, you get all the same kind of assay performance of our earlier GEM-X 3’ and 5’ assays. But when you have multiple samples, you can do this at a much lower per cost sample.”
“Response to a need”
10x says the launches are not a response to criticism lobbed against the company that it is trying to monopolize single cell analysis and the broader spatial biology field: “They’re a response to a need for people to scale their studies,” Schnall-Levin countered.
Earlier this year, 10x denied it was acting to squelch competition by aggressively litigating potential infringement of its patents, as alleged by the then-CEO of rival NanoString Technologies—since acquired by Bruker, where it anchors that company’s new spatial biology division—and a group of academic researchers in a GEN commentary.
Chromium instruments accounted for 40% ($7.641 million) of 10x’s $19.056 million in total instrument revenue for the third quarter this year, according to results released October 29. The most recently announced Chromium instrument—Chromium Xo, launched in September—is designed to run 10x’s GEM-X 3′ assay and deliver high-performance single cell analysis at a U.S. list price of $25,000.
Chromium Flex is among Chromium consumables that accounted for 76.5% ($96.536 million) of the $126.204 million in total consumables revenue reported in Q3.
10x reported $151.654 million in total Q3 revenue, down 1% from $153.644 million in the year-ago quarter. The company finished the first nine months of 2024 with $445.764 million in total revenue, up 2.5% from $434.748 million a year earlier. 10x shares rose 6% from $15.79 at yesterday’s close to $16.73 in early trading today as of 11 am ET, after falling 9% to $14.35 in post-market trading Tuesday in response to the results.
Bruker is set to report Q3 results on November 5. Bruker does not break down results for its Bruker Spatial Biology division, which combines results from NanoString with Canopy and a third company, Acuity Spatial Genomics.
Bruker Spatial is part of the BSI Nano segment, for which Bruker reported revenues of $492.9 million for the first half of this year, up 13% from $434.7 million in Q1–Q2 2023. Bruker finished January–June 2024 with $1.522 billion, up 11% from $1.367 billion from a year earlier.
