How New Technology Can Leverage Single-Cell Omics Techniques

Single-cell omics offers new insights into the complexities of biological systems through the analysis of cellular functions, disease mechanisms and drug responses.

Despite the high level of detail provided by single-cell omics, there are several renowned challenges commonly experienced within this area of research. For example, single-cell approaches are expensive and many studies are limited by the number of samples they can profile, with the process taking weeks or even months.

Scale Biosciences (ScaleBio) recently unveiled its new ScalePlex technology in an attempt to combat these difficulties. We spoke to Jason Koth, product management lead at ScaleBio, to learn more about the ScalePlex technology for leveraging and overcoming current limitations within single-cell genomics.

Isabel Ely (IE): What is the importance of single-cell omics?

Jason Koth (JK): Single-cell omics tools are critical in biological research because they allow scientists to profile more deeply the overall biological picture of how various cell types and states impact normal, disease and developmental biology within samples vs bulk methods. In a sample profiled with bulk methods, the varying cell proportions and different states are lost to an averaged representation. Single-cell methods can precisely detect these sample features. This enhanced resolution into heterogeneity allows better characterization of biology, which allows new understanding into the how and why of complex biology and what drives it.  More granular information about each cell’s potential contribution to complex diseases can support new hypotheses on biological pathways, mechanisms of disease and identification of more informative biomarkers.

IE: Can you tell us about ScalePlex technology? What research areas does it apply to and how does it simplify single-cell genomic studies?

JK: Single-cell approaches are expensive with many studies only able to profile a limited number of samples. With ScaleBio's massively parallelized barcoding technology, the cost of single-cell experiments is rapidly decreasing by up to 10-fold for a single sample compared to droplet methods. This enables researchers to think about moving from descriptive studies with only a few samples to larger studies with multiple time points, experimental conditions or across larger cohorts. ScalePlex now makes it easy to combine tens to hundreds of samples in a single experiment. We are especially excited about this technology in translational research and drug development.

Hundreds of patient samples, collected across different locations and at different times, can be easily collected and processed together. In addition, with its streamlined workflow, ScalePlex results in more cells being captured, enabling analysis of even a small number of cells, like those from biopsies.

IE: What differentiates ScalePlex technology from current practices applied in the laboratory within single-cell omics research?

JK: Compared to other multiplexing methods, ScalePlex enables more samples to be run in parallel, increasing lab efficiency and minimizing cost per sample. It's quicker to multiplex 96 samples than to hash 8 samples with antibodies or lipid-modified tags. This is because samples can be pooled directly after the ScalePlex tagging reaction without any washes. The novel modified oligo tag is quenched as part of the simultaneous sample fixation. This minimizes background signal and saves time compared to other methods that require washing away unbound tags prior to sample pooling. It also results in fewer cells being lost during processing.

Unlike other multiplexing methods, tedious optimization and titration steps are eliminated. The ScalePlex reagents are ready to use straight from the kit.

Finally, reagents are universal across experiments. The tags are species-agnostic and compatible with both cells and nuclei, unlike other methods. This makes the technology simple and broadly applicable across any sample a researcher might be interested in profiling.

IE: How does multiplexing work with ScalePlex technology?

JK: Multiplexing with ScalePlex is simple and scalable, which is one of the reasons our customers (and our team) are so excited about it. The technology uses a novel modified oligo that, when combined with samples during ScaleBio sample fixation, will add a unique molecular tag to all the cells or nuclei in that sample. Each ScalePlex oligo plate comes with 96 unique tags that can be used individually across different experiments, all at once from a single oligo plate. Alternatively, to increase multiplexing beyond 96, multiple oligo plates can be used in the same experiment, enabling hundreds of samples to be combined into a single run.

After samples are tagged during fixation, they are pooled together and then washed as a pool. This pooled washing streamlines the process instead of having to conduct individual washes before combining samples, which can add dozens more pipetting, washing and counting steps.

Following washing, the pooled samples are added to the first level indexing plate (RT index plate) and taken through the workflow as any other sample to generate sequencing-ready libraries. In analysis, the ScalePlex tags and RT indices identify each sample’s data uniquely to demultiplex back into each unique sample. This unique combination of ScalePlex tag and RT index makes it possible to label multiple pools of 96 samples and add them onto different sections of the RT index plate and profile hundreds of samples all with the same core workflow. 

IE: What are the current challenges faced in single-cell omics research? Does ScalePlex technology address some of these challenges and what else can be done?

JK: There are several challenges currently in single-cell omics research that restrict access to more labs or limit more ambitious and impactful research from being done. High costs per sample can make it prohibitive for many labs to conduct this type of experiment. For those that can utilize single-cell omics, studies larger than a handful of samples are typically out of reach. Additionally, limited throughput with existing technologies can mean processing more than a handful of samples can take weeks or months, restricting the scope and scale of research. Finally, with both prior challenges, running technical or biological replicates are often out of the question, which can limit the statistical power of studies.

ScalePlex combined with ScaleBio’s Single-Cell RNA sequencing kit can address all these challenges. It supports broader access to single-cell omics across the research community and thinks about the bigger questions it is applied to as well. With a simple, streamlined, flexible method for multiplexing, researchers can reduce sample costs to enable larger studies to be conducted and a greater number of samples in each run, doing much more with less. The ability to combine 96 samples or more in a single run, simply, allows the processing of many samples simultaneously with greater efficiency and reduced experiment time. With reductions in cost and increases in efficiency, it becomes possible to run biological and technical replicates across samples for greater statistical power than would be possible when studying just a handful of samples.

IE: What are your goals for the short- and long-term future in developing this technology further?

JK: In the near term, ScaleBio would like to work towards integrating the ScalePlex protocol with lab automation. With the flexibility for massive multiplexing of hundreds of different samples and conditions, automation can further streamline these experiments. This would make ambitious research questions routinely answerable for any lab – no matter the size or budget. We are very excited to see what new research questions the scientific community will use the technology for, with such a simple and streamlined method for multiplexing.

In the longer term, we are focused on developing the ScalePlex technology with our high-throughput platform (discussed earlier this year at the Advances in Genome Biology and Technology conference). This new platform will offer throughput of up to 2 million cells in a single experiment. When the ScalePlex technology is combined with drastically increased throughput in a simplified workflow, it will be exciting to see the creative and impactful research these differentiated technologies are applied to in disease research.

Jason Koth, product management lead at ScaleBio, was speaking to Dr. Isabel Ely, Science Writer for Technology Networks.

About the interviewee

Jason Koth leads product management at ScaleBio, helping facilitate the introduction of new single-cell omics technologies designed to leverage scale to unlock new fields of research. He previously held product marketing roles focused on single-cell genomics at 10x Genomics and BD. He earned his bachelor’s degree in chemical engineering from the University of California San Diego.