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2018 Top 10 Innovations

Biology happens on many levels, from ecosystems to electron transport chains. These tools may help spur discoveries at all of life's scales.

Dec 1, 2018
The Scientist Staff

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With the maturation of big data, whole-genome sequencing, and other expansive investigations, it can sometimes feel like researchers have traded in their microscopes for macroscopes. But this year’s Top 10 Innovations competition tells a different story: that of a single cell.

Many of the exciting laboratory tools that our independent panel of judges (whose bios and comments on each of the Top 10 products you’ll find below) selected for this year’s winning crop are geared toward prying open individual cells to access the data contained in their DNA, RNA, and/or proteins. The advantage of capturing these reams of biological information on the level of a single cell is revealing the variety within tissues not detectable in pooled samples. In cancer research, for example, such analyses may allow scientists to more accurately characterize tumor heterogeneity by sampling several thousand rapidly dividing cells on an individual basis to see how they differ from one another.

Also making a strong showing on this year’s list are products that enable and advance tried and true laboratory technologies, such as mass spectrometry and CRISPR-based genome editing. We at The Scientist are pleased to present the winners of our 2018 Top 10 Innovations competition, and we look forward to seeing the discoveries that bloom from their adoption.

Sphere Fluidics Cyto-Mine

About five years ago, employees at Sphere Fluidics asked 35 biopharmaceutical companies if the UK-based biotech firm’s single-cell analysis technology could be of any use. The responses indicated that there was a need, particularly among companies working on antibodies and cell lines. What evolved out of those conversations is the Cyto-Mine, a compact, benchtop apparatus that takes the place of what would ordinarily be accomplished by multiple instruments. “It’s essentially the world’s first integrated device specifically designed to automatically perform all the steps in antibody discovery and cell line development workflows,” says Rob Marchmont, the sales and marketing director at Sphere Fluidics, which began selling the instrument this summer.

The Cyto-Mine screens a sample of up to 200,000 cells by sorting them individually into their own tiny droplets, assessing them for the desired property (such as high production of a particular protein or antigen specificity), then dispensing the good ones onto microtiter plates, from which users can grow clones.

Tom Kelly, a scientist at pharmaceutical company Janssen, was an early tester of Cyto-Mine and now uses the finalized version (priced at $450,000) for selecting cell lines that produce large quantities of a biologic drug. He says the biggest advantage is the proof of clonality Cyto-Mine delivers, confirming that there’s just a single, verified cell in each well. His previous protocol included an extra step that doubled the processing time. “The time it takes to go from transfection to freezing vials in the old process would have been three months,” he says, “and now it’s six weeks.”

KOEHLER: “We often struggle to find a single, integrated platform that enables both screening and cell recovery for downstream analysis. Full automation and a system focused on gentle manipulation will increase the fidelity of experiments.”

Mission Bio Tapestri Precision Genomics Platform

 

Launched last December, the Tapestri Precision Genomics Platform was the first high-throughput instrument for single-cell DNA sequencing sample prep. Using droplet-based microfluidics technology, Tapestri first exposes cells to a protease that lyses the nucleus and frees the DNA from its condensed chromatin formation. Heat then denatures that protease before the system adds the reagents to amplify the loci of interest and to barcode them according to their cell of origin, readying the samples to be fed into a next-generation sequencer.

“It’s exciting,” says MD Anderson Cancer Center geneticist Nick Navin, whose group has used the instrument regularly for about a year to detect the combinations of mutations found in individual breast cancer cells. “That allows you to really understand the genetic substructure of a tumor,” he says, as well as “to reconstruct the evolution of the mutations.”

Tapestri can prep up to 10,000 cells simultaneously, compared with only 384 when sorting cells into wells of a plate. Moreover, says Navin, the instrument takes only about a day to prepare a sample, compared with five to seven days using the plate method.

The Tapestri costs $79,500, and consumables run about $795 to $1,300 per sample. Mission Bio offers several fixed panels that target loci relevant in various cancers, and can develop customized panels that target up to 300 loci of interest, and possibly more in the future, expanding Tapestri’s applications beyond oncology, says Dennis Eastburn, chief scientific officer at Mission Bio.

WILEY: “This new microfluidic platform for high-throughput single-cell DNA sequencing could be a powerful approach for analyzing tumor cell heterogeneity and understanding the mechanistic basis of tumor evolution."

Fluidic Analytics Fluidity One

Among the many potential applications of Fluidity One is “routine biophysics,” says Sean Devenish, the head of R&D at Fluidic Analytics, which makes the protein-analysis instrument. Devenish envisions labs routinely using the instrument for quality control, testing protein-containing solutions when they first arrive and again when they come out of the freezer to make sure the contents haven’t degraded. Users pipet 5 μL of sample onto a disposable microfluidic chip, then insert it into the benchtop Fluidity One instrument. The sample runs through a chamber in parallel with a stream of buffer, into which proteins diffuse. The instrument measures the rate of this diffusion to calculate the average size of the proteins; it also measures sample concentration.

Alex Büll, who studies protein aggregation in disease at the University of Düsseldorf in Germany, says he’s found Fluidity One useful for analyzing urine samples from patients. “It’s very difficult to actually estimate the concentrations properly, so we use the Fluidity One to determine the concentrations, and we also follow the aggregation of the proteins and the dimer/monomer equilibrium,” he explains. Fluidity One’s advantage over measuring light scattering (a standard technique for determining the size of proteins in solution) is that light scattering results are dominated by any aggregates in the solution, while Fluidity One delivers a “true average” size value for the proteins present, Büll says. Devenish adds that the instrument can also reveal whether proteins are bound to each other or to DNA, lipids, or nanoparticles.

Fluidity One costs $30,000, plus chips and reagents, which cost about $5 per run.

ZHANG: “Characterizing and performing quality control on purified proteins is critical for consistent results. This tool could be a great addition to any biochem lab.”

10X Genomics  Chromium Immune Repertoire Profiling Solution

With the Chromium Immune Repertoire Profiling Solution, researchers can study the body’s adaptive immune response to different types of infections and identify the specific cell types that respond to immune system activation, whether it’s triggered by bacteria, viruses, or even cancer. Released commercially in March, the 10X Genomics technology builds on the power of single-cell sequencing by allowing researchers to distinguish each and every T and B cell in a sample, along with the genetic sequence of the Y-shape receptors on each cell.

“I don’t think people realize that they can get all of that information from this product,” says Giovanna Prout, the director of strategic marketing for single cell genomics at 10X. “And, with some of the new products recently released, researchers can get even more.”

With DNA barcoding technology, the tool can now determine which type of T or B cell responds to a particular antigen. “Now you can look at clonal expansion of these cells in response to a certain virus or disease,” Prout explains. The barcoding technology also improves the analysis of cell phenotypes by combining gene expression with cell-surface protein expression data, because antibodies are connected to barcodes, rather than to the fluorescent tags used in flow cytometry. Because the barcodes are diverse, researchers can detect many more cell-surface markers simultaneously, providing an unprecedented look at the immune systems of both humans and mice. Each sample costs $1,500 to screen.

In Chris Klebanoff’s lab at Memorial Sloan Kettering Cancer Center, he and his colleagues are looking for novel T cells as a treatment for solid malignancies. “The 10x platform is unique in its ability to combine T-cell-receptor data with gene expression at the single-cell level in a user friendly manner,” says Smita Chandran, a senior research scientist in the lab. “I am most excited about its translational application to identify and zero in on unique T cells that are capable of mediating a tumor response.”

VAN VLIET: "Profiling the receptor sequencing among T cells and B cells with this approach provides an informative data set that can aid understanding of the initial starting population prior to any sorting or transduction strategies, and can help contribute to definitions of biological cell attributes of such cells.”

Fasmatech  Omnitrap

For protein scientists looking to analyze large molecules with tandem mass spectrometry, the Omnitrap device offers fresh capabilities. The platform is a radio frequency ion trap that processes proteins even at high molecular weights—a limitation of older trapping technologies—to gain information on protein sequences, structures, and molecular interactions. “The Omnitrap allows one to obtain unique information that was impossible, or nearly impossible, to obtain by other means,” says Roman Zubarev, a chemist at the Karolinska Institute who was the first Omnitrap customer.

Zubarev is leading a team to use the device as part of a project to perform so-called top-down sequencing of antibodies. Top-down analyses keep large protein structures intact, rather than digesting them as other analytical methods require, and Zubarev says the Omnitrap will be critical to the endeavor.

One of the product’s major advantages, according to Dimitris Papanastasiou, the founder and chief scientific officer of Athens-based Fasmatech, is the ability to fragment proteins in multiple ways. This allows users to look at a protein’s characteristics under different circumstances—and do so using one device. “It’s really unique,” he says.

Omnitrap is an add-on to Thermo Scientific’s Q Exactive Mass Spectrometer and costs €250,000 ($288,000 USD).

ZHANG: “Improvements in protein mass spectrometry will be transformative for biological research.”

AcouSort • AcouWash

In 2010, researchers at Lund University in Sweden developed the concept of using sound to migrate cells, a phenomenon called acoustophoresis. That December, they launched AcouSort to commercialize the technology. Earlier this year, the company officially launched its second product, AcouWash, which can wash cells from one medium to another, enrich or concentrate cell samples, and separate cells based on size, all using ultrasound. 

An acoustic wave “pushes particles or cells of a certain size into the center of [a] microchannel that the sample is passing through,” explains Jay Mallinson, lead engineer on the $50,000 benchtop machine. Researchers can adjust the amplitude of the acoustic wave depending on the size of the cells they are trying to isolate—larger cells actually need less force to move because there is more surface area to be pushed by the acoustic wave. Then, it’s just a matter of directing the flow through a splitter that separates the cells of interest from the background media.

AcouWash minimizes cell loss, which can happen with repeated washing and centrifugation steps—a big advantage when working with samples containing precious few cells, says Karolina Pircs, a postdoc in Johan Jakobsson’s molecular neurogenetics lab at Lund University. Pircs’s research involves directly reprogramming fibroblasts from Huntington’s patients and healthy controls into neurons. A protocol that she helped develop last year (EMBO Mol Med, 9:1117–131) converts 30 percent to 40 percent of the fibroblasts, meaning the researchers must sort the converted from unconverted cells. The AcouWash system, which she’s tested twice so far, yielded about 10 percent more cells than a traditional protocol involving six centrifugation steps, she says.

VAN VLIET: “While the function of this invention is simple, its capacity to handle small sample volumes at relatively low shear rates is an attractive option for intermittent sampling and analysis of cells during process development and manufacturing protocol optimization."

Horizon Discovery   Dharmacon Edit-R Fluorescent Cas9 Nuclease mRNA

To use the genome-editing tool CRISPR-Cas9, researchers typically insert DNA, coding for the various components of the tool, into cells they want to edit. But there’s no easy way of getting rid of this foreign DNA once it’s been incorporated into the host cell. 

Specifically, researchers may be concerned about the lingering presence of DNA that codes for the Cas9 nuclease. Often “you have the Cas9 still being expressed in the cell long after the edit has occurred,” says Amanda Haas, a product manager at UK-based gene-editing company Horizon Discovery. That means that the enzyme can still interact with host DNA, potentially leading to unwanted cuts in the genome at off-target sites.

One of the company’s latest products, Dharmacon Edit-R Fluorescent Cas9 Nuclease mRNA, aims to circumvent this problem by providing the RNA transcript instead of DNA for the Cas9 enzyme. Soon after a target cell has synthesized the protein—which is fluorescent to aid cell sorting, Haas notes—the mRNA is naturally degraded. So “while the edits you’ve made are permanent,” she explains, “you won’t have remnants of the editing system still present.”

Dharmacon Edit-R Fluorescent Cas9 Nuclease mRNA retails from Horizon Discovery at $400 for a ready-to-use tube of 20 micrograms—enough mRNA to do several experiments, Haas says. Horizon Discovery was unable to locate a user who could comment on the product.

KOELHER: “This reasonably priced tool enables FACS enrichment of edited cell populations. My lab would use this product, and I think it could impact several projects.”

Inscripta   MAD7

CRISPR gene-editing technology is a revolutionary tool in the biomedical sciences. But commercializing products that result from research that employed CRISPR-Cas9 or CRISPR-Cpf1 can end up being prohibitively expensive for many academics and small startups, as use of the nucleases is associated with costly licensing fees and royalties. 

So, after researchers at Colorado-based startup Inscripta discovered a new class of nucleases—named MADzymes as a nod to the impressive biological diversity of Madagascar—they made a collective decision. “We said, this is just too important a technology to hold onto,” explains Inscripta CEO Kevin Ness. “We’re going to give this enzyme out for free—truly free.”

As of December 2017, the company has made the entire sequence of its patented DNA-cutting enzyme, MAD7, available online for all research and development uses, whether they are commercial or noncommercial, domestic or international. Researchers wishing to commercialize the enzyme itself—by including the protein in a therapeutic, for example—are asked to pay a small royalty.

Louise Baskin, a product manager at Horizon Discovery, was part of a team that tested MAD7 and is currently using it to edit mammalian cells. “All of our data have pointed to it being as good as Cas9,” she says. Baskin adds that, because MAD7 has a different recognition region to Cas9, “it opens up genomic space in terms of where we can make those cuts.”

The sequence has been downloaded more than 1,000 times in the last year, and Ness says that Inscripta is exploring options for partnerships with potential distributors, so that researchers might buy the DNA or protein product directly.

 KOEHLER: “Another gene editing product and an alternative to Cas9. Inscripta aims to break down barriers related to cost and intellectual property to enable wider use of gene editing.”

NanoTemper Technologies   Tycho NT.6 

The developers of the Tycho NT.6 want to make quality control of protein samples in the lab a no-brainer. With older methods, says NanoTemper Technologies co-CEO Philipp Baaske, researchers would have long discussions “about if they should test the protein or not. Now, they can just do it.” A run on Tycho takes three minutes and requires 10 μL of sample. The instrument heats the sample at a rate of 30 °C/minute while measuring fluorescence from the protein’s tryptophan and tyrosine residues, which it compares to a reference value for that sample. Discrepancies from that reference value indicate that the protein may no longer be folded as it should be, which would affect its activity, or that the sample is contaminated or degraded.

Gabriel Birrane, who heads the X-ray crystallography core at Beth Israel Deaconess Medical Center in Boston, says that his group uses the Tycho in its work with insoluble bacterial proteins. “We’ve been able to use the Tycho to screen conditions” to identify those that will induce the proteins to fold, he says. Otherwise, Birrane adds, finding those conditions can be a difficult trial-and-error process. And his team has realized that the instrument is faster than running a gel when they need to verify that the sample coming off a column contains their protein of interest.

A desktop Tycho instrument, with consumables to perform 600 analysis points, costs $37,500.

ZHANG: “Thermal denaturing is a great tool to quickly assess protein quality and protein–nucleic acid binding. Biochemists should find good use for this device.” 

BD •  BD AbSeq Assay  

This technology enables researchers to simultaneously analyze RNA and protein expression in thousands of individual cells. Released commercially this July, the BD Life Sciences AbSeq Assay, for use with the BD Rhapsody single-cell analysis system, couples antibodies with oligonucleotides to estimate the abundances of proteins in cells from high-throughput sequencing runs. The antibody-oligonucleotide conjugates are sold as single-vial matrix tubes and are easy to scale for standard 2-microliter sample tests, which provide results on protein expression that are similar to flow cytometry data.

This combination of mRNA and protein data makes the AbSeq Assay powerful. Some single-cell, RNA-sequencing tools can’t provide a thorough analysis of the cells due to inefficient mRNA capture as well as mRNA instability and turnover, says John Chang, an immunology researcher at the University of California, San Diego, who uses the BD AbSeq Assay in his lab to study lymphocyte function during immune responses. “Assays that enable simultaneous analysis of RNA and proteins in the same single cells, such as BD AbSeq, can overcome this limitation and can lead to more accurate and comprehensive insights in many biologic systems.”

Specifically, notes Steve Kulisch, BD’s vice president of marketing for the product, researchers can begin to figure out how cancer patients’ tumors interact with their immune systems, data that have the potential to provide more-powerful, individualized cancer treatments. Currently the assay scans for a little more than 100 different combinations of human antibody-oligonucleotides, and more are in development, which should help researchers tease apart the intricacies of complex diseases without having to run more than one experiment.

Twenty-five tests cost $375, and the whole set-up runs $10,000 to $50,000, which breaks down to 10 to 18 cents a cell, depending on the experimental design, Kulisch says.

WILEY: “Uses antibodies to cell surface markers that have nucleotide tags attached to them so that you can easily distinguish different cell types in single-cell RNA-Seq experiments and compare results to flow cytometry results. A useful and innovative extension of antibody labeling and detection technologies. One of the first commercializations of this relatively new technology.”


The Judges

ANGELA KOEHLER

Institute Fellow in the Chemical Biology Program at the Broad Institute and a Group Leader for the National Cancer Institute’s Initiative for Chemical Genetics. She is also a Project Leader in the NCI Cancer Target Discovery and Development (CTD2) Center at the Broad Institute aimed at targeting causal cancer genes with small molecules.


Krystyn Van Vliet

Associate Provost and the Michael and Sonja Koerner Professor of Materials Science and Engineering and Biological Engineering at MIT. She is also the Director of Manufacturing Innovation at MIT’s Innovation Initiative, and Lead of the Singapore-MIT Alliance for Research & Technology BioSystems & Micromechanics team.


H. Steven Wiley

Senior Research Scientist and Laboratory Fellow at Pacific Northwest National Laboratory. He published some of the earliest computer models of receptor regulation and is known for developing a variety of quantitative biochemical and optical assays as a basis for validating computational models of cell processes.


Feng Zhang

Core member of the Broad Institute of MIT and Harvard and the James and Patricia Poitras Professor of Neuroscience at MIT. He is also an associate professor in the Departments of Brain and Cognitive Sciences and Biological Engineering at MIT.


Editor’s Note: The judges considered dozens of entries submitted for a variety of life-science products by companies and users. The judging panel is completely independent of The Scientist, and its members were invited to participate based on their familiarity with life-science tools and technologies. They have no financial ties to the products or companies involved in the competition. In this issue of The Scientist, any advertisements placed by winners named in this article were purchased after our independent judges selected the winning products and had no bearing on the outcome of the competition.

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