Molecular Medicine Israel

2017 Top 10 Innovations

From single-cell analysis to whole-genome sequencing, this year’s best new products shine on many levels.

Innovation comes in many forms, molded into various outlooks, adapted to shifting time frames. Sometimes, technological and conceptual progress is undergirded by a more expansive view to encompass the bigger picture—think evolutionary theory or the widespread applicability of Sanger sequencing. Other times, innovation, especially in the life sciences, is achieved by zeroing in on the minute components that make biology tick—receptors, cells, organelles.

This year’s Top 10 Innovations highlight breakthroughs on this fundamental scale. Winning products that include cutting-edge single-cell protein and gene expression analyses, souped-up Cas9 proteins for CRISPR-based genome editing, and culture systems for research organoids illustrate the innovative drilling down into fine-scale biology. Other winners, such as a handheld blood-testing device and a biomarker detection system, underscore the importance of technological development in the clinical laboratory.

In all, 2017 has brought us another bright crop of innovative products, selected by our independent panel of expert judges. The Scientist is proud to present this year’s Top 10 Innovations.
1- This new single-cell technology allows researchers to characterize cells based on the proteins they secrete—as many as 42 different cytokines, chemokines, and other molecule types at once. Commercially launched this February by Branford, Connecticut–based IsoPlexis, IsoCode chips contain thousands of long microchambers that house only single cells. Within each microchamber, 15 spatially separated slots contain up to three different antibodies targeting specific secreted proteins; upon binding, the antibodies fluoresce in three colors, allowing researchers to distinguish the proteins.

“The ability to profile thousands of individual T cells or immune cells at once, the ability to basically, for each of those immune cells, get between 30 and 45 secreted proteins per cell, that’s the real innovation,” says IsoPlexis CEO Sean Mackay. Existing technologies either measure cells en masse, losing granularity, or look at only a few secreted proteins per individual cell, he notes. “Instead of just a few, you can now look at 40 secreted proteins per cell—that’s a real big leap in the field.”

Among the potential applications for IsoCode chips is the analysis of CAR T cells, which are currently being developed for various blood cancers. For example, researchers at Kite, a Gilead company, have found that the assay—and the built-in algorithm that calculates the so-called polyfunctional strength index (PSI)—associates strongly with patients’ likelihood of response to the company’s recently approved CAR T-cell therapy for non-Hodgkin’s lymphoma. “It’s quite powerful,” says John Rossi, director of translational sciences at Kite. “Current assays that rely on a single-plex ELISA or even multiparametric flow cytometry don’t give you the level of resolution that the IsoPlexis platform can provide.”

IsoCode chips come in 10 different panels, ranging from 24 to 42 antibodies per panel, at a cost of $500–$600. The automated IsoLight imaging and workflow platform can be purchased starting at $200,000. But the IsoCode chips can also be paired with other fluorescence microscopy systems.

CRUICKSHANK-QUINN: “The IsoLight single-cell technology, with its ease-of-use, has the potential to impact cancer research for both biomarker discovery and patient monitoring.”

2- Abbott’s latest version of its handheld blood-testing device, the i-STAT Alinity, has all the bells and whistles to make point-of-care assays more user-friendly. Roughly the size of a 1980s cell phone, Alinity is packed with technology unthinkable three decades ago. Various cartridges loaded into the device can perform myriad tests on a blood sample of just several drops, including glucose levels and hematocrit, with results delivered to clinicians within minutes.

Narendra Soman, the director of R&D for Abbott’s Point of Care Diagnostics business, says one of the improvements in i-STAT is a large color touchscreen, which signals users with audio and visual cues if a patient’s levels fall into a concerning range. “The visual display is a fantastic feature,” reminiscent of a smartphone, says Geoff Herd, the point-of-care testing coordinator at Whangarei Hospital, New Zealand, in an email. His colleagues use Alinity in the maternity ward and emergency room. “The system has been so well designed it is easy for users to get test procedures right and hard to get them wrong,” he says.

“We added a lot more functionality for test results,” Soman adds. “Once a blood result is obtained, it can go from the instrument to a patient’s medical record.”

The gadget’s new, ergonomic design better suits the way health-care providers carry it around in the hospital. Before, i-STAT was designed to sit in a large pocket; now, Alinity’s curves conform to the shape of an armpit. “What we noticed was nurses, essentially, wanted their hands free to carry other things,” says Soman.

Alinity came on to the market a year ago, and is available in about four dozen countries for $7,000 to $12,500 USD, but is not yet available in the U.S. Soman says Abbott is waiting for a few more assays to be cleared by the US Food and Drug Administration before selling it stateside.

CRUICKSHANK-QUINN: “The i-STAT Alinity can be used in any setting due to its portability and ease-of-use to obtain information on the blood and organs. Only a few drops of blood with results in 2–10 minutes has immediate impact in point-of-care testing.”

3- Scientists can use animal-derived extracellular matrix (ECM) to grow research organoids in their labs. But Switzerland-based QGel makes fully synthetic ECMs that closely mimic the human ECM and has several advantages over those animal-derived products, says Colin Sanctuary, QGel’s cofounder. For one, QGel’s product, which was released in January, allows for the possibility to tune key structural and bioactive components of the ECM specific to the cell type of interest, so that it closely mimics the physiological environment inside the human body. QGel is also consistent from batch to batch, so it provides better replicability than animal-derived gels. And it’s compatible with liquid-handling robots, unlike animal-derived products, which can clog the machines and need to be kept at difficult-to-maintain temperatures. Sanctuary says he hopes to see organoids grown from patients’ cancer cells and used to craft personalized treatments. He predicts that if QGel rather than animal-derived ECMs are used to grow the organoids, their use in clinical treatment will be able to reach a large global scale and make a significant impact for those affected by disease.

Oncology researcher Silvia Goldoni of Novartis tells The Scientist her group uses QGel to grow cancer cell lines, which they plan to use for drug screening, and patient-derived cells. “One of the things we’re particularly interested in is the possibility to grow cells that historically have been very hard to grow,” she says, given that growing cells in 2-D, or “in the absence of important ECM elements or other supporting cells types . . . really hinders our ability to model certain cancers in vitro.”

A QGel Assay Kit for Organoids costs about $4,000 to $5,000, and enables approximately 3,000 experiments, Sanctuary says.

UNGER: “This clearly has the potential to be transformative at both a scientific level and an economic level to the business of developing drugs and medical device interventions, by providing accurate 3-D, in vitro human tissue such as organs and tumors including the extracellular matrix.”

4- Intabio’s Blaze system for detecting and identifying protein isoforms aims to save pharmaceutical companies loads of time in laboratory prep work. Protein analytics that ordinarily take a month, says Intabio CEO Lena Wu, could happen in just a day with Blaze.

The system, set to launch within the next few months, would be deployed for quality control in biologics manufacturing. Typically, analysts seeking to find any abnormalities within a biologic sample separate components by capillary isoelectric focusing, then identify any isoforms via mass spectrometry. The two-step process of selecting samples and scaling them up for mass spec is time-consuming, Wu explains.

Blaze speeds things up by integrating detection, quantitation, and identification into one microfluidic system that sends proteins for mass-spec analysis immediately after detection, obviating the laborious process of prepping material for mass spec separately. “It completely changes the paradigm of when you can get this critical information about the quality of the product you’re making,” says Wu.

John Teare, the director of Late-Stage Development Program Management at Bayer Pharmaceuticals, says he’s eager to test it out. He provided some of the biological material Intabio used to develop Blaze. “So many times we do isoelectric focusing and see an unusual peak and ask, `What is this?’” says Teare. “With Blaze you run it, and you say, `What’s the mass of that peak?’ And boom.”

Although pricing is still yet to be set, Wu estimates the device will cost between $70,000 and $200,000, and a reagent kit for 100 samples will run between $5 and $10.

UNGER: “This offers a truly dramatic increase in research productivity, which can immediately affect budgets and pipeline of products under development.”

5- This August, Lexington, Massachusetts–based Quanterix brought its Simoa biomarker detection technology to the lab bench, launching the compact SR-X system. The platform offers more than 80 different assays to test samples—typically blood or serum, but some assays are also compatible with cerebral spinal fluid or single-cell lysates—for the presence of cytokines, other markers of neurodegeneration or neuroinflammation, and more.

Simoa, the SR-X’s core technology, is also at the heart of the larger HD-1 system (the size of two side-by-side refrigerators), launched in 2014, explains Jeremy Lambert, director of product strategy at Quanterix. Because Simoa uses more magnetic beads relative to the proteins they’re targeting, each bead captures only a single protein. Those protein-carrying particles are then pelleted, washed, combined with an antibody detector, and flowed across an array of 200,000 microchambers that can house only a single particle; there, the antibody detector interacts with a fluorogenic reporter molecule. “The ability to count individual beads provides the very high sensitivity that enables detection of very low concentrations of proteins,” Lambert says. Researchers can look for up to six different target proteins in a single assay without compromising sensitivity, he adds.

The SR-X uses the same technology, but is much smaller. The size of a large microwave, it fits on a standard benchtop. And the SR-X’s assay prep—including the incubation of samples with capture beads, for example, and the washing step—are performed by the researcher before the samples are fed into the machine. “That gives a lot of flexibility to the end user, where they can vary the conditions of an assay,” Lambert says. These steps can be performed using conventional lab devices that are part of a standard ELISA workflow, he notes.

CRUICKSHANK-QUINN: “This benchtop instrument is able to detect protein and nucleic acid biomarkers directly from blood and tissue without the need for sample extraction and amplification steps.

6- Promega’s new protein detection system excels at measuring protein levels across the cell. “The basic idea of the HiBiT Tagging System was to provide a really simple, sensitive bioluminescent method to quantify the abundance of a protein of interest, whether it be in the cell or on the cell surface,” says Chris Eggers, a senior research scientist at Promega.

When the small and easily integrated 11-amino-acid tag (High BiT or HiBiT) interacts with the complementary Large BiT (LgBiT) 156-amino-acid component, they bind tightly and release detectable light. Researchers can incorporate the small HiBit tag just about anywhere on a protein of interest using CRISPR-Cas9, another preferred expression system, or one of Promega’s plasmids, which can be purchased for $395. Promega also offers the option to license the sequence of the HiBiT tag free of charge. Detection reagents start at $160 and, depending on which reagents and volume are needed, cost as much as $8,925.

Biologist Julien Sebag of the University of Iowa has been using the system to study G protein–coupled receptor (GPCR) trafficking. He is happy with its speed, especially compared to ELISA. His group tags GPCRs with HiBiT and then measures both extracellular levels and total levels of protein to determine what he calls the “trafficking ratio” of the receptor. “The sensitivity is very good as well, so that allows us to express the proteins at lower levels—more physiologically relevant levels—and still be able to detect them,” Sebag says.

UNGER: “Interesting improvements facilitate small-peptide tagging, and are appropriate to CRISPR-Cas9, both very promising areas.”

7- Genome-wide, pooled CRISPR screens can provide researchers with information about the role of specific genes involved in cell function—but are not without limitations. “While this is a powerful, useful format, it does have restrictions on the complexity of the phenotypic assay that can be used,” explains Louise Baskin, senior product manager at Dharmacon. “Everything in a pooled screen has to be almost an on-off—it has to be an increase in some sort of reporter signal, or more commonly, it’s simply cell death.”

Dharmacon’s Edit-R CRISPR-Cas9 screening platform, launched on the market in June 2017, instead provides users with an arrayed library of synthetic crRNA guides with a “one-well-per-gene” format, allowing for a much subtler assay, Baskin says. “You can measure 1, 10, 20 variations on a phenotype for a much more complex and rich data set.”
Dharmacon provides four distinct guide RNAs per gene, so customers “get a lot of redundancy,” Baskin notes. “Having multiple data points per gene really improves statistical power.” The catalog libraries, available in 96- or 384-well plate formats, come in sizes that can target from 50 to around 18,500 genes for between $2 and $15 per well, Baskin says, or between $8 and $60 per gene.

The University of California, San Francisco’s Judd Hultquist recently used Edit-R as part of a project to investigate HIV-host interactions in primary human T cells. “The ease of use, high efficiency, broad accessibility, and functional adaptability make this platform truly revolutionary,” Hultquist writes in an email to Dharmacon. “The work has opened up a lot of new scientific possibilities for us. . . . Having these reagents available to us, in 96-well format especially, made all the difference.”

CRUICKSHANK-QUINN: “This CRISPR library allows for rapid assessment and high-throughput screening of multiple targets across many genes to cover the entire human genome.

8- With its Chromium system, 10x Genomics aims to make transcriptome and whole-genome analysis more precise than ever. Using the single-cell system’s reagents and hardware, researchers partition their samples as single cells (or long DNA molecules), together with reagents and individually barcoded gel beads into individual oil droplets. Reagents lyse the cells and, together with barcoded beads, create a cDNA library of their RNA transcripts, which are then sequenced. The barcodes are specific to each droplet, and after Chromium software crunches the data, users can trace gene expression in individual cells. The result, says Mike Lucero, 10x Genomics’s head of strategic marketing, is “a digital count of each gene from hundreds of thousands of droplet compartments.”

The controller for the single-cell system costs about $75,000; there’s also a Chromium controller that adds in a whole-genome sequencing functionality, available for $125,000. In October of this year, the company rolled out the Chromium Single Cell V(D)J Solution, which analyzes the adaptive immune receptor and antibody repertoires of T and B cells, and measures gene expression from the same single-cell samples. To run experiments, purchasers need the controller plus reagents, chips, and complementary software. Lucero says Chromium has enabled customers to find new cell types and cell states and to track changes in gene expression over time in, for example, a developing embryo.

Michael Schatz, a computational biologist at Johns Hopkins University, says one of his uses for the Chromium system, which originally debuted in May 2016, has been in a project to map the newly sequenced domestic pepper genome. One property that makes the technology unique is its ability to differentiate whether a given allele came from the maternal or paternal chromosome, he says. “It does provide effectively a very new and powerful microscope to see things we’ve never been able to see before.”

KAMDAR: “Great technology for profiling single-cell gene expression, enabling deep profiling of complex cell populations.”

9- Mass spectrometry continues to march toward ever-greater sensitivity, selectivity, and speed. Thermo Fisher Scientific’s TSQ Altis Triple Stage Mass Spectrometer robustly and reliably quantitates most analyte types, even in complex samples such as plasma and tissue. This system can be used widely in analytical, forensic toxicology, and clinical research applications.

The Altis boasts triple quadrupoles, which allow researchers to target specific molecules and affords enhanced ion-transmission consistency. Another advantage of the system is the active-collision cell, where ionized samples collide with a neutral gas and fragment, which ensures fast, selective reaction monitoring and resulting boosts in productivity.

After Jun Qu, who works on the development and analysis of antibody drugs at the University at Buffalo in New York, did extensive beta testing with the Altis in May, he ordered one and awaits its arrival. Qu says he is impressed with the instrument’s ability to isolate a narrow window of a sample that includes the peptide of interest. Eliminating the unnecessary parts of samples containing hundreds of thousands of peptides helps avoid what Qu calls “chemical noise,” the signal from nontarget peptides that interfere with the target’s detection—a particularly important step for protein analysis.

“Regardless of the molecule type, from small to large, every organization faces some significant challenges [in] analysis, especially when it comes to achieving more sensitivity to meet today and tomorrow’s regulatory standards,” Debadeep Bhattacharyya, a senior marketing manager at Thermo Fisher Scientific, writes in an email to The Scientist. Bhattacharyya declined to provide pricing information for the Altis.

KAMDAR: “The new TSQ Altis mass spectrometers can develop quantitative methods for biotherapeutic proteins and target receptors with extreme sensitivity, selectivity, accuracy, and precision.”

10- The Cas9 protein’s cutting efficiency can be a limiting step in CRISPR-Cas9 genome editing. Thermo Fisher Scientific’s new Invitrogen TrueCut Cas9 Protein v2 has been specially engineered to maximize cleavage efficiency and therefore accelerate the process.

“Most of the labor in cell engineering is in isolating clones” that have been successfully edited, says Jon Chesnut, senior director of synthetic biology R&D at Thermo Fisher Scientific. “By improving the efficiency of the cleavage event . . . more cells in the population are going to be properly edited.” This makes it easier to identify the edited clones, he adds.

The TrueCut protein can achieve efficient editing not only in standard cell lines but also in stem cells and primary cells. Working with T cells, for example, “in one experiment we knocked out the [PD-1] receptor to 95 or greater percent,” says Chesnut. “It’s essentially a complete knockout of the receptor in one transfection.”

Olivier Humbert, a staff scientist at the Fred Hutchinson Cancer Research Center, uses the TrueCut system to edit blood stem cells with the aim of developing therapeutics for hemoglobino-pathies such as beta thalassemia. The protein “allows us to efficiently edit those stem cells, which can be a little tricky to work with,” he says. “We can genetically modify over 70 percent of those blood stem cells.”

Thermo Fisher Scientific offers TrueCut in two concentrations: 1 μg/μL for standard editing assays and 5 μg/μL for more challenging assays. At the lower concentration, the company offers 10 μg for $85 or 25 μg for $108; 100 μg of the higher concentration costs $230.

KAMDAR:“This is a next-generation CRISPR-Cas9 protein engineered to deliver maximum editing efficiency across a range of cell types and gene targets.”

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