Researchers recently used CRISPR single-guide RNAs to alter genes involved in pigmentation in frog embryos.
This year’s list of winners celebrates both large leaps and small (but important) steps in life science technology.
December 1, 2016|
Oftentimes innovation is incremental. After all, even big, brash new ideas have nuts and bolts that can be endlessly tweaked to improve performance, efficiency, and utility. This year’s Top 10 Innovations winners do include bold, new platforms that look primed to rev up discovery in basic biology, drug development, and clinical labs. But the list also features products that speak to the important, but often underappreciated, tinkering that drives life science innovation.
Just as geneticists might revel in the release of a new platform capable of generating long-read sequences with single-molecule resolution, synthetic biologists eagerly await the development of improved CRISPR-Cas9 guide RNAs and nucleases to facilitate ever more efficient and precise genome editing. Like biology itself, life science technologies are often more than the sum of their parts.
Also worth mentioning are the more clinically relevant innovations that made this year’s Top 10 list. Synthetic human kidney tissue that brings properties of the organs to the petri dish and specially designed panels that quantify a host of biomarkers in various samples promise not only to enhance work in the lab, but to change lives in the clinic. Advances like these remind us that innovation and the pace at which it occurs serve more than manufacturers, developers, and academics—they can serve humanity.
From a machine that allows for single-cell Western blotting to a microfluidic device that streamlines mass spectrometry, this year’s Top 10 Innovations are a celebration of transformative life-science advances, large and small.
Single-cell Western blotting is now available for purchase. Developed by Amy Herr’s lab at the University of California, Berkeley, Milo is a benchtop instrument that allows researchers to search for specific proteins in about 1,000 single cells at once. Users simply pipette a cell suspension on top of a 1-by-3-inch glass microscope slide covered in a 30-micron thick gel layer dotted with 6,400 microwells. As the cells settle into the gel, some wells will remain empty, but about 1,000 will collect individual cells for analysis. Researchers then add reagents to chemically lyse the cells and denature the proteins. Next, they apply a charge to pull the proteins into the space between the wells and use UV light to activate chemicals in the gel that lock the protein bands into place.
“People who are doing conventional Westerns can’t see heterogeneity, because they’re looking at a bulk level,” says Kelly Gardner, a former graduate student in the Herr lab and current director of marketing at ProteinSimple. “Milo gives you access [to] identify subpopulations.” A description of the technology was first published in June 2014, and strong interest from the scientific community led Herr, Gardner, and their colleague Josh Molho to launch Zephyrus Biosciences, which was acquired by ProteinSimple’s parent company Bio-Techne in March. The company declined to give the exact price of a Milo unit, but stated that Milo’s cost is comparable to a benchtop flow cytometer, and that interested researchers can request a quote on the website. The company was also unable to provide user comment due to the newness of the product.
Unger: A novel use of a custom chip that eliminates the transfer step and allows efficient large-scale tests of thousands of single cells. As price keeps coming down, this should allow the detailed efficient testing of many problematic (e.g., poor flow) proteins, and give info about individual cellular responses, which is an important area of inquiry today.
Fishman: This is an example of the potential for scalability of a known technology at lower cost and using less space. This also saves researchers’ time by testing protein-expression heterogeneity in their cells, simultaneously.
A crucial stage of drug development is testing whether a candidate compound damages the kidneys, but existing cell cultures and animal models can only approximate the human kidney. ExVive Human Kidney Tissue from Organovo is a replica of the kidney proximal tube created using 3-D bioprinting. It offers drug developers a reliable means of testing for renal toxicity.
Currently, few preclinical tests can determine whether a potential drug is toxic in humans, making investing in clinical testing risky for developers. Identifying renal toxicity early on reduces that risk. More importantly, “you’re really talking about doing no harm to the patients that are going to be in the clinical trial,” says Organovo Chief Scientific Officer Sharon Presnell.
Bioprinting operates on a similar principle to 3-D plastic printing, explains Presnell, but “instead of putting beads of polymer into a printer, we’re putting little aggregates of cells.” Organovo, which won a spot in 2014’s Top 10 Innovations for its ExVive Liver Tissue, produces tissue samples on a contract basis, and pricing can vary widely depending on the number and type of samples a client requires.
The replica kidney tissue could be applied outside of toxicology too, as a platform for experiments on kidney tissue that would not be otherwise feasible, Presnell says.
“It seems to have integrity like a native kidney tissue,” says Caroline Lee, a metabolism and pharmacokinetics researcher at Ardea Biosciences who profiled transport protein expression in the artificial tissue. Lee found that directional transport proteins were oriented correctly along the membrane. “You can see drugs going in the right direction,” she says. “It’s pretty remarkable.”
Unger: Based on quite a novel and bold approach to copying the detailed morphology and function of kidney tissues, this innovation offers major advantages over conventional cell culture methods, which have limited predictive capacity at the tissue level.
Fishman: This technology can be used instead of preclinical animal trials, reducing our reliance on laboratory animals to test new compounds. It also has the potential to transform drug development by better mimicking human kidney biology to test for the renal toxicity of new drugs.
At less than a third the size and weight—and half the cost—of Pacific Biosciences’s original long-read sequencer, the Sequel System is the company’s latest offering in single molecule, real-time (SMRT) sequencing.
Sequel, which debuted last fall, generates the same long reads and single-molecule resolution accomplished by the company’s older SMRT sequencer, called the PacBio RS II. Compared with the RS II, Sequel “is a higher throughput version of SMRT sequencing, which allows the faster generation of more data to tackle larger genomes and biology requiring higher molecular depth as well as metagenomic samples in the same relative time frame,” says Robert Sebra of the Icahn School of Medicine at Mount Sinai in New York City who has used the system since December 2015.
Sebra, who worked at PacBio from 2007 to 2012, has used SMRT technology for various applications over the past six years, including de novo human genome sequencing. “It’s very flexible for both R&D and production sequencing,” he says. “There’s essentially no systematic error, enabling higher quality value sequence data in tandem with longer reads to help discover previously unknown genomic features.”
Sequel is also particularly useful for metagenomics and infectious disease research. It was recently used to produce a reference genome sequence of a Korean individual, says Jonas Korlach, chief scientific officer at PacBio and coinventor of SMRT sequencing (Nature, 538:243-47, 2016). In October, leaders of the Genome 10K (G10K) and Bird 10,000 Genomes (B10K) initiatives announced their choice of SMRT sequencing as a principal technology.
With a list price of US$350,000, a PacBio sequencer is within reach for more labs. “Now, SMRT sequencing is for everyone,” says Korlach.
Fishman: The Sequel System is an improvement on Pacific Biosciences’s earlier systems in that it provides higher throughput and more scalability at a lower cost.
StrÖmvik: Though not affordable for small labs, high-throughput, long-read sequencing is essential for any group working on large and complex genomes, metagenomics, and metatranscriptomes.
Axion BioSystems makes in vitro optogenetics more precise and more replicable than ever, thanks to its new Lumos light-delivery system, first shipped in December 2015. The apparatus contains 48 wells, each with four individually controllable LEDs that can flash different wavelengths of light—blue, green, orange, and red—with microsecond precision. When positioned above a microarray culture plate with a recorder fixed beneath, the setup allows researchers the ability to precisely stimulate, manipulate, and measure a variety of cultured cells.
Geneticist David Goldstein is poised to use the Lumos in his Columbia University lab to study the behavior of cultured human neuronal networks with mutations that cause different forms of epilepsy. “What we’ve been looking for for a long time now, in a precision medicine context for epilepsy, is a medium-complexity in vitro model . . . but [one that is] still high-throughput enough so we can screen compounds,” he says.
Cultured neuronal networks tend to synchronize their synaptic firing, decreasing the amount of information that experimentalists can extract from their behavior. “To elicit more complex behavior that might reveal the effects of the mutations, what we want to be able to do is kind of tune activity in the networks while we’re monitoring the response,” Goldstein says, adding that he expects data from the Lumos to come in over the next year. “That’s exactly what this system allows us to do.”
The Lumos costs US$26,000.
Unger: This system for high-throughput optical stimulation in multiwell plates is the first large-scale practical implementation in the emerging field of biophotonics.
Platt: The platform . . . now puts unique control in the hands of the researcher. Using high-power LEDs that span several wavelengths increases the customization ability to go with specific light-manipulated protein manipulation.
With its user-friendly nature, the CRISPR-Cas9 technique is often lauded as the technology that will democratize gene editing. Thermo Fisher Scientific’s new LentiArray CRISPR Libraries, introduced in September, make applying the tool in screening assays even more accessible to researchers. The company has developed reagents that, when introduced to any variety of human cells—from HeLa to induced pluripotent cells—knock out genes, one-by-one, using CRISPR.
Northwestern University’s Simone Sredni, who studies an aggressive childhood cancer called rhabdoid tumors, participated in beta testing the libraries by screening the effects of mutating 160 kinases in patients’ tumor cells to find those that affected cell proliferation and growth. Her preliminary data came back in three months, and she identified some kinases whose impairment did indeed slow growth. “It really happened fast,” she says, taking only a little more than a year to get to the point now where she is testing inhibitors against those kinases in vivo in animal models. “This is something I wouldn’t be able to find if it wasn’t for the screen.”
The libraries come in a variety of flavors. Customers can choose from 19 different gene sets, customize their array, or conduct an unbiased screen of about 18,000 genes. “It’s not only the most efficient screening technology on the market, but it gives us a lot of latitude in creating different types of experiments for different applications,” says Jon Chesnut, the senior director of synthetic biology R&D at Thermo Fisher Scientific.
Starting at US$10,000 per library, it can be a bit costly, says Sredni, but for labs doing high-throughput screens, the price may be worth it.
StrÖmvik: Anything taking CRISPR technology to a high-throughput level is worth at least a look!
Wiley: This is a great enabling system. You can assemble this type of library yourself, but this product offers a streamlined way to start mapping genes to function.
In 2008, when NanoString debuted its nCounter analysis system—an automated microscope that tallies color-coded barcodes hooked to target molecules—the plan was to mature the technology from quantifying mRNAs to counting DNA sequences and proteins as well. This year, the company met its goal and unveiled its nCounter Vantage 3D Panels.
“The Vantage assays were expanded to allow the digital counting of mRNAs, DNAs, proteins, and even phosphorylation status of proteins all at the same time,” says NanoString’s senior vice president of R&D, Joe Beechem. In April, NanoString released the first Vantage assays, designed to digitally count RNAs in lung cancer and leukemia samples, proteins related to solid tumor biology and immune-cell signaling, and single nucleotide variations in DNA.
Gordon Mills, chair of the Department of Systems Biology at the University of Texas MD Anderson Cancer Center in Houston, helped develop the Vantage panels and uses them in MD Anderson’s Zayed Institute for Personalized Cancer Therapy, which he codirects. “There are many platforms that one can take to the [human sample testing] laboratory,” he says. “But none of them [except the nCounter Vantage system] had the robustness, the ease of use, and the potential to do DNA, RNA, and protein at the same time on a patient sample.”
The nCounter analysis system ranges from US$149,000 to US$280,000, and the nCounter Vantage 3D Panels run from US$275 per sample and upward. In the near future, NanoString and Mills’s laboratory plan to roll out new Vantage panels that add the dimension of measuring the spatial orientation of molecular components at the single-cell scale.
Wiley: Potentially, this product is the biggest technological breakthrough by enabling the simultaneous detection of DNA, RNA, and protein abundance in the same small sample.
StrÖmvik: Currently very geared toward cancer research, this system will hopefully also have other applications. One instrument can measure up to 800 different selected DNA, RNA, or protein molecules.
ZipChip is a microfluidic device that radically speeds up mass spectrometry, requires minimum sample volumes, and broadens the range of materials that a mass spectrometer can handle. The small box, less than a foot long, mounts directly onto a mass spec and works by processing samples through a microfluidic chip the size of a microscope slide.
Normally, preparing mass spec samples is time-consuming and error-prone. ZipChip reduces potential complications. “With our front end, we’re able to analyze samples with almost no prep at all, even if they have salt, detergents, or different matrices present,” says Chris Petty, cofounder of 908 Devices, the maker of ZipChip.
ZipChip uses capillary electrophoresis to separate sample components in just two to three minutes when liquid chromatography columns would require up to an hour, Petty says. The device provides better separation for samples, such as proteins, antibodies, and antibody-drug conjugates, that are difficult to separate with other techniques, says Petty. Plus, it only needs a few nanoliters of material. The device costs US$30,000. An autosampler adds another US$20,000 to the price tag.
Michael Pacold, who studies metabolomics at New York University, says that integrating a prototype of ZipChip into his lab has enabled him to take on a wider range of projects because he can gather data faster and from more sources. “A lot of clinical studies will only let you take a few microliters of plasma from a bank,” he says. “Without something like the ZipChip, those studies were not accessible. Now they are.”
Platt: The capillary electrophoresis, sample separation, and direct spraying to accompany mass spec units will allow for smaller volumes (nanoliters for ZipChip) and potentially lower the cost and improve sample identification while reducing preparation time.
Unger: This uses integrated microfluidic technology to quite dramatically speed up separations as a front end to mass spec (MS) methods, without damaging the integrity of the sample. This should support the continuing widespread use of MS methods both for research and for production of bio therapeutics.
For the third year in a row, Horizon’s HAP1 cells have earned a spot in The Scientist’s Top 10 Innovations. In 2014, CRISPR-generated knockout cell lines (then sold by Haplogen) won. Last year, Horizon made the list for cells with custom-made deletions. And in October 2015, Horizon launched its Turbo GFP Tagged HAP1 Cells, which made this year’s list for their ability to fluorescently tag proteins of interest without requiring that the gene be overexpressed.
Daniella Steel, Horizon’s senior product manager for cell lines, says one of the main advantages of using these cells over antibody labeling is simplicity. “Unlike antibodies, you don’t need validation or optimization, and you can visualize these cells live.”
Emma Lundberg of the KTH Royal Institute of Technology in Sweden recently received a batch of the cells for her work on the Human Protein Atlas project. She is in charge of mapping the subcellular locations of proteins using confocal microscopy and says that overexpression can sometimes lead to artifacts or misplacement of proteins. “The good thing is you know where you have your tag, and where you have it is expressed at the endogenous level,” she says. “And HAP1 cells are easy to work with for imaging applications.”
Custom-made cells cost US$3,400 and take about 16 weeks to develop. Horizon is also growing a collection of cell lines that tag proteins localized to particular organelles (those cost US$1,450). Lundberg says the price is reasonable considering how much time a lab would have to spend developing and validating its own cell line.
Platt: The promise of these genetically modified cells is that they will take advantage of CRISPR-Cas9 technology to tag genes with TurboGFP such that when they are expressed, they. . . can be followed without additional immunolabeling.
Fishman: TurboGFP uses CRISPR-Cas9 self-releasing tag to provide researchers with tagged proteins. The proteins are tagged endogenously, which is preferable to exogenous models, and provides them reliably and at lower cost.
With modern microscopes, researchers turn to high-powered cameras to help them capture images of what’s in their sample. “Every year, these cameras have gotten better and better and better,” says Rachit Mohindra, product manager at Photometrics, a company that specializes in microscopy cameras and other imaging systems for life science research. “They’re basically perfect.” To improve on perfection is tough, he admits, but he thinks he and his colleagues have done just that with their 4.2 megapixel Prime sCMOS camera. Released at the beginning of 2016, the camera has a built-in algorithm to reduce shot noise—the variation inherent in measurements taken using light microscopes—without having to acquire many extra images and then average across them, or increase the light intensity, which can damage samples. “You’re able to maintain your low levels of light, keep [target cells] alive for longer, and get nice data,” Mohindra says. The Prime camera improves signal-to-noise ratio three to five times, he adds, which is “equivalent of being able to turn down the light by a factor of 10.”
The Prime sCMOS camera’s built-in algorithm also reduces the total amount of data collected by a researcher, hastening processing and analysis times. “It takes about 30 seconds per frame to process if you do it offline,” Mohindra says. “When you have a camera that acquires at 100 frames per second, that’s 5 minutes for 1 second’s worth of data.” But with the Prime camera, he says, researchers can process the data immediately.
“The real-time filtering and high frame rates of the Photometrics Prime sCMOS camera enable us to capture even more super-resolution microscopy data and to better characterize variability in the structure of chromatin,” Kyle Douglass of École Polytechnique Fédérale de Lausanne in Switzerland noted on the company’s website. The Prime sCMOS camera costs US$15,950.
STRÖMVIK: Increasing demand for high-quality scientific imaging increases the information to be processed. Adding the field-programmable gate array-technology to the camera itself seems like the way to go.
Along with its LentiArray CRISPR Libraries, another arrow in Thermo Fisher Scientific’s quiver of CRISPR reagents made this year’s Top 10 Innovations—the GeneArt Platinum Cas9 Nuclease. Recombinant Streptococcus pyogenes Cas9 protein purified from E. coli, the GeneArt Platinum Cas9 contains a nuclear localization signal that aids in delivery to the nuclei of target cells.
“The things that we knew were important were consistent quality, activity, and purity,” says Jason Potter, Thermo Fisher senior staff scientist and R&D manager of genome-editing tools and synthetic biology. “So we made sure, through extensive testing, that we had a very robust purification process.”
Potter’s team at Thermo Fisher published a paper last year showing that GeneArt Cas9 achieved cleavage efficiencies as high as 85 percent in a variety of cell lines (J Biotech, 208:44-53, 2015).
Matthew Porteus, a Stanford University stem cell biologist, uses GeneArt Platinum Cas9 in his studies of ex vivo gene editing to treat blood diseases—research that he’s currently doing with mouse cells, but has partnered with Thermo Fisher to move into clinical testing. While using the CRISPR/Cas9 system is an efficient and specific way to accomplish genome editing, “our problem was that in the early preps of Cas9 protein that were commercially available, they had toxicity to them,” he says. “[GeneArt Platinum Cas9] really became the gold standard protein that allowed us to do experiments that gave us results that we had not been achieving using any other reagent.”
A 25 µg vial of GeneArt Platinum Cas9 Nuclease costs US$150, and customers can also tap into experts at Thermo Fisher who can help design experiments or talk through protocols. “The trick for genome editing is to take people by the hand and tell them exactly the pipetting schemes and what you need to do to be more successful,” says Thermo Fisher vice president and general manager of synthetic biology Helge Bastian.
WILEY: By avoiding the need for vector-based Cas9 expression, this reagent can greatly accelerate the typical CRISPR-Cas9 workflow, at least in certain cell lines.
Associate Professor in the Biomedical Ethics Unit and the Department of the Social Studies of Medicine and an Associate Member of the Sociology Department and the Institute for Health and Social Policy at McGill University. Fishman holds a Ph.D. in Sociology from the University of California, San Francisco.
H. STEVEN WILEY
Senior Research Scientist and Laboratory Fellow at Pacific Northwest National Laboratory. Wiley 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.
Associate Professor at Georgia Tech University and Director of Graduate Admissions and Recruiting for the Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. Platt studies tissue remodeling, systems biology, and a number of diseases using both computational and experimental approaches.
Associate Professor of Administrative Services at Boston University. Unger has founded and participated in numerous companies, including Kurzweil Computer Products, Inc., which became Xerox Imaging Systems. He is also cofounder and chair emeritus of the MIT Enterprise Forum.
Associate Professor and Chair of the Department of Plant Science at McGill University’s McGill Centre for Bioinformatics. Strömvik studies functional anatomy resulting from gene expression in crop and forest plants.
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.