Human Cell Atlas: The next frontier

Reprinted from the October 2016 AltTox Digest; used by permission.

Now that the human genome has been mapped, the next frontier is to map the human cellular phenotypes. An understanding of all the types of human cells and how they interact in the various tissues and organs will provide the new level of understanding of human biology needed to accomplish medical breakthroughs, understand physiological processes such as human development and aging, and understand pathophysiological processes such as disease and toxicity.

Cells are the basic building blocks of all human tissues and organs. Beginning in the embryo, cells divide and begin to specialize into the different cell types that make up the human body.

General estimates identify several hundred major cell types, however, new methods of characterizing cells show that even within what appears to be a homogenous population there is great variability.

The technique used to identify cells at the level of the single cell is single-cell messenger RNA sequencing (RNA-seq), where every messenger RNA species in a sample is sequenced and identified.  Credit: Genome Research Limited

The technique used to identify cells at the level of the single cell is single-cell messenger RNA sequencing (RNA-seq), where every messenger RNA species in a sample is sequenced and identified. Credit: Genome Research Limited

Recent government funding initiatives have spurred innovation and progress in studying cells at the level of the single cell. In 2014, the US National Institutes of Health (NIH) awarded $7.9 million to 25 projects studying various aspects of single cell analysis as part of the Single Cell Analysis Program (SCAP).

On October 13-14, 2016 an international group of renowned researchers met in London to discuss building the Human Cell Atlas. The Human Cell Atlas will be more than just a catalogue of static cell types. Like SCAP, it involves addressing the many challenges in characterizing human cell heterogeneity.

For more on single cell analysis and the new international effort to develop the Human Cell Atlas, see the entire article, “The Human Cell Atlas: An international effort,” on AltTox.org.

alternative toxicity testing Human Cell Atlas Single Cell Analysis Program
Credit: The Wyss Institute at Harvard University

Can Organs-On-Chips Repair The Flawed System Of Drug Discovery?

Reposted from Life Science Leader.

By Trisha Gladd, Life Science Connect Editor

There is an ecosystem of many stakeholders who play a role in the discovery of new drugs, and each of them have a vested interest in making the drug discovery system work successfully and efficiently.  Yet, the realities of a flawed system are evident in the facts and figures.  A Phase 1 clinical trial for one compound can cost close to $15 million and take years to complete. Data published on www.fdareview.org also shows that only about 10 percent of drugs entering Phase 1 trials actually make it to market, which translates to considerable financial losses for those in the other 90 percent.


Recently, a wide range of these stakeholders – from pharmaceutical companies and academic researchers, to disease foundations and CROs – have signed on to work with Emulate, Inc., a privately held company at the forefront of a new technology, called ‘Organs-on-Chips.’  James Coon, CEO of Emulate, and his team of scientific researchers, designers and engineers are aiming to change the way drug candidates are evaluated in the laboratory by using Organs-on-Chips technology an alternative to today’s cell culture and animal testing techniques.  In the past week, two new collaborators have joined forces with Emulate: a CRO, Covance Drug Development, and a major cancer research center, the Ellison Institute for Transformative Medicine at USC.  This adds to the growing list of partners – including Johnson & Johnson, Merck, the Michael J. Fox Foundation for Parkinson’s Disease, and the government defense agency DARPA – who are putting their hopes and expertise on the line to advance Organs-on-Chips technology into the mainstream of the drug-development process.

Coon says one of the reasons so few drugs make it to market is due to the conventional in vitro models and animal models currently being used by the pharmaceutical industry. To identify viable drug candidates, these models rely on data points from static human cell cultures in plastic dishes that do not represent the broader living biology of human tissues and organ systems, or on studies in animals that do not always directly translate to human biology. Organs-on-Chips technology offers a new approach.  By placing living human cells in an engineered microenvironment that recreates what’s happening within tissue systems, Coon says the technology offers the ability to create the smallest functional unit of a human organ, which gives a biological context that is much more effective at predicting human response than today’s cell cultures or animal testing.

Organs-on-Chip is a technology originally designed by Donald E. Ingber M.D. Ph.D., founding director of The Wyss Institute for Biologically Inspired Engineering at Harvard University, and Dan Dongeun Huh, Ph.D., assistant professor in the department of engineering at the University of Pennsylvania, that combines microfabrication techniques and engineering principals to create living, functioning human organs inside engineered microenvironments. Measuring in a size similar to a AA battery, each chip is made of a clear flexible polymer that contains tiny hollow channels lined by living human cells. Just as if cells from a patient’s body were biopsied and then studied, these translucent devices can be created by scientists to use as a window into the inner workings of human organs.

Since spinning out of The Wyss Institute for Biologically Inspired Engineering in July 2014, Emulate has evolved its Organs-on-Chips technology to become a commercially-viable product platform for use in industry.  By housing the Organs-on-Chips within an automated system Emulate offers a way for researchers and product developers to not only conduct experiments that are predictive of normal human physiology, but they also can create different disease states within the Organs-on-Chips to help determine appropriate therapeutic intervention. This lab-ready automated system includes three components: the Organs-on-Chips, the instrumentation that automates the use of those chips, and the software apps that allows scientists to collect and analyze data.  Because Emulate is integrating their Organs-on-Chips technology into a ‘plug-and-play’ system, end users can easily conduct experiments to meet customized needs within their own labs.

“In collaborations announced over the last year, industry leaders, such as Merck, the Michael J. Fox Foundation and Johnson & Johnson, are recognizing that the Organs-on-Chips technology can be valuable in predicting human response in applications throughout the drug development process and are now engaged in using the technology for a wider range of applications,” says Coon. “This includes early-stage processes, such as discovering new drug targets and understanding disease mechanisms, as well as late-stage testing of the efficacy and safety of new drug compounds.”

How Would Organs-on-Chips Impact The Future Of Animal Testing?

While it seems Organs-on-Chips has the potential to eliminate animal testing, Coon says that, as of right now, that is unlikely. “We live in a world where there is a regulatory system in place that is built around standards using animal testing,” he explains. “As a result, some of our early partners are using Organs-on-Chips to augment their existing pre-clinical models, and over time, we may be able to increasingly replace animals in the development process.” When it comes to the three guiding principles supporting the humane use of animal testing in scientific research—replace, reduce, and refine—Coon says Organs-on-Chips can play a role in each area. “By serving in a role side-by-side with animal testing, the technology can generate human-relevant data that has the ability to guide the refinement of the animal models that are selected for regulatory submissions,” explains Coon. “This could ultimately reduce the ineffective or unnecessary animal studies as well as the number of animals required.”

Consistent with the way new standards are accepted for regulatory filings with FDA and other agencies, the Organs-on-Chips technology will be evaluated for future adoption for regulatory uses as the body of data using Organs-on-Chips continues to grow over time. As of right now, it is a technology that is used part of the R&D process, and continues to be evaluated for adoption as a standard practice for regulatory filings.

Industry Partnerships Drive Commercialization Potential

In 2015, Organs-on-Chips was named the overall winner of the London Design Museum’s Design of the Year award. This marked the first time this award was presented to a product from the field of medicine. Some of pharma’s biggest names also have recognized the potential of this technology. As mentioned, Emulate has entered into a strategic collaboration with Merck. Together, the two companies are working to deploy Organs-on-Chips across certain Merck drug discovery programs with the goal of improving models of human inflammatory diseases and better predicting human response of therapeutic candidates. In addition, Johnson & Johnson Innovation and Janssen Biotech are also in a strategic collaboration with Emulate to use Organs-on-Chips to drive the clinical goals for three Janssen R&D programs.

When it comes to partnerships, Coon says one of the things they have been careful about very early on is not chasing money. “Our goal is to strategically align with companies that help us advance our core business, which is to develop the technology platform, the instrumentation, and the software,” he explains. “All of our partners have brought not just funding but also expertise.,. These partnerships allow us to have the kind of insight that offers a jump-start to move forward in different therapeutic areas we wouldn’t normally have access to.”

Emulate continues to have an active collaboration with The Wyss Institute as well. This includes a $37 million agreement between The Wyss Institute and the Defense Advanced Research Projects Agency (DARPA) to integrate 10 human Organs-on-Chips to study complex human physiology. This project provides foundational research that opened the door for Emulate to envision its overall mission, which is to develop and commercialize the Organs-on-Chips technology into an automated system that is used by industry to emulate human biology, in order to understand how diseases, medicines, chemicals and foods affect human health. “Everything we’ve done with DARPA has given us the insight to not only be able to deliver technically on the science and the biology, but to also scale manufacturing of the chips up and create a stronger foundation for product development,” says Coon.

Emulate is expanding its current product portfolio, which includes Lung-Chip, Liver-Chip, Intestine-Chip and Kidney-Chip, for additional organs such as Skin-Chip, Heart-Chip, Brain-Chip. As the product platform becomes widely adopted and more researchers are using it across multiple industries, Emulate will need to be able to produce millions of chips to move closer to launching Organs-on-Chips as a commercial product. A major step toward the commercialization of Organs-on-Chips was made earlier this year when Emulate secured $28 million of its Series B financing to accelerate its technology into a commercially-available “Human Emulation System.” As stated in a press release on its site, the financing will position Emulate “to accelerate its R&D effort, expedite the launch of its products and expand strategic relationships with industry and academic partners in order to evolve the company towards profitability.”

Since the early stages of research at the Wyss Institute in 2009 to Emulate’s founding in July 2014, experts from design, engineering, medicine, biology, and the physical sciences have shared a common goal of working together to develop Organs-on-Chips to create transformative change. As Emulate continues to advance its product platform, the industry will move closer to a solution that helps develop new therapeutic solutions for patients and offers a less costly way to develop innovative medicines. In addition, the company is also currently working with partners to develop Organs-on-Chips with individual patient stem cells, for use in precision medicine and personalized health applications. Through a focus on improved disease understanding and accuracy of human response, Organs-on-Chips drives efficiency at all levels of drug development and offers possibilities in patient care the industry has yet to see.


Credit: The Wyss Institute at Harvard University

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Animal-free skin allergy testing

With the recent approval of the human Cell Line Activation Test (h-CLAT) for skin sensitization (allergy), toxicologists now have a battery of methods that allows them to test for sensitization without using animals.mice

Testing a chemical substance for skin irritation or corrosion is pretty straight-forward: the substance is applied to a skin sample (there are many non-animal in vitro options) and damage will be seen relatively quickly. But to learn if the chemical has the potential to cause skin allergies, testing is more complicated. Skin sensitization is a two-stage process. In the first stage, a chemical exposure “primes” the immune system. Additional exposures then provoke an allergic response (inflammation, redness, itching, etc). Because of the biological complexity of the process, skin sensitization testing is usually conducted on mice or guinea pigs.

But mice and guinea pigs don’t always react the same way as humans would to potential skin allergens. To replace these animal tests with more human-relevant methods, toxicologists have long recommended developing a battery of in vitro tests that could be combined in an Integrated Testing Strategy – where each test method captures a different part of the skin sensitization process. The biological processes that underlie the skin allergy reaction are pretty well understood, and have been described (the Organisation on Economic Co-operation and Development (OECD) has published a description of this process – the Adverse Outcome Pathway leading to skin allergies). Two of the pieces of this strategy are already in place: the OECD approved the use of the Direct Peptide Reactivity Assay (DPRA) and the KeratinoSens test – each measuring a different step in the sensitization process. The DRPA assays measures whether a chemical can react with proteins in a way that causes the protein to become an allergen. The KeratinoSens assay measures activation of genes involved in the allergic reaction in skin cells (keratinocytes). The h-CLAT method completes the battery of tests: it detects biomarkers that indicate activation of immune (dendritic) cells in the skin.

Many countries require that chemicals used in manufacturing, agriculture, medicine, and cosmetics be tested for their potential to cause skin allergies in humans. Without approved in vitro options, REACH regulations in the EU alone would force industry to use hundreds of thousands of animals for skin sensitization testing. The animal-free, 3-test strategy is a “textbook” example of the mechanistic, pathway-based approach to chemical testing promoted by the Human Toxicology Project Consortium. Use of this strategy has the potential to greatly reduce the numbers of animals used for skin sensitization testing, while also reducing the cost and time it takes to produce human-relevant results.

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From the Wyss Institute press release: "These fluorescence confocal microscopy images show both a high magnification view (left) of a region of the human brain capillary endothelium within the endothelium lined tube (shown at lower magnification at right) that, in combination with surrounding human pericytes and astrocytes, comprise the blood-brain barrier (cell junctions linking adjacent endothelial cells are shown in magenta). " Credit: Wyss Institute at Harvard University

“Blood-brain barrier on-a-chip”

Scientists at the Wyss Institute have created a 3-dimensional in vitro model of the human blood-brain-barrier (BBB)-“on-a-chip.”  The device will make it possible for researchers to test drugs, chemicals, and disease factors that interact with the BBB, without using animals – and in a 3-dimensional environment that mimics that of the human BBB in vivo.

The BBB is a semi-permeable cellular structure that allows some nutrients and substances to enter the blood flow in the brain, and keeps other elements (such as bacteria and potential toxins) out. Because it is so effective, it can also prevent useful treatments from reaching targets in the brain. Researchers need to understand how and why certain substances can pass through the barrier, in part so they can design therapeutic drugs accordingly, and so they can design other substances to prevent neurotoxicity.

From the Wyss Institute press release: "These fluorescence confocal microscopy images show both a high magnification view (left) of a region of the human brain capillary endothelium within the endothelium lined tube (shown at lower magnification at right) that, in combination with surrounding human pericytes and astrocytes, comprise the blood-brain barrier (cell junctions linking adjacent endothelial cells are shown in magenta). " Credit: Wyss Institute at Harvard University

From the Wyss Institute press release: “These fluorescence confocal microscopy images show both a high magnification view (left) of a region of the human brain capillary endothelium within the endothelium lined tube (shown at lower magnification at right) that, in combination with surrounding human pericytes and astrocytes, comprise the blood-brain barrier (cell junctions linking adjacent endothelial cells are shown in magenta). ” Credit: Wyss Institute at Harvard University

To create the device, the Wyss Institute team carved a tiny channel in a polymer chip and filled it with a gel matrix containing human astrocytes, the cells that comprise the extra-tight “barrier” around blood vessels in the brain. Another channel was tunneled through this matrix and seeded with human pericyte cells (contractile cells which control the “gaps” through which substances can enter the neurological bloodstream) and then with human endothelial cells (the cells that line the interior of a blood vessel). The cells “self-assembled” into the same layers and connections they exhibit in blood vessels in vivo.

To test the model, the team introduced a protein known to cause inflammation – one that has been associated with a number of central nervous system diseases and disorders, including Alzheimer’s, multiple sclerosis, and stroke (among others). The in vitro BBB responded by producing protective proteins. The device can thus be used to study neuroinflammation, and to test new treatments.

Read more in the Wyss Institute’s press release.

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Human Toxicology Project Consortium at the Society of Toxicology meeting in New Orleans

You’ll find the Human Toxicology Project Consortium at the Society of Toxicology’s annual meeting in New Orleans next week – in the ToxExpo center, poster sessions, workshops, and seminars.

  • Visit HTPC’s informational booth at ToxExpo, booth #1704.
  • HTPC is co-sponsoring a “hands-on” seminar, “Creating an Adverse Outcome Pathway in the AOP Wiki,” on Tuesday, March 15, from 5-7PM in the Hilton Riverside.  More details about the seminar can be found here.
  • HTPC is also once again co-sponsoring and presenting at the annual SOT Satellite Meeting, Updates on Activities Related to 21st Century Toxicology and Related Efforts: Invited Presentations and Open Microphone, on Thursday, March 17, 12:30 PM to 4:00 PM, Hilton New Orleans Riverside, Jefferson Ballroom. As always, this informative meeting features a number of invited presentations, and also allows time for an “open microphone” segment in which participants are welcome to give brief presentations on germane topics.

The draft program is as follows:

12:30 PM—Box Lunch (for pre-registered participants) and Welcome by Thomas Hartung, Johns Hopkins University

1:00 PM—Invited Speakers (10 minute presentations each followed by 5 minute of discussion)

ToxCast Update: Russell Thomas, US Environmental Protection Agency

EDSP21 Update: David Dix, US Environmental Protection Agency

Tox21 Update: Richard Paules, US National Toxicology Program

Hamner TT21C Update: Melvin Andersen, Hamner Institutes

NICEATM Update: Warren Casey, NICEATM

SEURAT/EU Tox-Risk Update: Michael Schwarz, University of Tuebingen

CAAT’s Read-Across Initiative and Human Toxome-Related Activity Update: Thomas Hartung, Johns Hopkins

Human Toxicology Project Consortium Update: Catherine Willett, HTPC

Evidence-Based Toxicology Update: Martin Stephens, Johns Hopkins

3:15 PM—Open Microphone for Additional Presentations and Discussion

4:00 PM—Adjourn

  • Kate Willett will also present a poster in the Regulation and Policy session, Wednesday, March 16, 1:15 PM to 4:45 PM: “Regulatory Acceptance of Non-standard Toxicological Methods through Increased use of Integrated Approaches to Testing and Assessment (IATA)” (Abstract #3003/Poster #P143).

Corporate members and partners of HTPC will be presenting at SOT next week, as well.  Scientists from each of the member corporations are coauthors on the following posters:

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