high-throughput screening

Ushering In a New Generation of Chemical Screening

By Richard Judson

I work with EPA colleagues and other scientists around the world to integrate advances in biology, biotechnology, chemistry, and computer science to evaluate thousands of chemicals. Part of our research is supporting EPA’s Endocrine Disruptor Screening Program, exploring the potential for chemicals to disrupt normal growth and development in humans and other animals.

The work we do is helping usher in a new generation of faster, more efficient, and far less costly chemical screening methods. We use automated technologies, called high-throughput screening assays, to expose cells and proteins to chemicals. We then screen them to identify any that exhibited changes in biological activity that may suggest the potential for endocrine disruption.

My partners and I are excited to announce that we have recently published two papers on results of our work. We used the innovative methods described above to screen chemicals for their potential to mimic normal estrogen hormones, substances that direct development and reproduction. Exposure to chemicals that mimic estrogen pose a range of potential health risks, including birth defects and certain types of cancer.

The first paper, published in Nature Scientific Reports, describes the results of screening approximately 10,500 chemicals. The screening included 88 duplicates of the same chemicals, which validated the reliability of the assays. It also included 39 reference chemicals—those whose estrogen-receptor activity have been well established through traditional testing methods. Using the reference chemicals showed that the assays could accurately identify chemicals that were both positive and negative for their ability to mimic natural estrogens.

Robotic arm moving samples for screening

Robotic arm moves samples for automated chemical screening, part of the Tox 21 collaboration.

This paper is a product of Tox21, a federal collaboration pooling expertise and resources among EPA, the National Toxicology Program (National Institute of Environmental Health Sciences), the Food and Drug Administration, and the National Center for Advancing Translational Sciences (NCATS). Tox21 was established to study how high-throughput screening methods can be used to evaluate thousands of chemicals. These assays were run on the NCATS ultra-high-throughput robotic screening system (pictured).

The second paper (selected by the American Chemical Society’s Environmental Science and Technology journal as an editor’s choice) describes the results of screening 1,814 chemicals (including 36 reference chemicals). The screening was performed using a panel of 13 high-throughput estrogen receptor assays that use a diverse set of cell types and assay technologies.The results indicate that such a panel can accurately predict estrogenic responses. It demonstrates how the resulting data could be used for chemical prioritization as part of the Agency’s Endocrine Disruptor Screening Program.

In December 2013, we publicly released our high-throughput screening data through user-friendly web applications called interactive Chemical Safety for Sustainability (iCSS) Dashboards. I encourage anyone with an interest in this research to take a look at the data and to also participate in EPA’s Second ToxCast Data Summit. The summit is scheduled for September 29-30, 2014 in Research Triangle Park, NC.

The goal of the summit is to bring together the user community (industry, non-governmental organizations, academia, governmental agencies and more) to present their ideas for ways to use the large amount of high-throughput screening data to help inform chemical policy and regulatory decisions.

About the Author: EPA scientist Dr. Richard Judson develops databases and computer applications to model and predict toxicological effects of a wide range of chemicals. He is a member of the EPA Computational Toxicology research team where he leads the effort in bioinformatics. Dr. Judson has a BA in Chemistry and Chemical Physics from Rice University and an MA and PhD in Chemistry from Princeton University.

Information About the Papers

Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Ruili Huang, Srilatha Sakamuru, Matt T. Martin, David M. Reif, Richard S. Judson, Keith A. Houck, Warren Casey, Jui-Hua Hsieh, Keith Shockley, Patricia Ceger, Jennifer Fostel, Kristine L. Witt, Weida Tong, Daniel M. Rotroff,2 Tongan Zhao, Paul Shinn, Anton Simeonov, David J. Dix, Christopher P. Austin, Robert J Kavlock, Raymond R. Tice, Menghang Xia. Nature Scientific Reports

Predictive Endocrine Testing in the 21st Century Using in Vitro Assays of Estrogen Receptor Signaling Responses. Daniel M. Rotroff, Matt T. Martin, David J. Dix, Dayne L. Filer, Keith A. Houck, Thomas B. Knudsen, Nisha S. Sipes, David M. Reif, Menghang Xia, Ruili Huang, and Richard S. Judson. Environmental Science & Technology

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

Please share this post. However, please don't change the title or the content. If you do make changes, don't attribute the edited title or content to EPA or the author.

Advancing Chemical Testing by the Thousands

Reposted from EPA Connect, the official blog of EPA leadership.

By Bob Kavlock

Bob Kavlock PortraitStudying thousands of chemicals at a time with the use of high-tech computer screening models and automated, often robot-assisted processes sounds like science fiction. But it’s not. EPA scientists are doing just that, leading the advancement of “high-throughput screening,” fast, efficient processes used to expose hundreds of living cells or isolated proteins to chemicals and then screen them for changes in biological activity—clues to potential adverse health effects related to chemical exposure.

This scientific advance is positioned to transform how we understand the safety of chemicals going forward. Twenty years ago, using high-throughput screening to test chemicals for potential human health risks seemed like technology that belonged in a science fiction television series rather than in real life.

Back then there were several large data gaps that would not allow us to extrapolate from the isolated biological changes we observe on a cellular level to adverse human health effects. However, through our computational toxicology (CompTox) research, which integrates, biology,

Robotic arm moving samples for screening

Robotic arm moves samples for automated chemical screening.

biotechnology, chemistry, and computer science, that is changing. We are helping to transform the paradigm of chemical testing from one that relies almost solely on expensive and time-consuming animal testing methods to one that uses the full power of modern molecular biology and robotics.

A significant part of this effort is the Toxicity Forecaster (ToxCast), launched in 2007. ToxCast allows us to prioritize potentially toxic chemicals for more extensive testing as well as giving us the opportunity to test newer, possibly safer alternatives to existing chemicals. By 2013, we evaluated more than 2,000 chemicals from industrial and consumer products to food additives using more than 500 high-throughput screening assays.

Read the rest of the post. 

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

Please share this post. However, please don't change the title or the content. If you do make changes, don't attribute the edited title or content to EPA or the author.

Release the Data! New Chemical Data, Workshops, and Challenges

By Matthew T. Martin

Scientist prepares a well-plate for high-throughput screening.

Scientist preparing a well-plate for high-throughput screening.

Ever open that cabinet under the kitchen sink, grab that bright blue bottle of window cleaner and wonder exactly what sort of chemicals are floating around in it? Many of you have at one time or another, and for those of you who have never given it a second thought rest assured that my colleagues and I at EPA are dedicated to identifying and categorizing all of the chemicals we might be exposed to on any given day. However, due the expensive, time-consuming process of traditional testing, which assesses one chemical at a time, only a small fraction of the tens of thousands of chemicals currently in commerce have been adequately assessed for potential human and environmental health risks.

To close this data gap and better evaluate potential health risks, we have worked hard in recent years to accelerate the pace of chemical testing. I am proud to say that we have now completed phase two of the multi-year Toxicity Forecaster (ToxCast) project and are publically releasing ToxCast data on 1,800 chemicals evaluated in over 700 high-throughput screening assays. This is a significant accomplishment that we want to share with the scientific community.

The new data is accessible through the new interactive Chemical Safety for Sustainability (iCSS) Dashboard, a web-based application for users to access and interact with the data freely at their own discretion. Users can select the chemicals and data of interest and then score the information to help inform chemical safety decisions.

As part of the data release, I hope the scientific community will take advantage of this new windfall of data and become involved in the ToxCast project by participating in the Predictive Toxicology Challenges. The first two challenges of the series, available through TopCoder and InnoCentive crowd sourcing technology, will ask the scientific and technology community to develop new algorithms to predict lowest effect levels (LELs) of chemicals using the new ToxCast data. Winners will receive monetary prizes to help fund their own planned research, and their solutions will help us determine innovative ways to use ToxCast data to inform decisions made about the chemical safety.

Also, beginning January 14,we are also hosting several stakeholder outreach workshops and webinars to address potential challenges with data translation, accessibility, and any other troubleshooting issues that might arise during the initial data launch. This is an opportunity for the scientific community to provide input on data usage and offer immediate feedback about the new data and the iCSS dashboard.

About the author: Matthew T. Martin is a research biologist within EPA’s National Center for Computational Toxicology, where he is part of the ToxCast team and leads the CSS task for developing predictive models of toxicity using high-throughput screening data. He also serves as the project lead for developing the new CSS Dashboard Web Application.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

Please share this post. However, please don't change the title or the content. If you do make changes, don't attribute the edited title or content to EPA or the author.