Suzanne Fitzpatrick

3S - Systematic, systemic, and systems biology and toxicology

Summary A biological system is more than the sum of its parts – it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass “systemic toxicities”; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to recapitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organon-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the challenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

Lessons from Toxicology: Developing a 21st-Century Paradigm for Medical Research

Summary Biomedical developments in the 21st century provide an unprecedented opportunity to gain a dynamic systems-level and human-specific understanding of the causes and pathophysiologies of disease. This understanding is a vital need, in view of continuing failures in health research, drug discovery, and clinical translation. The full potential of advanced approaches may not be achieved within a 20th-century conceptual framework dominated by animal models. Novel technologies are being integrated into environmental health research and are also applicable to disease research, but these advances need a new medical research and drug discovery paradigm to gain maximal benefits. We suggest a new conceptual framework that repurposes the 21st-century transition underway in toxicology. Human disease should be conceived as resulting from integrated extrinsic and intrinsic causes, with research focused on modern human-specific models to understand disease pathways at multiple biological levels that are analogous to adverse outcome pathways in toxicology. Systems biology tools should be used to integrate and interpret data about disease causation and pathophysiology. Such an approach promises progress in overcoming the current roadblocks to understanding human disease and successful drug discovery and translation. A discourse should begin now to identify and consider the many challenges and questions that need to be solved.

Good cell culture practice for stem cells and stem-cell-derived models

The first guidance on Good Cell Culture Practice (GCCP) dates back to 2005. This document expands this to include aspects of quality assurance for in vitro cell culture focusing on the increasingly diverse cell types and culture formats used in research, product development, testing and manufacture of biotechnology products and cell-based medicines. It provides a set of basic principles of best practice that can be used in training new personnel, reviewing and improving local procedures, and helping to assure standard practices and conditions for the comparison of data between laboratories and experimentation performed at different times. This includes recommendations for the documentation and reporting of culture conditions. It is intended as guidance to facilitate the generation of reliable data from cell culture systems, and is not intended to conflict with local or higher level legislation or regulatory requirements. It may not be possible to meet all recommendations in this guidance for practical, legal or other reasons. However, when it is necessary to divert from the principles of GCCP, the risk of decreasing the quality of work and the safety of laboratory staff should be addressed and any conclusions or alternative approaches justified. This workshop report is considered a first step toward a revised GCCP 2.0.

The Emergence of Systematic Review in Toxicology

The Evidence-based Toxicology Collaboration hosted a workshop on “The Emergence of Systematic Review and Related Evidence-based Approaches in Toxicology,” on November 21, 2014 in Baltimore, Maryland. The workshop featured speakers from agencies and organizations applying systematic review approaches to questions in toxicology, speakers with experience in conducting systematic reviews in medicine and healthcare, and stakeholders in industry, government, academia, and non-governmental organizations. Based on the workshop presentations and discussion, here we address the state of systematic review methods in toxicology, historical antecedents in both medicine and toxicology, challenges to the translation of systematic review from medicine to toxicology, and thoughts on the way forward. We conclude with a recommendation that as various agencies and organizations adapt systematic review methods, they continue to work together to ensure that there is a harmonized process for how the basic elements of systematic review methods are applied in toxicology.

Developing microphysiological systems for use as regulatory tools--challenges and opportunities.

In the last few years, scientists have made important progress in developing systems using human cells to test the effects of drugs and other substances. These systems have the potential to improve toxicity testing beyond currently available tools. The innovative new tools, which are known as microsystems, microphysiological systems, or organs on a chip, can aid in the development of medical products so that toxicity may be identified earlier in product development. This may lower costs and speed new treatments to patients. Experts believe that these systems may eventually enable scientists to test more environmental compounds more efficiently.

Reproductive and developmental toxicity testing: from in vivo to in vitro.

On April 16, 2012, the U.S. Food and Drug Administration (FDA) held a workshop cosponsored by the National Institute of environmental Health Sciences, the Center for Alternatives to Animal testing (CAAt) at the Johns Hopkins Bloomberg School of Public Health, and the Middle Atlantic Reproduction and teratology Association to discuss emerging in vitro tools for predicting reproductive and developmental toxicity. this workshop, with 350 registered participants including those participating via webstream, provided an opportunity to discuss the evidence needed to evaluate and validate new test methods and to integrate these methods into regulatory decision making. During drug development, pharmaceutical companies use a variety of in vivo and in vitro developmental and reproductive toxicology (DARt) tests to predict the safety of new compounds. the results inform internal decision making and labeling, helping companies determine, for example, whether a compound would be safe for particular populations (e.g., women of childbearing age). In vivo testing for effects on embryofetal development in two animal species – one rodent species (usually rats or mice) and one nonrodent species (typically rabbits) is generally required by FDA to support clinical trials and labeling for use in pregnancy, explained Ed Fisher (FDA). Currently, companies employ in vitro tests using humanor animal-derived cells or cell lines or different animal models (e.g., zebrafish) only as a way to rapidly screen compounds prior to, or in conjunction with, in vivo testing, added Abigail Jacobs (FDA). For a variety of reasons, animal toxicity is sometimes a poor predictor of human toxicity, noted David Gerhold (National Institutes of Health – NIH) and other participants. Validated in vitro tests have the potential to increase the relevance of toxicity testing for humans and to reduce, refine, or replace in vivo animal testing. In fact, Gerhold continued, the National Research Council (NRC) report, Toxicity Testing in the 21st Century: A Vision and Strategy (NRC, 2007), envisions a future in which toxicity testing relies primarily on the in vitro study of human-derived cells or cell lines. Furthermore, the in vivo DARt methods used for regulatory purposes have changed little in the past few decades, explained Jesse Goodman (FDA), despite dramatic advances in basic scientific research. Modernizing toxicology to improve preclinical predictions of product safety, continued Goodman, is one of the priorities identified in FDA’s strategic plan for regulatory science (US FDA, 2011). But how should scientists validate emerging in vitro assays or batteries of tests? And what is the current status of ongoing validation efforts? Participants addressed these and related questions, focusing on the ability of in vitro test methods to predict in vivo outcomes and the potential to incorporate these new methods into regulatory decision making. Ultimately, Fisher and other participants said, to be accepted by both pharmaceutical companies and regulators, new methods must provide protection that is equivalent to, or better than, existing in vivo approaches.

FutureTox III: Bridges for Translation

Future Tox III, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in November 2015. Building upon Future Tox I and II, Future Tox III was focused on developing the high throughput risk assessment paradigm and taking the science of in vitro data and in silico models forward to explore the question-what progress is being made to address challenges in implementing the emerging big-data toolbox for risk assessment and regulatory decision-making. This article reports on the outcome of the workshop including 2 examples of where advancements in predictive toxicology approaches are being applied within Federal agencies, where opportunities remain within the exposome and AOP domains, and how collectively the toxicology community across multiple sectors can continue to bridge the translation from historical approaches to Tox21 implementation relative to risk assessment and regulatory decision-making.

Status of acute systemic toxicity testing requirements and data uses by U.S. regulatory agencies

Acute systemic toxicity data are used by a number of U.S. federal agencies, most commonly for hazard classification and labeling and/or risk assessment for acute chemical exposures. To identify opportunities for the implementation of non-animal approaches to produce these data, the regulatory needs and uses for acute systemic toxicity information must first be clarified. Thus, we reviewed acute systemic toxicity testing requirements for six U.S. agencies (Consumer Product Safety Commission, Department of Defense, Department of Transportation, Environmental Protection Agency, Food and Drug Administration, Occupational Safety and Health Administration) and noted whether there is flexibility in satisfying data needs with methods that replace or reduce animal use. Understanding the current regulatory use and acceptance of non-animal data is a necessary starting point for future method development, optimization, and validation efforts. The current review will inform the development of a national strategy and roadmap for implementing non-animal approaches to assess potential hazards associated with acute exposures to industrial chemicals and medical products. The Acute Toxicity Workgroup of the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM), U.S. agencies, non-governmental organizations, and other stakeholders will work to execute this strategy.

Use of Adverse Outcome Pathways in Human Risk Assessment and Toxicology

Mechanistic information has been used for many years to inform chemical hazard and risk assessments. NRC reports and several agency strategic plans in recent years promote the large-scale use of mechanistic information, organized in the form of pathways at different levels of biological organization as a basis to underpin a dramatic change in the way chemical assessment is performed. As a result, there now exist international collaborations to develop the data and knowledge bases, guidance and principles for development and use of “Adverse Outcome Pathways” (AOPs). Many of the principles for developing and using pathways are based on experience with Mode of Action frameworks for human health risk assessment. Expert groups within the Organization for Economic Cooperation and Development (OECD) are publishing guidance and partnering with the US EPA and European Commissions Joint Research Centre (JRC) to develop a public knowledge base for building AOPs on a large scale. Although this direction is fairly new, there are many pathways already in development. In addition, pathway-based approaches are increasingly being applied to a variety of assessments of hazard in a number of sectors. This chapter describes the genesis of the AOP concept, the development of the necessary tools based on international collaborations, and provides some examples of the use of AOPs in human health risk assessment.

Recommendations toward a human pathway-based approach to disease research

Failures in the current paradigm for drug development have resulted in soaring research and development costs and reduced numbers of new drug approvals. Over 90% of new drug programs fail, the majority terminated at the level of Phase 2/3 clinical trials, largely because of efficacy failures or unexplained toxicity. A recent workshop brought together members from research institutions, regulatory agencies, industry, academia, and nongovernmental organizations to discuss how existing programs could be better applied to understanding human biology and improving drug discovery. Recommendations include increased emphasis on human relevance, better access and curation of data, and improved interdisciplinary and international collaboration.