Periodic Reporting for period 2 - PrecisionTox (Toward Precision Toxicology: New Approach Methodologies for Chemical Safety)
Reporting period: 2022-08-01 to 2024-01-31
Our society depends on a healthy environment. Yet the direct effects on human health of most industrial chemicals are largely unknown because the innovations in this important economic sector have historically outpaced our abilities to test their safety.
Part of this dilemma stems from a historical reliance on observing toxicological adverse health effects on mice or rats as surrogates for humans because of our shared mammalian biology. However, these traditional approaches using models by “analogy” (i.e. mice are human) are notoriously unsustainable and unethical, and there is increasing evidence that no single species can reliably be used to predict the effects of harmful chemicals on humans.
PrecisionTox is unique in its concept of using a diversity of distantly related (more ethically acceptable) organisms as human surrogates by “homology” (i.e. toxicity by descent). Our main scientific objective is to demonstrate that toxicity to humans can be better deduced by a ‘comparative toxicology’ approach – by exposing an evolutionarily diverse suite of model test species (fruit flies, nematodes, water fleas, and embryos of zebrafish and clawed frogs) and a human cell line to chemicals and by mapping the origins of toxicity pathways based on repeated measurements of genetic and metabolic changes indicative of adversity. The anticipated impact is the discovery of many conserved pathways to toxicity and their biomarkers that can be useful for environmental and human health protection.
Work relating to the second objective is beginning to detect the degree to which genetic variation among individuals determines the level of susceptibility to toxicity by studying fruit fly populations and globally diverse human cell lines with known DNA variation, which may potentially serve as a ‘susceptibility model’ for human populations. This concept of "quantitative susceptibility" stems from statistical genetic evidence that the heritable basis for individual differences is often found in genes and pathways shared among species. The anticipated impact is a new method to set regulatory limits on chemical exposure based on variations in people’s genetic susceptibility to adverse outcomes.
The project’s final objective is to translate the research from PrecisionTox into a brighter future for chemical risk management. Our aim here is to work to resolve specific risk management problems by conducting case studies with risk managers and regulators and to build a model of how new approach methodologies (NAMs) made from the knowledge of conserved pathways to toxicity (with their biomarkers) will be incorporated into future chemical risk governance structures. Ultimately, at its core, this is an exercise in overcoming ‘socio-technical barriers’ to the uptake of NAMs and marketplace engineering.
Part of this dilemma stems from a historical reliance on observing toxicological adverse health effects on mice or rats as surrogates for humans because of our shared mammalian biology. However, these traditional approaches using models by “analogy” (i.e. mice are human) are notoriously unsustainable and unethical, and there is increasing evidence that no single species can reliably be used to predict the effects of harmful chemicals on humans.
PrecisionTox is unique in its concept of using a diversity of distantly related (more ethically acceptable) organisms as human surrogates by “homology” (i.e. toxicity by descent). Our main scientific objective is to demonstrate that toxicity to humans can be better deduced by a ‘comparative toxicology’ approach – by exposing an evolutionarily diverse suite of model test species (fruit flies, nematodes, water fleas, and embryos of zebrafish and clawed frogs) and a human cell line to chemicals and by mapping the origins of toxicity pathways based on repeated measurements of genetic and metabolic changes indicative of adversity. The anticipated impact is the discovery of many conserved pathways to toxicity and their biomarkers that can be useful for environmental and human health protection.
Work relating to the second objective is beginning to detect the degree to which genetic variation among individuals determines the level of susceptibility to toxicity by studying fruit fly populations and globally diverse human cell lines with known DNA variation, which may potentially serve as a ‘susceptibility model’ for human populations. This concept of "quantitative susceptibility" stems from statistical genetic evidence that the heritable basis for individual differences is often found in genes and pathways shared among species. The anticipated impact is a new method to set regulatory limits on chemical exposure based on variations in people’s genetic susceptibility to adverse outcomes.
The project’s final objective is to translate the research from PrecisionTox into a brighter future for chemical risk management. Our aim here is to work to resolve specific risk management problems by conducting case studies with risk managers and regulators and to build a model of how new approach methodologies (NAMs) made from the knowledge of conserved pathways to toxicity (with their biomarkers) will be incorporated into future chemical risk governance structures. Ultimately, at its core, this is an exercise in overcoming ‘socio-technical barriers’ to the uptake of NAMs and marketplace engineering.
After 36 months of H2020 support, PrecisionTox remains a uniquely interdisciplinary project. Its dual mission is to offer a new evolutionary genetic understanding of chemical toxicity causing adversity to humans and how this change in perspective may be integrated within current and future regulatory paradigms. Whereas the first reporting period was focused on the logistical and strategic work towards its objectives, the second reporting period was primarily focused on reaching “production mode”, which began in earnest at the end of 2023 following the completion of the unanticipated R&D for RNA sequencing and the completion of the Chemicals Library. Our achievements during months 19-36 include:
• Completed chemicals library of 250 substances with information about their chemical class, diversity in terms of structure, physical-chemical properties, toxicity modes of action (if known) and database/literature-derived associations with disease pathology, genes and putative metabolic biomarkers
• Conducted harmonised toxicity testing experiments on 90 substances with comparative toxicology results based on 58 substances for a first “phylogenetic toxicity analysis " to allow cross-species extrapolation
• Conducted a pilot project informed experimental design that produces a larger volume and diversity of omics data per species for each tested chemical
• Validated a customised methodology for RNA sequencing for integration with procedures for high-throughput sample processing for metabolomics and transcriptomics data
• Uploaded pilot project data and results to the Data Commons, which benefits from an additional data processing pipeline (for RNA sequencing data) and can be accessed by browsing the results using a highly modular and adaptable PrecisionTox Data Explorer application
• Produced early-stage discoveries on modes of action shared between Daphnia and Drosophila.
• Genome-wide screening of genetic variation for toxicity is also producing publishable results
• Submitted the report on the socio-technological barriers to the uptake of NAMs in chemical regulation
• Progress is made on (i) the development of 2/3 case studies with Nordic regulators, (ii) possible steps towards solutions and governance reform for the uptake of NAMS in regulation, (iii) legislative mapping of key EU chemical-related legislation and case law. (iv) developing reporting templates and other informational support for the regulatory use of NAMs data and results.
• Completed chemicals library of 250 substances with information about their chemical class, diversity in terms of structure, physical-chemical properties, toxicity modes of action (if known) and database/literature-derived associations with disease pathology, genes and putative metabolic biomarkers
• Conducted harmonised toxicity testing experiments on 90 substances with comparative toxicology results based on 58 substances for a first “phylogenetic toxicity analysis " to allow cross-species extrapolation
• Conducted a pilot project informed experimental design that produces a larger volume and diversity of omics data per species for each tested chemical
• Validated a customised methodology for RNA sequencing for integration with procedures for high-throughput sample processing for metabolomics and transcriptomics data
• Uploaded pilot project data and results to the Data Commons, which benefits from an additional data processing pipeline (for RNA sequencing data) and can be accessed by browsing the results using a highly modular and adaptable PrecisionTox Data Explorer application
• Produced early-stage discoveries on modes of action shared between Daphnia and Drosophila.
• Genome-wide screening of genetic variation for toxicity is also producing publishable results
• Submitted the report on the socio-technological barriers to the uptake of NAMs in chemical regulation
• Progress is made on (i) the development of 2/3 case studies with Nordic regulators, (ii) possible steps towards solutions and governance reform for the uptake of NAMS in regulation, (iii) legislative mapping of key EU chemical-related legislation and case law. (iv) developing reporting templates and other informational support for the regulatory use of NAMs data and results.
Progress beyond the state of the art is primarily found in the incremental understanding of the real-world challenges of pursuing a project of this scale and complexity. These include pushing technical and technological boundaries in (i) automation for high throughput screening accounting for differences among species, (ii) advancing the detection and interpretation of molecular signals of toxicity, (iii) implementing computational methods for associating these signals to identifiable pathways to toxicity using machine learning, (iv) the theory and practice of F.A.I.R. data management, and (v) the theory and practice of breaking through techno-social barriers for the regulatory uptake of NAMs.
As the new knowledge from this project emerges for demonstrating its concepts, it is on track to accelerate the pace of regulating chemicals as groups by promoting a more mechanistic and integrative approach to assessing chemical hazards. Given the interdisciplinarity of PrecisionTox by uniting science with law (and provided we succeed) we continue to expect (i) legal, political, and/or regulatory frameworks to take advantage of NAMs in chemical safety assessment, (ii) defined avenues for the early commercial adoption of NAMs across a wide range of mechanisms which depend upon the level of certainty of biomarkers at establishing causation between chemicals and their adverse health effects, and (iii) results that are relevant in the formulation of the next legislative tools for chemical safety.
As the new knowledge from this project emerges for demonstrating its concepts, it is on track to accelerate the pace of regulating chemicals as groups by promoting a more mechanistic and integrative approach to assessing chemical hazards. Given the interdisciplinarity of PrecisionTox by uniting science with law (and provided we succeed) we continue to expect (i) legal, political, and/or regulatory frameworks to take advantage of NAMs in chemical safety assessment, (ii) defined avenues for the early commercial adoption of NAMs across a wide range of mechanisms which depend upon the level of certainty of biomarkers at establishing causation between chemicals and their adverse health effects, and (iii) results that are relevant in the formulation of the next legislative tools for chemical safety.