NAMs Dictionary

A is for AOP

An Adverse outcome Pathway (AOP) captures the sequence of events that leads from the exposure to a chemical to a final negative effect on a biological system. Every AOP starts with a Molecular Initiating Event (MIE), representing the interaction between a substance and an organism. Examples of this interaction are the binding of a receptor, a protein changing cellular compartment or DNA damage. The MIE will then trigger a second event called Key Event (KE), which will lead to the next KE and so on. Finally, this sequence of KE causes a final negative effect on the entire biological organisms called Adverse Outcome (AO).  

To better understand how an AOP is defined, it can be helpful to imagine it as a “biological domino” where each event prompts the next until the final and last AO. The AOP describes each domino tile (KIE, KE and AO) and how they interact, essentially drawing a photograph of the entire cascade.

The interaction between each domino’s step is called the Key Event Relationship and is defined thanks to three main aspects:

Biological plausibility: biological knowledge that a specific KE will lead to another KE

Empirical support: biological data that links two KEs

Quantitative understanding: biological data concerning the conditions where one KE leads to another KE

AOPs are an essential tool for chemical risk assessment: they represent the scientific understanding of how chemicals interact and damage the human body.

References:

Wikipedia: https://bit.ly/3qLs7qF
Scientific publication: A review of in Silico Tools as Alternatives to Animal Testing: Principles, Resources and Applications. J. C. Madden et al., DOI: 10.1177/0261192920965977
OECD: https://bit.ly/3cmuXdi
AOP wiki: https://aopwiki.org/
Nice and clear video on AOPs: https://www.youtube.com/watch?v=rIcILqg3SFA

B is for BIOKINETICS

> Biokinetics give insight into the absorption, distribution, metabolism and excretion of chemicals in organisms.

> They play a critical role in next-generation risk evaluations that move towards NAMs, as they are required for the design of in vitro studies and quantitative in vitro-to-in vivo extrapolation

> NAMs for biokinetics can guide the development of NAMs for toxicity assessment by advancing the understanding of the physiology and kinetic characteristics of relevant organs.

C is for

C.Elegans

> The Caenorhabditis elegans is a tiny worm widely used in biomedical research.

> Considered as “non-sentient”, this nematode is cheap to maintain and complex enough to have a nervous, digestive and hormonal system, so that it can replace more expensive animals like rats and mice in toxicological studies and still provide data on the whole organism ; therefore it fulfils the 3Rs objectives (Replacement, Reduction and Refinement)

Listen to VOXLAB podcact on C.Elegans

Read: Wikipedia

Video “Investigating the ecotoxic effects of oxybenzone on C. elegans”

D is for

Drosophila melanogaster 

The Drosophilia melanogasteris a small invertebrate that goes through specific phases during development. Each stage has been deeply described, especially regarding brain formation. This feature, in combination with easy access to strains of Drosophilawith genetic alterations, makes this fly a perfect model for neurodevelopmental toxicology. Considered as non-sentient, it fulfils the 3Rs objectives.

Scientific publication: Drosophila as a Model for Developmental Toxicology: Using and Extending the Drosophotoxicology Model, J. G. Affleck, V. K. Walker, DOI: 10.1007/978-1-4939-9182-2_10

video 

article NC3RS

podcast VOXLAB by PrecisionTox

E is for ECVAM

The European Centre for the Validation of Alternative Methods(ECVAM) was established in 1991 pursuant to a requirement in Directive 86/609/EEC that the European Commission (EC) and its member states actively support the development, validation, and acceptance of methods to replace, reduce, or refine the use of animals in laboratories.

 

The aim of EURL ECVAM is twofold:

to promote the scientific and regulatory acceptance of non-animal tests which are of importance to biomedical sciences, through research, test development and validation and the establishment of a specialised database service

to co-ordinate at the European level the independent evaluation of the relevance and reliability of tests for specific purposes, so that chemicals and products of various kinds, including medicines, vaccines, medical devices, cosmetics, household products and agricultural products, can be manufactured, transported and used more economically and more safely, whilst the current reliance on animal test procedures is progressively reduced.

 

F is for serum Free

Serum-free media are media designed to grow a specific cell type or perform a specific application in the absence of serum. The use of serum-free media (SFM) represents an important tool, that allows cell culture to be done with a defined set of conditions as free as possible of confounding variables.


Advantages of using serum-free media include:Easier purification and downstream processing.
– Precise evaluations of cellular function.
– Increased definition.
– More consistent performance

Serum-free medium has fewer possible interfering factors due to low nutrient levels. … In serum-free media, the protein concentration is low, resulting in low levels of contaminants. As a result, the target protein is easier to purify with higher recovery. Serum-free alternatives better serve animal welfare.

G is for GIVIMP

In the past several decades, there has been a substantial increase in the availability of in vitro test methods for evaluating chemical safety in an international regulatory context.  To foster confidence in in vitro alternatives to animal testing, the test methods and conditions under which data are generated must adhere to defined standards to ensure resulting data are rigorous and reproducible.  Created by The Organisation for Economic Cooperation and Development (OECD), Good In vitro Method Practices (GIVIMP) for the development and implementation of in vitro methods for regulatory use in human safety assessment aims to help reduce the uncertainties in cell and tissue-based in vitro method derived chemical safety predictions.  GIVIMP provides guidance for test method developers and end users of resulting data on key elementes of in vitro methods. GIVIMP tackles ten important aspects related to in vitro work: (1) Roles and responsibilities, (2) Quality considerations, (3) Facilities (4) Apparatus, material and reagents, (5) Test systems, (6) Test and reference/control items, (7) Standard operating procedures (SOPs), (8) Performance of the method, (9) Reporting of results, (10) Storage and retention of records and materials.

H is for Horizon Europe

Since 2020 we are involved in 3 major EU projects: ONTOX, PrecisionTox and Panoramix

Those project are financed by Horizon Europe is the EU’s key funding programme for research and innovation with a budget of €95.5 billion.

It tackles climate change, helps to achieve the UN’s Sustainable Development Goals and boosts the EU’s competitiveness and growth.

 

It relies on 3 pillars:

  • Excellent Science
  • Global Challenges and European Industrial Competitiveness
  • Innovative Europe

I is for

induced Pluripotent Stem Cells

iPSC are derived from skin or blood cells that have been reprogrammed back into an embryonic-like pluripotent state that enables the development of an unlimited source of any type of human cell needed for therapeutic purposes.

iPSC offer a unique chance to model human disease and are already being used to make new discoveries about premature aging, congenital heart disease, cancer, and more.

The primary advantages of iPSCs compared to other stem cells are: a) iPSCs can be created from the tissue of the same patient that will receive the transplantation, thus avoiding immune rejection, and b) the lack of ethical implications because cells are harvested from a willing adult without harming them.

However, there are constraints for ESC use in cell replacement therapy. The first constraint is the immune incompatibility between the donor cells and the recipient, which can result in the rejection of transplanted cells. The second constraint is ethical, because the embryo dies during the isolation of ESCs.

J is for JRC

The mission of the JRC (Joint Research* Centre) is to provide customer-driven scientific and technical support for the conception, development, implementation and monitoring of EU policies.

JRC plays a key role in the supports of projects by ensuring their respect and understanding of the legal frame, taking part into the research, disseminating results and promoting the methods and thei application.

Indeed The European Centre for the Validation of Alternative Methods (EURL ECVAM) is part of JRC.  (cf. Letter E)

*Joint research is a system which can be expected to produce more creative research outcomes by establishing common research themes with private companies, universities, and public research institutes and promoting research cooperatively while exchanging opinions from a standpoint of mutual equality.

K is for Key Event

Key events, in AOPs, are identified steps along the pathway that represent intermediate events, typically at the different levels of biological organization which are experimentally or toxicologically associated with an adverse outcome pathway (OECD, 2012)

Key event (KE) :

  • A measureable change in biological state that is essential, but not necessarily sufficient for the progression from a defined biological perturbation toward a specific AO.​
  • Represented as nodes in an AOP diagram or AOP network.​
  • Provide verifiability to an AOP description.

Key event relationship (KER)

  • Define a directed relationship between a pair of KEs, identifying one as upstream and the other as downstream.
  • Supported by biological plausibility and empirical evidence.
  • Represented as a directed edge (i.e., an arrow) in an AOP diagram or AOP network.
  • Unit of inference or extrapolation within an AOP.

 

L is for LIVe2022

LIVe2022 intends to be a unique exchange platform for scientists interested in in vitro respiratory researches, stakeholders from academia, pharma, biotech, chemical, tobacco, consumer goods, medical devices industries, CROs and regulatory agencies.

M is for Machine Learning

In recent times, machine learning has become increasingly prominent in predictive toxicology shifting from in vivo studies toward in silico studies. Currently, in vitro methods together with other computational methods such as quantitative structure–activity relationship modeling and absorption, distribution, metabolism and excretion calculations are being used. Machine learning and its applications in predictive toxicology include support vector machines (SVMs), random forest (RF) and decision trees (DTs), neural networks, regression models, naïve Bayes, k-nearest neighbors, and ensemble learning.

N is for NAMs

The term “new approach methodologies” (NAMs) emerged as a descriptive reference to any non-animal-based approaches that can be used to provide information in the context of chemical hazard and risk assessment.


NAMs meet the goals of 3Rs regarding animal testing: replace, reduce, refine of the use of animals for scientific purpose.


NAMs can be either in silico methods (machine learning, computer-based modeling,  AI…) or in vitro (organ in a dish,  organ on a chip, cell culture …)

O is for OMICs

“The word omics refers to a field of study in biological sciences that ends with -omics, such as genomics, transcriptomics, proteomics, or metabolomics. The ending -ome is used to address the objects of study of such fields, such as the genome, proteome, transcriptome, or metabolome, respectively. More specifically genomics is the science that studies the structure, function, evolution, and mapping of genomes and aims at characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes and messenger molecules.”

“Advances in omics technologies have begun to enable personalized medicine at an extraordinarily detailed molecular level.”

P is for PBPK

Physiological based pharmacokinetic modeling and simulation (PBPK) is a computer modeling approach that incorporates blood flow and tissue composition of organs to define the pharmacokinetics (PK) of drugs.

« Although PBPK models do have some limitations, the potential benefit from PBPK modeling technique is huge. PBPK models can be applied to investigate drug pharmacokinetics under different physiological and pathological conditions or in different age groups, to support decision-making during drug discovery, to provide, perhaps most important, data that can save time and resources, especially in early drug development phases and in pediatric clinical trials, and potentially to help clinical trials become more “confirmatory” rather than “exploratory”. »

  • Most PBPK models are developed and tested with experimental animal data. With the goal of replacing animal experiments, New Approach Methodologies (NAMs) are necessary to combine and integrate various datasets into PBPK models:
  • In vitro experiments relevant to absorption, distribution, metabolism and excretion (ADME) processes
  • Development and refinement of in vitro to in vivo extrapolation (IVIVE) techniques
  • QSAR predictions
  • Training is an important part in the acceptance of PBPK modeling in decision making.

Q is for QSAR

Quantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities.  Using these data, QSAR models are developed and validated following OECD guidelines and best practices of modeling. Then, QSAR models are used to identify chemical compounds predicted to be active against selected endpoints from large chemical libraries. Therefore, QSAR models can be a good alternative to animal testing, which would otherwise be necessary to determine the toxicity of unknown substances.

R is for Risk Assessment

The risk-assessment process integrates many disciplines of toxicology. It has both qualitative and quantitative components and consists of four general steps: hazard identification, dose-response assessment, exposure assessment, and risk characterization(NRC 1983, 1994).

In risk assessment, alternatives to animal testing include sophisticated tests using human cells and tissues (also known as in vitro methods), advanced computer-modeling techniques (often referred to as in silico models), and studies with human volunteers.

S is for Sentient

Beings can be either sentient or non sentient

•Beings/organisms that cannot feel pain due to the lack of a central nervous systems are considered non-sentient and are not protected as animal in EU legal standards. This includes bacteria, archaea, protists, fungi, plants and certain animals.

In developing NAMs, non sentient are very useful. In fact, greater accuracy can be achieved by using a diverse range of biomedical model species — fruit flies, water fleas, round worms, and embryos of frogs and zebrafish — along with human cell lines to observe what happens when organisms are exposed to chemicals

T is for Transferability


The ability of a test method or of a procedure to be accurately and reliably performed in different, competent laboratories (NIEHS, 2003).

U is for U Curves

U-Shaped Dose-Responses in Biology, Toxicology, and Public Health – annualreviews

U-shaped dose-response curves: their occurrence and implications for risk assessment – pubmed

V is for Validation

W is for Water fleas

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