Reproducibility of animal research in light of biological variation.

Context-dependent biological variation presents a unique challenge to the reproducibility of results in experimental animal research, because organisms' responses to experimental treatments can vary with both genotype and environmental conditions. In March 2019, experts in animal biology, experimental design and statistics convened in Blonay, Switzerland, to discuss strategies addressing this challenge. In contrast to the current gold standard of rigorous standardization in experimental animal research, we recommend the use of systematic heterogenization of study samples and conditions by actively incorporating biological variation into study design through diversifying study samples and conditions. Here we provide the scientific rationale for this approach in the hope that researchers, regulators, funders and editors can embrace this paradigm shift. We also present a road map towards better practices in view of improving the reproducibility of animal research.

The use of animals in physiological science: the past, the presence, and the future.

Physiology is a scientific discipline of how people's and animals' bodies function that requires traditionally suitable experimental models that often rely on animals. However, at the end of the 50th of the last century, researchers themselves addressed concerns about the use of animals for biomedical science and physiology in particular. At that time, the so-called 3R strategy was implicated where the three "R" stand for replacement, reduction, and refinement. When addressing these concerns, researchers nevertheless realized that a critical dispute about experimental models in the light of the 3R initiative may require further attention to other points such as robustness, registration, reporting, reproducibility, and rigor of the work. The question that has to be addressed now is first whether the use of animals in physiology changed in the post-3R period, whether it led to a replacement, reduction, or refinement of animal handling, and most importantly, how this affected the scientific progress in (patho)physiology. In order to address open questions concerning the relationship between the use of animals and physiological research, complete volumes of the Pflügers Archiv - European Journal of Physiology were analyzed every 10 years starting in 1950 and ending in 2020 and compared to volumes of the Journal of Physiology. It analyzed how scientists organize their projects published in the journal and what kind of models they used. The results show that physiological science has dramatically changed in the last 70 years. Replacement, reduction, and refinement were achieved to a certain level. However, during the last years, no further achievement could be seen. It seems that a certain level of animal testing is required for biomedical science and physiology in particular. Physiological studies in the present time are dominated by investigation of the physiological function of small rodents mainly mice and rats with only a few exceptions. The analysis also shows that in the future, researchers must have a critical look at further requirements of their research such as data robustness, improvement of reproducibility of data, and generation of rigor data as a prerequisite to improve our physiological view on life.

A 3-year evaluation of preclinicaltrials.eu reveals room for improvement in preregistration of animal studies.

In 2018, the first registry dedicated to preregistration of animal study protocols was launched. Despite international support, the overall number of (pre)registered protocols is still low, illustrating the need for pushing the preregistration agenda among researchers and policymakers.

Meta-analysis of variation suggests that embracing variability improves both replicability and generalizability in preclinical research.

The replicability of research results has been a cause of increasing concern to the scientific community. The long-held belief that experimental standardization begets replicability has also been recently challenged, with the observation that the reduction of variability within studies can lead to idiosyncratic, lab-specific results that cannot be replicated. An alternative approach is to, instead, deliberately introduce heterogeneity, known as "heterogenization" of experimental design. Here, we explore a novel perspective in the heterogenization program in a meta-analysis of variability in observed phenotypic outcomes in both control and experimental animal models of ischemic stroke. First, by quantifying interindividual variability across control groups, we illustrate that the amount of heterogeneity in disease state (infarct volume) differs according to methodological approach, for example, in disease induction methods and disease models. We argue that such methods may improve replicability by creating diverse and representative distribution of baseline disease state in the reference group, against which treatment efficacy is assessed. Second, we illustrate how meta-analysis can be used to simultaneously assess efficacy and stability (i.e., mean effect and among-individual variability). We identify treatments that have efficacy and are generalizable to the population level (i.e., low interindividual variability), as well as those where there is high interindividual variability in response; for these, latter treatments translation to a clinical setting may require nuance. We argue that by embracing rather than seeking to minimize variability in phenotypic outcomes, we can motivate the shift toward heterogenization and improve both the replicability and generalizability of preclinical research.

Epidemiology and reporting characteristics of preclinical systematic reviews.

In an effort to better utilize published evidence obtained from animal experiments, systematic reviews of preclinical studies are increasingly more common-along with the methods and tools to appraise them (e.g., SYstematic Review Center for Laboratory animal Experimentation [SYRCLE's] risk of bias tool). We performed a cross-sectional study of a sample of recent preclinical systematic reviews (2015-2018) and examined a range of epidemiological characteristics and used a 46-item checklist to assess reporting details. We identified 442 reviews published across 43 countries in 23 different disease domains that used 26 animal species. Reporting of key details to ensure transparency and reproducibility was inconsistent across reviews and within article sections. Items were most completely reported in the title, introduction, and results sections of the reviews, while least reported in the methods and discussion sections. Less than half of reviews reported that a risk of bias assessment for internal and external validity was undertaken, and none reported methods for evaluating construct validity. Our results demonstrate that a considerable number of preclinical systematic reviews investigating diverse topics have been conducted; however, their quality of reporting is inconsistent. Our study provides the justification and evidence to inform the development of guidelines for conducting and reporting preclinical systematic reviews.

Endeavours made by trade associations, pharmaceutical companies and regulators in the replacement, reduction and refinement of animal experimentation in safety testing of pharmaceuticals.

Following the European Commission decision to develop a roadmap to phase out animal testing and the signing of the US Modernisation Act, there is additional pressure on regulators and the pharmaceutical industry to abandon animal experimentation in safety testing. Often, endeavours already made by governments, regulators, trade associations, and industry to replace, reduce and refine animal experimentation (3Rs) are unnoticed. Herein, we review such endeavours to promote wider application and acceptance of 3Rs. ICH guidelines have stated 3Rs objectives and have enjoyed many successes driven by global consensus. Initiatives driven by US and European regulators such as the removal of the Abnormal Toxicity Test are neutralised by reticent regional regulators. Stream-lined testing requirements have been proposed for new modalities, oncology, impurity management and animal pharmacokinetics/metabolism. Use of virtual controls, value of the second toxicity species, information sharing and expectations for life-threatening diseases, human specific or well-characterised targets are currently being scrutinised. Despite much effort, progress falls short of the ambitious intent of decisionmakers. From a clinical safety and litigation perspective pharmaceutical companies and regulators are reluctant to step away from current paradigms unless replacement approaches are validated and globally accepted. Such consensus has historically been best achieved through ICH initiatives.

Still to ARRIVE at adequate reporting of orthodontic studies involving animal models.

BACKGROUND: The ARRIVE 2.0 guidelines were introduced to improve the reporting of animal studies. The aim of this study was to assess the reporting adherence of orthodontic speciality animal studies in relation to ARRIVE 2.0 guidelines. Associations between the reporting and study characteristics were explored. MATERIALS AND METHOD: An electronic database search was undertaken using Medline via PubMed (www.pubmed.ncbi.nlm.nih.gov) to identify studies meeting the eligibility criteria published between 1 January 2018 and 31 December 2023. Data extraction was performed in duplicate and independently. Descriptive statistics and frequency distributions for the responses to each checklist item were calculated. Mean values for adequate reporting per ARRIVE item were calculated. A sum score was calculated by adding the responses (0 = not reported, 1 = inadequate reporting, 2 = adequate reporting) per item and sub-questions. On an exploratory basis, univariable linear regression between summary score and study characteristics (year of publication, continent of authorship, type of centre, and number of authors) was performed. RESULTS: Three hundred and eighty-four studies were analysed. Variability in the adequate reporting of the ARRIVE 2.0 guideline items was evident. In particular, in 32% of studies, there was a lack of reporting of the priori sample size calculation. Overall, the mean reporting score for the sample was 57.9 (SD 6.7 and range 34-74). There were no associations between score and study characteristics except for a weak association for year of publication with a small improvement over time (each additional year). CONCLUSIONS: The reporting of animal studies relevant to the speciality of orthodontics is sub-optimal in relation to the ARRIVE 2.0 guidelines. There was a tendency for the non-reporting of items pertaining to study sample size, eligibility, methods to reduce bias and interpretation/scientific implications. Greater awareness and reporting adherence to the ARRIVE 2.0 guidelines are required to reduce research waste involving animal models.

Reproducibility of preclinical animal research improves with heterogeneity of study samples.

Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research. Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke, myocardial infarction, and breast cancer, we compared the accuracy of effect size estimates between single-laboratory and multi-laboratory study designs. Single-laboratory studies generally failed to predict effect size accurately, and larger sample sizes rendered effect size estimates even less accurate. By contrast, multi-laboratory designs including as few as 2 to 4 laboratories increased coverage probability by up to 42 percentage points without a need for larger sample sizes. These findings demonstrate that within-study standardization is a major cause of poor reproducibility. More representative study samples are required to improve the external validity and reproducibility of preclinical animal research and to prevent wasting animals and resources for inconclusive research.

Implementation of the principles of the 3Rs of animal testing at CDER: Past, present and future.

The safety testing of pharmaceutical candidates has traditionally relied on data gathered from studies in animals, and these sources of information remain a vital component of the safety assessment for new drug and biologic products. However, there are clearly ethical implications that attend the use of animals for safety testing, and FDA fully supports the principles of the 3Rs, as it relates to animal usage; these being to replace, reduce and refine. We provide an overview of some of the events and activities (legal and programmatic) that have had, and continue to have, the greatest impact on animal use in pharmaceutical development, and highlight some ongoing efforts to further meet the challenge of achieving our mission as humanely as possible.

Genomic, microbial and environmental standardization in animal experimentation limiting immunological discovery.

BACKGROUND: The use of inbred mice housed under standardized environmental conditions has been critical in identifying immuno-pathological mechanisms in different infectious and inflammatory diseases as well as revealing new therapeutic targets for clinical trials. Unfortunately, only a small percentage of preclinical intervention studies using well-defined mouse models of disease have progressed to clinically-effective treatments in patients. The reasons for this lack of bench-to-bedside transition are not completely understood; however, emerging data suggest that genetic diversity and housing environment may greatly influence muring immunity and inflammation. RESULTS: Accumulating evidence suggests that certain immune responses and/or disease phenotypes observed in inbred mice may be quite different than those observed in their outbred counterparts. These differences have been thought to contribute to differing immune responses to foreign and/or auto-antigens in mice vs. humans. There is also a growing literature demonstrating that mice housed under specific pathogen free conditions possess an immature immune system that remarkably affects their ability to respond to pathogens and/or inflammation when compared with mice exposed to a more diverse spectrum of microorganisms. Furthermore, recent studies demonstrate that mice develop chronic cold stress when housed at standard animal care facility temperatures (i.e. 22-24 °C). These temperatures have been shown alter immune responses to foreign and auto-antigens when compared with mice housed at their thermo-neutral body temperature of 30-32 °C. CONCLUSIONS: Exposure of genetically diverse mice to a spectrum of environmentally-relevant microorganisms at housing temperatures that approximate their thermo-neutral zone may improve the chances of identifying new and more potent therapeutics to treat infectious and inflammatory diseases.

The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research.

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the "ARRIVE Essential 10," which constitutes the minimum requirement, and the "Recommended Set," which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.

Rethinking 3R strategies: Digging deeper into AnimalTestInfo promotes transparency in in vivo biomedical research.

In the European Union (EU), animal welfare is seen as a matter of great importance. However, with respect to animal experimentation, European citizens feel quite uninformed. The European Directive 2010/63/EU for the protection of laboratory animals aims for greater transparency and requires that a comprehensible, nontechnical summary (NTS) of each authorised research project involving animals is published by the respective Member State. However, the NTSs remain sleeping beauties if their contents are not easily and systematically accessible. The German web-based NTS database AnimalTestInfo is a unique channel for scientists to communicate their work, and provides the opportunity for large-scale analyses of planned animal studies to inform researchers and the public. For an in-depth meta-analysis, we classified the duly completed NTSs submitted to AnimalTestInfo in 2014 and 2015 according to the International Classification of Diseases and Related Health Problems (ICD) system. Indexing the NTSs with ICD codes provided a fine-grained overview of the prospective uses of experimental animals. Using this approach, transparency, especially for highly controversial animal research involving, for example, nonhuman primates, is fostered, as it enables pinpointing the envisaged beneficiary down to the level of the addressed disease. Moreover, research areas with many planned projects involving animals can be specified in detail. The development of 3R (replacement, reduction, and refinement) measures in these research areas may be most efficient, as a large number of experimental animals would benefit from it. Indexing NTSs with ICD codes can support governments and funding agencies in advancing target-oriented funding of 3R research. Data drawn from NTSs can provide a basis for the development, validation, and implementation of directed 3R strategies as well as guidance for rethinking the role of animal research models.

Quality of interventional animal experiments in Chinese journals: compliance with ARRIVE guidelines.

BACKGROUND: In view of the inadequacy and incompleteness of currently-reported animal experiments and their overall poor quality, we retrospectively evaluated the reporting quality of animal experiments published in Chinese journals adhering to the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines. RESULTS: The databases CNKI, WanFang, VIP, and CBM were searched from inception until July 2018. Two appropriately-trained reviewers screened and extracted articles independently. The ARRIVE guidelines were used to assess the quality of the published reports of animal experiments. The compliance rate of every item was analyzed relative to their date of publication. A total of 4342 studies were included, of which 73.0% had been cited ≤5 times. Only 29.0% (1261/4342) were published in journals listed in the Chinese Science Citation Database. The results indicate that the compliance rate of approximately half of the sub-items (51.3%, 20/39) was less than 50%, of which 65.0% (13/20) was even less than 10%. CONCLUSIONS: The reporting quality of animal experiments in Chinese journals is not at a high level. Following publication of the ARRIVE guidelines in 2010, the compliance rate of the majority of its requirements has improved to some extent. However, less attention has been paid to the ethics and welfare of experimental animals, and a number of specific items in the Methods, Results, and Discussion sections continue to not be reported in sufficient detail. Therefore, it is necessary to popularize the ARRIVE guidelines, advocate researchers to adhere to them in the future, and in particular promote the use of the guidelines in specialized journals in order that the design, implementation, and reporting of animal experiments is promoted, to ultimately improve their quality.

It's Time to Reconsider The Principles of Humane Experimental Technique.

In the 60 years since the publication of The Principles of Humane Experimental Technique, the Three Rs (Reduction, Refinement, Replacement) proposed by William Russell and Rex Burch have gradually been accepted throughout the world as ways of facing up to the ethical and scientific dilemmas involved in animal experimentation. However, the scale of animal use and the use of animals as models of humans has continued, seemingly almost unchallenged in much of the scientific community, despite the warnings about models, species differences and human variation spelled out in the The Principles. In this Comment, it is proposed that it is time to move away from the animal welfare focus of the Three Rs, in favour of a wider concept of humanity, which also embraces human welfare. In addition, since less than 10% of new drugs successfully pass from preclinical testing, which is highly reliant on animal procedures, to acceptance for clinical use, it is argued that the aim should not be to directly replace animal testing with non-animal methods with similar aims and which produce similar results, but to take advantage of developments in cell and molecular biology and in computer science, to devise new, different, appropriate, specific and intelligent stand-alone preclinical testing strategies that are applicable to particular human situations.

Standards and guidelines for canine clinical genetic testing laboratories.

This publication represents a proposed approach to quality standards and guidelines for canine clinical genetic testing laboratories. Currently, there are no guidelines for laboratories performing clinical testing on dogs. Thus, there is no consensus set of protocols that set the minimal standards of quality among these laboratories, potentially causing variable results between laboratories, inconsistencies in reporting, and the inability to share information that could impact testing among organizations. A minimal standard for quality in testing is needed as breeders use the information from genetic testing to make breeding choices and irreversible decisions regarding spay, neuter or euthanasia. Incorrect results can have significant impact on the health of the dogs being tested and on their subsequent progeny. Because of the potentially serious consequences of an incorrect result or incorrect interpretation, results should be reviewed by and reported by individuals who meet a minimum standard of qualifications. Quality guidelines for canine genetic testing laboratories should include not only the analytical phase, but also the preanalytical and postanalytical phases, as this document attempts to address.

Quality assurance checklist and additional considerations for canine clinical genetic testing laboratories: a follow-up to the published standards and guidelines.

There is currently no oversight for canine clinical genetic testing laboratories. We published an initial set of standards and guidelines with the goal of providing a basis for which canine testing laboratories could evaluate their quality assurance programs. To further those standards and guidelines, we have developed a checklist that can be used as a self-evaluation to identify gaps in their programs for continual quality improvement over time. Because there is currently no organization willing to oversee an external proficiency program, the checklist provides the first step toward an internal, self-assessment that can be used periodically to monitor improvements. In addition, we attempt to address concerns from the canine community regarding rare or private mutations, genetic screening using array-based technologies, non-peer reviewed tests that are being offered, and the clinical validity of certain mutations in particular breeds. Through coordination, conversation and hard work, the canine genetic testing community can strive to organize to improve testing and to provide more transparency to consumers and better outcomes for dogs.

Variations in hepatic lipid species of age-matched male mice fed a methionine-choline-deficient diet and housed in different animal facilities.

BACKGROUND: Non-alcoholic steatohepatitis (NASH) is a common disease and feeding mice a methionine-choline-deficient (MCD) diet is a frequently used model to study its pathophysiology. Genetic and environmental factors influence NASH development and liver lipid content, which was studied herein using C57BL/6 J mice bred in two different animal facilities. METHODS: Age-matched male C57BL/6 J mice bred in two different animal facilities (later on referred to as WT1 and WT2) at the University Hospital of Regensburg were fed identical MCD or control chows for 2 weeks. Hepatic gene and protein expression and lipid composition were determined. RESULTS: NASH was associated with increased hepatic triglycerides, which were actually higher in WT1 than WT2 liver in both dietary groups. Cholesterol contributes to hepatic injury but was only elevated in WT2 NASH liver. Ceramides account for insulin resistance and cell death, and ceramide species d18:1/16:0 and d18:1/18:0 were higher in the NASH liver of both groups. Saturated sphingomyelins only declined in WT1 NASH liver. Lysophosphatidylcholine concentrations were quite normal in NASH and only one of the 12 altered phosphatidylcholine species declined in NASH liver of both groups. Very few phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol species were comparably regulated in NASH liver of both animal groups. Seven of these lipid species declined and two increased in NASH. Notably, hepatic mRNA expression of proinflammatory (F4/80, CD68, IL-6, TNF and chemerin) and profibrotic genes (TGF beta and alpha SMA) was comparable in WT1 and WT2 mice. CONCLUSIONS: Mice housed and bred in different animal facilities had comparable disease severity of NASH whereas liver lipids varied among the groups. Thus, there was no specific lipid signature for NASH in the MCD model.

Use of the guinea pig in studies on the development and prevention of acquired sensorineural hearing loss, with an emphasis on noise.

Guinea pigs have been used in diverse studies to better understand acquired hearing loss induced by noise and ototoxic drugs. The guinea pig has its best hearing at slightly higher frequencies relative to humans, but its hearing is more similar to humans than the rat or mouse. Like other rodents, it is more vulnerable to noise injury than the human or nonhuman primate models. There is a wealth of information on auditory function and vulnerability of the inner ear to diverse insults in the guinea pig. With respect to the assessment of potential otoprotective agents, guinea pigs are also docile animals that are relatively easy to dose via systemic injections or gavage. Of interest, the cochlea and the round window are easily accessible, notably for direct cochlear therapy, as in the chinchilla, making the guinea pig a most relevant and suitable model for hearing. This article reviews the use of the guinea pig in basic auditory research, provides detailed discussion of its use in studies on noise injury and other injuries leading to acquired sensorineural hearing loss, and lists some therapeutics assessed in these laboratory animal models to prevent acquired sensorineural hearing loss.

3Rs as part of preclinical neuropsychiatric translational crisis, and ARRIVE guidelines as part of solution.

OBJECTIVE: The ongoing translational and reproducibility crisis dominates preclinical research today as results from animal studies often disappoint when transferred to human clinical studies. This problem is especially relevant in the field of brain diseases and translational neuropsychiatry. METHODS: Here, we discuss if the 3R concept could be part of the translational crisis. RESULTS: The focus has been on the second R, which is to reduce the variation between the experimental animals, so that the number of animals per study can be reduced. However, the risk of obtaining false results has also increased. We, therefore, recommend that researchers use a broader perspective as also suggest by Russell and Burch who founded the 3Rs when considering the 3R concept, which involves the translational aspects described in detail in their 3R book from 1959. CONCLUSION: This may together with systematic reviews and well-designed and well-performed animal studies and accurate reporting of the results indeed contribute to solving the translational crisis in preclinical research.

Cultures of care? Animals and science in Britain.

It is becoming increasingly common to hear life scientists say that high quality life science research relies upon high quality laboratory animal care. However, the idea that animal care is a crucial part of scientific knowledge production is at odds with previous social science and historical scholarship regarding laboratory animals. How are we to understand this discrepancy? To begin to address this question, this paper seeks to disentangle the values of scientists in identifying animal care as important to the production of high quality scientific research. To do this, we conducted a survey of scientists working in the United Kingdom who use animals in their research. The survey found that being British is associated with thinking that animal care is a crucial part of conducting high quality science. To understand this finding, we draw upon the concept of 'civic epistemologies' (Jasanoff 2005; Prainsack 2006) and argue that 'animals' and 'care' in Britain may converge in taken-for-granted assumptions about what constitutes good scientific knowledge. These ideas travel through things like state regulations or the editorial policies of science journals, but do not necessarily carry the embodied civic epistemology of 'animals' and 'science' from which such modes of regulating laboratory animal welfare comes.