- Pre-registration nursing students
- No definition of master’s degree in nursing described in the publication
After the search, we collated and uploaded all the identified records into EndNote v.X8 (Clarivate Analytics, Philadelphia, Pennsylvania) and removed any duplicates. Two independent reviewers (MCS and SA) screened the titles and abstracts for assessment in line with the inclusion criteria. They retrieved and assessed the full texts of the selected studies while applying the inclusion criteria. Any disagreements about the eligibility of studies were resolved by discussion or, if no consensus could be reached, by involving experienced researchers (MZ-S and RP).
The first reviewer (MCS) extracted data from the selected publications. For this purpose, an extraction tool developed by the authors was used. This tool comprised the following criteria: author(s), year of publication, country, research question, design, case definition, data sources, and methodologic and data-analysis triangulation. First, we extracted and summarized information about the case study design. Second, we narratively summarized the way in which the data and methodological triangulation were described. Finally, we summarized the information on within-case or cross-case analysis. This process was performed using Microsoft Excel. One reviewer (MCS) extracted data, whereas another reviewer (SA) cross-checked the data extraction, making suggestions for additions or edits. Any disagreements between the reviewers were resolved through discussion.
A total of 149 records were identified in 2 databases. We removed 20 duplicates and screened 129 reports by title and abstract. A total of 46 reports were assessed for eligibility. Through hand searches, we identified 117 additional records. Of these, we excluded 98 reports after title and abstract screening. A total of 17 reports were assessed for eligibility. From the 2 databases and the hand search, 63 reports were assessed for eligibility. Ultimately, we included 8 articles for data extraction. No further articles were included after the reference list screening of the included studies. A PRISMA flow diagram of the study selection and inclusion process is presented in Figure 1 . As shown in Tables 2 and and3, 3 , the articles included in this scoping review were published between 2010 and 2022 in Canada (n = 3), the United States (n = 2), Australia (n = 2), and Scotland (n = 1).
PRISMA flow diagram.
Characteristics of Articles Included.
Author | Contandriopoulos et al | Flinter | Hogan et al | Hungerford et al | O’Rourke | Roots and MacDonald | Schadewaldt et al | Strachan et al |
---|---|---|---|---|---|---|---|---|
Country | Canada | The United States | The United States | Australia | Canada | Canada | Australia | Scotland |
How or why research question | No information on the research question | Several how or why research questions | What and how research question | No information on the research question | Several how or why research questions | No information on the research question | What research question | What and why research questions |
Design and referenced author of methodological guidance | Six qualitative case studies Robert K. Yin | Multiple-case studies design Robert K. Yin | Multiple-case studies design Robert E. Stake | Case study design Robert K. Yin | Qualitative single-case study Robert K. Yin Robert E. Stake Sharan Merriam | Single-case study design Robert K. Yin Sharan Merriam | Multiple-case studies design Robert K. Yin Robert E. Stake | Multiple-case studies design |
Case definition | Team of health professionals (Small group) | Nurse practitioners (Individuals) | Primary care practices (Organization) | Community-based NP model of practice (Organization) | NP-led practice (Organization) | Primary care practices (Organization) | No information on case definition | Health board (Organization) |
Overview of Within-Method, Between/Across-Method, and Data-Analysis Triangulation.
Author | Contandriopoulos et al | Flinter | Hogan et al | Hungerford et al | O’Rourke | Roots and MacDonald | Schadewaldt et al | Strachan et al |
---|---|---|---|---|---|---|---|---|
Within-method triangulation (using within-method triangulation use at least 2 data-collection procedures from the same design approach) | ||||||||
: | ||||||||
Interviews | X | x | x | x | x | |||
Observations | x | x | ||||||
Public documents | x | x | x | |||||
Electronic health records | x | |||||||
Between/across-method (using both qualitative and quantitative data-collection procedures in the same study) | ||||||||
: | ||||||||
: | ||||||||
Interviews | x | x | x | |||||
Observations | x | x | ||||||
Public documents | x | x | ||||||
Electronic health records | x | |||||||
: | ||||||||
Self-assessment | x | |||||||
Service records | x | |||||||
Questionnaires | x | |||||||
Data-analysis triangulation (combination of 2 or more methods of analyzing data) | ||||||||
: | ||||||||
: | ||||||||
Deductive | x | x | x | |||||
Inductive | x | x | ||||||
Thematic | x | x | ||||||
Content | ||||||||
: | ||||||||
Descriptive analysis | x | x | x | |||||
: | ||||||||
: | ||||||||
Deductive | x | x | x | x | ||||
Inductive | x | x | ||||||
Thematic | x | |||||||
Content | x |
The following sections describe the research question, case definition, and case study design. Case studies are most appropriate when asking “how” or “why” questions. 1 According to Yin, 1 how and why questions are explanatory and lead to the use of case studies, histories, and experiments as the preferred research methods. In 1 study from Canada, eg, the following research question was presented: “How and why did stakeholders participate in the system change process that led to the introduction of the first nurse practitioner-led Clinic in Ontario?” (p7) 19 Once the research question has been formulated, the case should be defined and, subsequently, the case study design chosen. 1 In typical case studies with mixed methods, the 2 types of data are gathered concurrently in a convergent design and the results merged to examine a case and/or compare multiple cases. 10
“How” or “why” questions were found in 4 studies. 16 , 17 , 19 , 22 Two studies additionally asked “what” questions. Three studies described an exploratory approach, and 1 study presented an explanatory approach. Of these 4 studies, 3 studies chose a qualitative approach 17 , 19 , 22 and 1 opted for mixed methods with a convergent design. 16
In the remaining studies, either the research questions were not clearly stated or no “how” or “why” questions were formulated. For example, “what” questions were found in 1 study. 21 No information was provided on exploratory, descriptive, and explanatory approaches. Schadewaldt et al 21 chose mixed methods with a convergent design.
A total of 5 studies defined the case as an organizational unit. 17 , 18 - 20 , 22 Of the 8 articles, 4 reported multiple-case studies. 16 , 17 , 22 , 23 Another 2 publications involved single-case studies. 19 , 20 Moreover, 2 publications did not state the case study design explicitly.
This section describes within-method triangulation, which involves employing at least 2 data-collection procedures within the same design approach. 6 , 7 This can also be called data source triangulation. 8 Next, we present the single data-collection procedures in detail. In 5 studies, information on within-method triangulation was found. 15 , 17 - 19 , 22 Studies describing a quantitative approach and the triangulation of 2 or more quantitative data-collection procedures could not be included in this scoping review.
Five studies used qualitative data-collection procedures. Two studies combined face-to-face interviews and documents. 15 , 19 One study mixed in-depth interviews with observations, 18 and 1 study combined face-to-face interviews and documentation. 22 One study contained face-to-face interviews, observations, and documentation. 17 The combination of different qualitative data-collection procedures was used to present the case context in an authentic and complex way, to elicit the perspectives of the participants, and to obtain a holistic description and explanation of the cases under study.
All 5 studies used qualitative interviews as the primary data-collection procedure. 15 , 17 - 19 , 22 Face-to-face, in-depth, and semi-structured interviews were conducted. The topics covered in the interviews included processes in the introduction of new care services and experiences of barriers and facilitators to collaborative work in general practices. Two studies did not specify the type of interviews conducted and did not report sample questions. 15 , 18
In 2 studies, qualitative observations were carried out. 17 , 18 During the observations, the physical design of the clinical patients’ rooms and office spaces was examined. 17 Hungerford et al 18 did not explain what information was collected during the observations. In both studies, the type of observation was not specified. Observations were generally recorded as field notes.
In 3 studies, various qualitative public documents were studied. 15 , 19 , 22 These documents included role description, education curriculum, governance frameworks, websites, and newspapers with information about the implementation of the role and general practice. Only 1 study failed to specify the type of document and the collected data. 15
In 1 study, qualitative documentation was investigated. 17 This included a review of dashboards (eg, provider productivity reports or provider quality dashboards in the electronic health record) and quality performance reports (eg, practice-wide or co-management team-wide performance reports).
This section describes the between/across methods, which involve employing both qualitative and quantitative data-collection procedures in the same study. 6 , 7 This procedure can also be denoted “methodologic triangulation.” 8 Subsequently, we present the individual data-collection procedures. In 3 studies, information on between/across triangulation was found. 16 , 20 , 21
Three studies used qualitative and quantitative data-collection procedures. One study combined face-to-face interviews, documentation, and self-assessments. 16 One study employed semi-structured interviews, direct observation, documents, and service records, 20 and another study combined face-to-face interviews, non-participant observation, documents, and questionnaires. 23
All 3 studies used qualitative interviews as the primary data-collection procedure. 16 , 20 , 23 Face-to-face and semi-structured interviews were conducted. In the interviews, data were collected on the introduction of new care services and experiences of barriers to and facilitators of collaborative work in general practices.
In 2 studies, direct and non-participant qualitative observations were conducted. 20 , 23 During the observations, the interaction between health professionals or the organization and the clinical context was observed. Observations were generally recorded as field notes.
In 2 studies, various qualitative public documents were examined. 20 , 23 These documents included role description, newspapers, websites, and practice documents (eg, flyers). In the documents, information on the role implementation and role description of NPs was collected.
In 1 study, qualitative individual journals were studied. 16 These included reflective journals from NPs, who performed the role in primary health care.
Only 1 study involved quantitative service records. 20 These service records were obtained from the primary care practices and the respective health authorities. They were collected before and after the implementation of an NP role to identify changes in patients’ access to health care, the volume of patients served, and patients’ use of acute care services.
In 2 studies, quantitative questionnaires were used to gather information about the teams’ satisfaction with collaboration. 16 , 21 In 1 study, 3 validated scales were used. The scales measured experience, satisfaction, and belief in the benefits of collaboration. 21 Psychometric performance indicators of these scales were provided. However, the time points of data collection were not specified; similarly, whether the questionnaires were completed online or by hand was not mentioned. A competency self-assessment tool was used in another study. 16 The assessment comprised 70 items and included topics such as health promotion, protection, disease prevention and treatment, the NP-patient relationship, the teaching-coaching function, the professional role, managing and negotiating health care delivery systems, monitoring and ensuring the quality of health care practice, and cultural competence. Psychometric performance indicators were provided. The assessment was completed online with 2 measurement time points (pre self-assessment and post self-assessment).
This section describes data-analysis triangulation, which involves the combination of 2 or more methods of analyzing data. 6 Subsequently, we present within-case analysis and cross-case analysis.
Three studies combined qualitative and quantitative methods of analysis. 16 , 20 , 21 Two studies involved deductive and inductive qualitative analysis, and qualitative data were analyzed thematically. 20 , 21 One used deductive qualitative analysis. 16 The method of analysis was not specified in the studies. Quantitative data were analyzed using descriptive statistics in 3 studies. 16 , 20 , 23 The descriptive statistics comprised the calculation of the mean, median, and frequencies.
Two studies combined deductive and inductive qualitative analysis, 19 , 22 and 2 studies only used deductive qualitative analysis. 15 , 18 Qualitative data were analyzed thematically in 1 study, 22 and data were treated with content analysis in the other. 19 The method of analysis was not specified in the 2 studies.
In 7 studies, a within-case analysis was performed. 15 - 20 , 22 Six studies used qualitative data for the within-case analysis, and 1 study employed qualitative and quantitative data. Data were analyzed separately, consecutively, or in parallel. The themes generated from qualitative data were compared and then summarized. The individual cases were presented mostly as a narrative description. Quantitative data were integrated into the qualitative description with tables and graphs. Qualitative and quantitative data were also presented as a narrative description.
Of the multiple-case studies, 5 carried out cross-case analyses. 15 - 17 , 20 , 22 Three studies described the cross-case analysis using qualitative data. Two studies reported a combination of qualitative and quantitative data for the cross-case analysis. In each multiple-case study, the individual cases were contrasted to identify the differences and similarities between the cases. One study did not specify whether a within-case or a cross-case analysis was conducted. 23
This section describes confirmation or contradiction through qualitative and quantitative data. 1 , 4 Qualitative and quantitative data were reported separately, with little connection between them. As a result, the conclusions on neither the comparisons nor the contradictions could be clearly determined.
In 3 studies, the consistency of the results of different types of qualitative data was highlighted. 16 , 19 , 21 In particular, documentation and interviews or interviews and observations were contrasted:
Both types of data showed that NPs and general practitioners wanted to have more time in common to discuss patient cases and engage in personal exchanges. 21 In addition, the qualitative and quantitative data confirmed the individual progression of NPs from less competent to more competent. 16 One study pointed out that qualitative and quantitative data obtained similar results for the cases. 20 For example, integrating NPs improved patient access by increasing appointment availability.
Although questionnaire results indicated that NPs and general practitioners experienced high levels of collaboration and satisfaction with the collaborative relationship, the qualitative results drew a more ambivalent picture of NPs’ and general practitioners’ experiences with collaboration. 21
The studies included in this scoping review evidenced various research questions. The recommended formats (ie, how or why questions) were not applied consistently. Therefore, no case study design should be applied because the research question is the major guide for determining the research design. 2 Furthermore, case definitions and designs were applied variably. The lack of standardization is reflected in differences in the reporting of these case studies. Generally, case study research is viewed as allowing much more freedom and flexibility. 5 , 24 However, this flexibility and the lack of uniform specifications lead to confusion.
Methodologic triangulation, as described in the literature, can be somewhat confusing as it can refer to either data-collection methods or research designs. 6 , 8 For example, methodologic triangulation can allude to qualitative and quantitative methods, indicating a paradigmatic connection. Methodologic triangulation can also point to qualitative and quantitative data-collection methods, analysis, and interpretation without specific philosophical stances. 6 , 8 Regarding “data-collection methods with no philosophical stances,” we would recommend using the wording “data source triangulation” instead. Thus, the demarcation between the method and the data-collection procedures will be clearer.
Yin 1 advocated the use of multiple sources of evidence so that a case or cases can be investigated more comprehensively and accurately. Most studies included multiple data-collection procedures. Five studies employed a variety of qualitative data-collection procedures, and 3 studies used qualitative and quantitative data-collection procedures (mixed methods). In contrast, no study contained 2 or more quantitative data-collection procedures. In particular, quantitative data-collection procedures—such as validated, reliable questionnaires, scales, or assessments—were not used exhaustively. The prerequisites for using multiple data-collection procedures are availability, the knowledge and skill of the researcher, and sufficient financial funds. 1 To meet these prerequisites, research teams consisting of members with different levels of training and experience are necessary. Multidisciplinary research teams need to be aware of the strengths and weaknesses of different data sources and collection procedures. 1
When using multiple data sources and analysis methods, it is necessary to present the results in a coherent manner. Although the importance of multiple data sources and analysis has been emphasized, 1 , 5 the description of triangulation has tended to be brief. Thus, traceability of the research process is not always ensured. The sparse description of the data-analysis triangulation procedure may be due to the limited number of words in publications or the complexity involved in merging the different data sources.
Only a few concrete recommendations regarding the operationalization of the data-analysis triangulation with the qualitative data process were found. 25 A total of 3 approaches have been proposed 25 : (1) the intuitive approach, in which researchers intuitively connect information from different data sources; (2) the procedural approach, in which each comparative or contrasting step in triangulation is documented to ensure transparency and replicability; and (3) the intersubjective approach, which necessitates a group of researchers agreeing on the steps in the triangulation process. For each case study, one of these 3 approaches needs to be selected, carefully carried out, and documented. Thus, in-depth examination of the data can take place. Farmer et al 25 concluded that most researchers take the intuitive approach; therefore, triangulation is not clearly articulated. This trend is also evident in our scoping review.
Few studies in this scoping review used a combination of qualitative and quantitative analysis. However, creating a comprehensive stand-alone picture of a case from both qualitative and quantitative methods is challenging. Findings derived from different data types may not automatically coalesce into a coherent whole. 4 O’Cathain et al 26 described 3 techniques for combining the results of qualitative and quantitative methods: (1) developing a triangulation protocol; (2) following a thread by selecting a theme from 1 component and following it across the other components; and (3) developing a mixed-methods matrix.
The most detailed description of the conducting of triangulation is the triangulation protocol. The triangulation protocol takes place at the interpretation stage of the research process. 26 This protocol was developed for multiple qualitative data but can also be applied to a combination of qualitative and quantitative data. 25 , 26 It is possible to determine agreement, partial agreement, “silence,” or dissonance between the results of qualitative and quantitative data. The protocol is intended to bring together the various themes from the qualitative and quantitative results and identify overarching meta-themes. 25 , 26
The “following a thread” technique is used in the analysis stage of the research process. To begin, each data source is analyzed to identify the most important themes that need further investigation. Subsequently, the research team selects 1 theme from 1 data source and follows it up in the other data source, thereby creating a thread. The individual steps of this technique are not specified. 26 , 27
A mixed-methods matrix is used at the end of the analysis. 26 All the data collected on a defined case are examined together in 1 large matrix, paying attention to cases rather than variables or themes. In a mixed-methods matrix (eg, a table), the rows represent the cases for which both qualitative and quantitative data exist. The columns show the findings for each case. This technique allows the research team to look for congruency, surprises, and paradoxes among the findings as well as patterns across multiple cases. In our review, we identified only one of these 3 approaches in the study by Roots and MacDonald. 20 These authors mentioned that a causal network analysis was performed using a matrix. However, no further details were given, and reference was made to a later publication. We could not find this publication.
Because it focused on the implementation of NPs in primary health care, the setting of this scoping review was narrow. However, triangulation is essential for research in this area. This type of research was found to provide a good basis for understanding methodologic and data-analysis triangulation. Despite the lack of traceability in the description of the data and methodological triangulation, we believe that case studies are an appropriate design for exploring new nursing roles in existing health care systems. This is evidenced by the fact that case study research is widely used in many social science disciplines as well as in professional practice. 1 To strengthen this research method and increase the traceability in the research process, we recommend using the reporting guideline and reporting checklist by Rodgers et al. 9 This reporting checklist needs to be complemented with methodologic and data-analysis triangulation. A procedural approach needs to be followed in which each comparative step of the triangulation is documented. 25 A triangulation protocol or a mixed-methods matrix can be used for this purpose. 26 If there is a word limit in a publication, the triangulation protocol or mixed-methods matrix needs to be identified. A schematic representation of methodologic and data-analysis triangulation in case studies can be found in Figure 2 .
Schematic representation of methodologic and data-analysis triangulation in case studies (own work).
This study suffered from several limitations that must be acknowledged. Given the nature of scoping reviews, we did not analyze the evidence reported in the studies. However, 2 reviewers independently reviewed all the full-text reports with respect to the inclusion criteria. The focus on the primary care setting with NPs (master’s degree) was very narrow, and only a few studies qualified. Thus, possible important methodological aspects that would have contributed to answering the questions were omitted. Studies describing the triangulation of 2 or more quantitative data-collection procedures could not be included in this scoping review due to the inclusion and exclusion criteria.
Given the various processes described for methodologic and data-analysis triangulation, we can conclude that triangulation in case studies is poorly standardized. Consequently, the traceability of the research process is not always given. Triangulation is complicated by the confusion of terminology. To advance case study research in nursing, we encourage authors to reflect critically on methodologic and data-analysis triangulation and use existing tools, such as the triangulation protocol or mixed-methods matrix and the reporting guideline checklist by Rodgers et al, 9 to ensure more transparent reporting.
Acknowledgments.
The authors thank Simona Aeschlimann for her support during the screening process.
The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Funding: The author(s) received no financial support for the research, authorship, and/or publication of this article.
Supplemental Material: Supplemental material for this article is available online.
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Traditional risk assessment methodologies in toxicology have relied upon animal testing, despite concerns regarding interspecies consistency, reproducibility, costs, and ethics. New Approach Methodologies (NAMs), including cell culture and multi-level omics analyses, hold promise by providing mechanistic information rather than assessing organ pathology. However, NAMs face limitations, like lacking a whole organism and restricted toxicokinetic interactions. This is an inherent challenge when it comes to the use of omics data from in vitro studies for the prediction of organ toxicity in vivo. One solution in this context are comparative in vitro–in vivo studies as they allow for a more detailed assessment of the transferability of the respective NAM data. Hence, hepatotoxic and nephrotoxic pesticide active substances were tested in human cell lines and the results subsequently related to the biology underlying established effects in vivo. To this end, substances were tested in HepaRG and RPTEC/tERT1 cells at non-cytotoxic concentrations and analyzed for effects on the transcriptome and parts of the proteome using quantitative real-time PCR arrays and multiplexed microsphere-based sandwich immunoassays, respectively. Transcriptomics data were analyzed using three bioinformatics tools. Where possible, in vitro endpoints were connected to in vivo observations. Targeted protein analysis revealed various affected pathways, with generally fewer effects present in RPTEC/tERT1. The strongest transcriptional impact was observed for Chlorotoluron in HepaRG cells (increased CYP1A1 and CYP1A2 expression). A comprehensive comparison of early cellular responses with data from in vivo studies revealed that transcriptomics outperformed targeted protein analysis, correctly predicting up to 50% of in vivo effects.
Comparison of base-line and chemical-induced transcriptomic responses in heparg and rptec/tert1 cells using tempo-seq.
Avoid common mistakes on your manuscript.
Given the at times heated discussions about regulatory toxicology in the political and public domain, the quite remarkable track record of toxicological health protection sometimes tends to go unnoticed. Not only are chemical scares such as the chemically induced massive acute health impacts in the 1950ies, 60ies and 70ies a thing of the past (Herzler et al. 2021 ), but in many parts of the world, there are now regulatory frameworks in place which aim at the early identification of potential health risks from chemicals. Within Europe, the most notable in terms of impact are probably REACH (EC 2006 ) and the regulations on pesticides (EC 2009 ) both of which still overwhelmingly rely on animal data for their risk assessments. This has manifold reasons, one being the historical reliability of animal-based systems for the prediction of adversity in humans. However, there are a number of challenges to this traditional approach. These comprise capacity issues when it comes to the testing of thousands of new or hitherto untested substances, the testing of mixtures, the ever-daunting question of species specificity or the limitation of current in vivo studies regarding less accessible endpoints such as for example immunotoxicity or developmental neurotoxicity.
Over recent years, so-called New Approach Methodologies (NAMs) have thus attracted increased attention and importance for regulatory toxicology. The United States Environmental Protection Agency (US EPA 2018 ) defines NAM as ‘…a broadly descriptive reference to any technology, methodology, approach, or combination thereof that can be used to provide information on chemical hazard and risk assessment that avoids the use of intact animals… ’. One instance of an attempt to replace an animal test with an in vitro test system is the embryonic stem cell test in the area of developmental toxicology (Buesen et al. 2004 ; Seiler et al. 2006 ). This stand-alone test was first evaluated for assessing the embryotoxic potential of chemicals as early on as 2004 (Genschow et al. 2004 ). While its establishment as a regulatory prediction model took several more years, one major outcome was the realization that the use of NAMs in general is greatly improved when used as part of a biologically and toxicologically meaningful testing battery (Marx-Stoelting et al. 2009 ; Schenk et al. 2010 ). It should be noted that despite all the potential of such testing batteries a tentative one to one replacement of animal studies is neither practical nor straight forward. The reason is not only the complexity of the endpoints in question but also practical constraints. This was recently exemplified by Landsiedel et al. who pointed out that with the number of different organs and tissues tested during one sub-chronic rodent study, and assuming that 5 NAMs are needed to address the adverse outcomes in any of those organs, it would take decades just to replace this one study. Any regulatory use of NAMs should hence preferably rely on their direct use (Landsiedel et al. 2022 ).
An example from the field of hepatotoxicity testing is the in vitro toolbox for steatosis that was developed by Luckert et al. ( 2018 ) based on the adverse outcome pathway (AOP) concept by Vinken ( 2015 ). The authors employed five assays covering relevant key events from the AOP in HepaRG cells after incubation with the test substance Cyproconazole. Concomitantly, transcript and protein marker patterns for the identification of steatotic compounds were established in HepaRG cells (Lichtenstein et al. 2020 ). The findings were subsequently brought together in a proposed protocol for AOP-based analysis of liver steatosis in vitro (Karaca et al. 2023a ).
One promising use for such cell-based systems is their combination with multi-level omics. In conjunction with sufficient biological and mechanistic knowledge, the wealth of information provided by multi-omics data should potentially allow some prediction of substance-induced adversity. That said any such prediction can of course only be reliable within the established limits of such systems such as the lack of a whole organism and incomplete toxicokinetics and restrictions on adequately capturing the effects of long-term exposure (Schmeisser et al. 2023 ). Regulatory use and trust in cell-based systems will, therefore, strongly rely on how they compare to the outcome of studies based on systemic data (Schmeisser et al. 2023 ).
Pesticide active substances are a group of compounds with profound in vivo data. Some examples for active substances commonly used in PPPs are the fungicides Cyproconazole, Fluxapyroxad, Azoxystrobin and Thiabendazole, as well as the herbicide Chlorotoluron and the multi-purpose substance 2-Phenylphenol. For these compounds, several short- and long-term studies in rodents have been conducted and multiple adverse effects in target organs like liver or kidneys were observed (see Table 1 ). Liver steatosis, as one potential adverse health outcome, has been associated with triazole fungicides, such as Cyproconazole, but other active substances such as Azoxystrobin are suspected to interfere with the lipid metabolism as well (Gao et al. 2014 ; Luckert et al. 2018 ). Potential modes of action for adverse effects include the activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which has been shown for Cyproconazole and Fluxapyroxad (Marx-Stoelting et al. 2017 ; Tamura et al. 2013 ; Zahn et al. 2018 ). Notably, even when an active substance is considered to be of low acute toxicity, e.g. Chlorotoluron, Thiabendazole and 2-Phenylphenol (EC 2015 ; US EPA 2002 ; WHO 1996 ), they might still exhibit adverse chronic effects (Mizutani et al. 1990 ; WHO 1996 ). This is the reason why pesticide active substances and plant protection products (PPP) are assessed extensively before their placing on the market (EC 2009 ).
The target organs most frequently affected by pesticide active ingredients are the liver and kidneys (Nielsen et al. 2012 ). Hence, an in vitro test system aimed at the prediction of pesticide organ toxicity should be able to model effects on these two target organs. One of the best options currently available for hepatotoxicity studies in vitro is the cell line HepaRG (Ashraf et al. 2018 ). Before their use in toxicological assays, the cells undergo a differentiation process resulting in CYP-dependent activities close to the levels in primary human hepatocytes (Andersson et al. 2012 ; Hart et al. 2010 ). They also feature the capability to induce or inhibit a variety of CYP enzymes (Antherieu et al. 2010 ; Hartman et al. 2020 ) and the expression of phase II enzymes, membrane transporters and transcription factors (Aninat et al. 2006 ). Antherieu et al. ( 2012 ) demonstrated that HepaRG cells can sustain various types of chemically induced hepatotoxicity following acute and repeated exposure. Hence, HepaRG cells have the potential to replace the use of primary human hepatocytes in the study of acute and chronic effects of xenobiotics in the liver. In 2012, the European Commission Joint Research Centre’s European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM) coordinated a validation study finding differentiated HepaRG cells as a reliable and relevant tool for CYP enzyme activity studies (EURL ECVAM 2012 ). This led to the proposal of a respective draft test guideline by the OECD in 2019 (OECD 2019 ). Additionally, as part of the US EPA Tox21 project, HepaRG cells were used for an assay assessing toxicogenomics (Franzosa et al. 2021 ).
A promising test system for investigations of nephrotoxicity is the tERT1 immortalized renal proximal tubular epithelial cell line RPTEC/tERT1 (further referred to as RPTEC). These non-cancerous cells have been found to closely resemble primary counterparts showing typical morphology and functionality (Shah et al. 2017 ; Wieser et al. 2008 ). Aschauer et al. ( 2015 ) demonstrated the applicability of RPTEC for investigation of repeated-dose nephrotoxicity using a transcriptomic-based approach. Simon et al. ( 2014 ) showed similar toxicological responses of RPTEC and the target tissue to exposure to benzo[ a ]pyrene and cadmium. Conclusively, RPTEC can be a useful tool for toxicological studies.
In the present study, six pesticide active substances were analyzed in two cell lines, namely the liver cell line HepaRG and the kidney cell line RPTEC. Assays were performed following exposure to the highest non-cytotoxic concentration and comprised targeted protein and transcriptomics analysis. Triggered pathways were identified and compared with established results from in vivo experiments.
All test substances were purchased in analytical grade (purity ≥ 98.0%) from Sigma-Aldrich, Pestanal® (Taufkirchen, Germany): Cyproconazole, CAS no. 94361–06-5, catalog no. 46068, batch no. BCCD4066; Fluxapyroxad, CAS no. 907204–31-3, catalog no. 37047, batch no. BCCF6749; Azoxystrobin, CAS no. 131860–33-8, catalog no. 31697, batch no. BCCF6593; Chlorotoluron, CAS no. 15545–48-9, catalog no. 45400, batch no. BCBW1414; Thiabendazole, CAS no. 148–79-8, catalog no. 45684, batch no. BCBV5436; 2-Phenylphenol, CAS no. 90–43-7, catalog no. 45529, batch no. BCCF1784. William’s E medium, fetal calf serum (FCS) good forte (catalog no. P40-47500, batch no. P131102), recombinant human insulin and l -glutamine were acquired from PAN-Biotech GmbH (Aidenbach, Germany), FCS superior (catalog no. S0615, batch no. 0001659021) from Bio&Sell (Feucht bei Nürnberg, Germany). Dimethyl sulfoxide (DMSO, purity ≥ 99.8%), hydrocortisone-hemisuccinate (HC/HS), hydrocortisone, epidermal growth factor (EGF) and neutral red (NR) were purchased from Sigma-Aldrich (Taufkirchen, Germany). Dulbecco’s modified eagle medium (DMEM) and Ham’s F Nutrition mix were obtained from Gibco® Life Technologies (Karlsruhe, Germany), trypsin–EDTA, Penicillin–Streptomycin and insulin-transferrin-selenium from Capricorn Scientific GmbH (Ebsdorfergrund, Germany).
HepaRG cells were obtained from Biopredic International (Sant Grégoire, France) and kept in 75 cm 2 flasks under humid conditions at 37 °C and 5% CO 2 . Cells were grown in proliferation medium consisting of William’s E medium with 2 mM l -glutamine, supplemented with 10% FCS good forte, 100 U mL −1 penicillin, 100 µg mL −1 streptomycin, 0.05% human insulin and 50 µM HC/HS for 2 weeks. Then, HepaRG cells were passaged using trypsin–EDTA solution and seeded in 75 cm 2 flasks, 6-well, 12-well and 96-well plates at a density of 20 000 cells per cm 2 . Cells in cell culture dishes were maintained in proliferation medium for another 2 weeks before the medium was changed to differentiation medium (i.e., proliferation medium supplemented by 1.7% DMSO) and cells were cultured for another 2 weeks. Thereafter, cells were used in experiments within 4 weeks, while media was changed to treatment media (i.e., proliferation media supplemented by 0.5% DMSO and 2% FCS) 2 days prior to the experiments.
The RPTEC cell line was obtained from Evercyte GmbH (Vienna, Austria) and cultivated as previously described (Aschauer et al. 2013 ; Wieser et al. 2008 ). Cells were grown in a 1:1 mixture of DMEM and Ham’s F-12 Nutrient Mix, supplemented with 2.5% FCS superior, 100 U mL −1 penicillin, 100 µg mL −1 streptomycin, 2 mM l -glutamine, 36 ng mL −1 hydrocortisone, 10 ng mL −1 EGF, 5 µg mL −1 insulin, 5 µg mL −1 transferrin and 5 ng mL −1 selenium. RPTEC were cultivated in 75 cm 2 flasks until they reached near confluence. Then, cells were passaged using trypsin–EDTA and seeded at 30% density in 75 cm 2 flasks for further sub-cultivation and 6-well, 12-well and 96-well plates for experiments. To obtain complete differentiation, cells in cell culture dishes were maintained for 14 days before they were used in experiments.
All substances were dissolved in DMSO and diluted in the respective medium to a final DMSO concentration of 0.5% before incubation. HepaRG treatment medium and 0.5% DMSO in RPTEC medium served as solvent controls for HepaRG cells and RPTEC, respectively. At least 3 biological replicates, i.e., independent experiments, were performed for each assay.
Cell viability was investigated with the WST-1 assay (Immunservice, Hamburg, Germany), according to the manufacturer’s protocol and subsequent NR uptake assay according to Repetto et al. ( 2008 ). HepaRG cells and RPTEC were seeded in 96-well plates and incubated with the test substances for 72 h. Triton X-100 (0.01%, Thermo Fisher Scientific, Darmstadt, Germany) was used as positive control for reduced cell viability. At the end of the incubation period, 10 µL WST-1 solution was added to each well and incubated for 30 min at 37 °C. The tetrazolium salt WST-1 is metabolized by cellular mitochondrial dehydrogenases of living cells to a formazan derivative, the absorbance of which was measured at 450 nm with an Infinite M200 PRO plate reader (Tecan, Maennedorf, Switzerland). The reading of each well was related to the absorbance value at the reference wavelength of 620 nm, and blank values were subtracted before the relation to the solvent control.
Afterwards the NR uptake assay was performed, where incorporation of NR into lysosomes of viable cells is measured. One day prior to the assay, NR medium was prepared by diluting a 4 mg mL −1 NR stock solution in PBS 1:100 with the respective cell culture medium for HepaRG cells and RPTEC, and incubated at 37 °C over night. After the WST-1 measurement, the incubation medium was removed and cells were washed twice with PBS. Subsequently, 100 µL NR medium, previously centrifuged for 10 min at 600 × g , was added and incubated for 2 h. Afterwards, cells were washed twice with PBS, and 100 µL destaining solution (49.5:49.5:1 ethanol absolute, distilled water, glacial acetic acid) per well was added. Plates were shaken at 500 rotations min −1 for 10 min and fluorescence of NR was measured with an Infinite M200 PRO plate reader (Tecan, Maennedorf, Switzerland) at 530 nm excitation and 645 nm emission. Each reading was subtracted by the blank value and normalized to the solvent control.
Marker proteins and protein modifications were analyzed by Signatope GmbH (Tübingen, Germany) with a multiplexed microsphere-based sandwich immunoassay. Cells were seeded in 6-well plates and incubated with the test substances for 36 and 72 h. Protein extraction was performed by adding 250 µL pre-cooled extraction buffer, supplied by the company, to the cells in each well and subsequent incubation for 30 min at 4 °C. Cell lysates were transferred to 1.5 mL reaction tubes and centrifuged for 30 min at 4 °C and 15 000 × g . The supernatant was aliquoted in 60 µL batches and stored at -80 °C until shipment. After thawing, aliquots were directly used and not frozen again. Samples were analyzed for 8 proteins and protein modifications, each representing a marker for a certain form of toxicity (Table 2 ).
RT-qPCR was conducted to ensure well performing RNA for subsequent PCR profiler arrays. Cells were seeded in 12-well plates and incubated with the test substances for 36 h. RNA extraction was performed with the RNA easy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s manual. Yield RNA concentration and purity were analyzed with a Nanodrop spectrometer (NanoDrop 2000, Thermo Fischer Scientific, Darmstadt, Germany) and RNA samples were stored at -80 °C until further use. Reverse transcription to cDNA was conducted using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Waltham, MA, USA) according to the manufacturer’s protocol with a GeneAmp ® PCR System 9700 (Applied Biosystems, Darmstadt, Germany) and cDNA samples were stored at – 20 °C. RT-qPCR was performed with Maxima SYBR Green/ROX Master Mix (Thermo Fisher Scientific, Darmstadt, Germany) according to manufacturer’s protocol. In brief, 9 µL master mix, consisting of 5 µL Maxima SYBR Green/ROX qPCR Master Mix, 0.6 µL each of forward and reverse primers (2.5 µM) and 2.8 µL nuclease-free water, was added to each well of a 384-well plate. Primer sequences are shown in Online Resource 1. Subsequently, 20 ng cDNA was added to each well to a final volume of 10 µL and RT-qPCR was performed with an ABI 7900HT Fast Real-Time PCR system instrument (Applied Biosystems, Darmstadt, Germany). In brief, activation took place at 95 °C for 15 min, followed by 40 cycles of 15 s at 95 °C and 60 s at 60 °C, followed by 15 min at 60 °C and default melting curve analysis. Data were processed using 7900 software v241 and Microsoft Excel 2021. Threshold cycle (C T ) was set to 0.5, melting curve was checked and manual baseline correction was performed for each gene individually. Yield C T -values were extracted to Microsoft Excel 2021 and relative gene expression was obtained with the 2 −ΔΔCt method according to Livak and Schmittgen ( 2001 ). GUSB and HPRT1 served as endogenous control genes for HepaRG cells, GUSB and GAPDH were used for RPTEC. Primer efficiency was tested beforehand according to Schmittgen and Livak ( 2008 ). Only RNA samples showing amplification in RT-qPCR were used for further analysis with PCR profiler arrays. For quality control purposes, yield 2 −ΔΔCt values from RT-qPCR and PCR profiler arrays were compared and had to be within the same range (Online Resource 1).
For performing the PCR profiler array, cDNA was synthesized from 1 µg RNA using the RT 2 First Strand Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol with a GeneAmp® PCR System 9700 (Applied Biosystems, Darmstadt, Germany). Subsequently, the RT 2 Profiler™ PCR Array Human Molecular Toxicology Pathway Finder or Nephrotoxicity (Qiagen, Venlo, Netherlands) was conducted with RT 2 SYBR ® Green ROX qPCR Mastermix (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol. RT-qPCR was performed with an ABI 7900HT Fast Real-Time PCR system instrument (Applied Biosystems, Darmstadt, Germany), where activation of polymerase took place for 10 min at 95 °C, followed by 40 cycles of 15 s at 95 °C and 60 s at 60 °C and default melting curve analysis. Data were analyzed using 7900 software v241 and Excel 2021. C T was set to 0.2, melting curve was checked and manual baseline correction was performed. Yield C T -values were extracted and further analyzed.
Further evaluation of PCR array data was performed with functional class scoring methods such as Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as with the bioinformatics analysis and search tool Ingenuity Pathway Analysis Software (IPA). Following the manufacturer’s instructions, yield C T -values were uploaded to the Qiagen Gene Globe Webportal Footnote 1 and analyzed using the standard ΔΔC T method referring to an untreated control. A cut-off C T was set to 35, all 5 built-in housekeeping genes were manually selected as reference genes and their arithmetic mean used for normalization. Means of fold regulation and p-values were calculated and further evaluated with the bioinformatics tools following the protocol provided in Online Resource 2. The processed results from HepaRG cells and RPTEC were used as input data individually, as well as combined. For the combined analysis, duplicate genes that were present on both arrays were removed.
To generate a first overview, the percentage of differentially expressed genes (DEG) per pathway was determined as previously published (Heise et al. 2018 ). Genes were assorted to pathways as suggested on the manufacturer’s web page. Footnote 2 The percentage of DEG was calculated as number of genes whose expression significantly differed by a fold change of 2, as determined by Student’s t- test (p < 0.05), related to the total number of genes in the pathway.
The freely available web tools GOrilla Footnote 3 and ShinyGO 0.80 Footnote 4 were used for GO enrichment and KEGG analysis, respectively (Eden et al. 2007 , 2009 ; Ge et al. 2020 ). Detailed protocols are provided in Online Resource 2 together with the R code for determining DEG and background genes (see Data availability), which was adapted from Feiertag et al. ( 2023 ).
In addition to GO enrichment and KEGG analysis, further evaluation of PCR array data was performed with the bioinformatics analysis and search tool IPA (Qiagen, Hilden, Germany, analysis date: Nov. 2023) as previously published (Karaca et al. 2023b ). IPA is a commercial bioinformatics tool for analyzing RNA data, predicting pathway activation and functional interrelations using a curated pathway database. Using Fisher’s exact test, IPA identifies overrepresented pathways by measuring significant overlaps between user-provided gene lists and predefined gene sets. Means of fold regulation and p -values were uploaded to IPA following the protocol provided in Online Resource 2. Cut-off was set to – 1.5 and + 1.5 for fold regulation and 0.05 for the p -value. Fold regulation represents fold change results in a biologically meaningful way. In case the fold change is greater than 1, the fold regulation is equal to the fold change. For fold change values less than 1, the fold regulation is the negative inverse of the fold change. No further filtering was applied and an IPA core analysis was run. One Excel spread sheet per substance was obtained including all predicted diseases or functions annotations, the associated categories, the p-value of overlap as well as the number and names of the DEG found in the respective annotation (Online Resource 3). Predicted effects on other organs than the liver or the kidneys, such as heart or lungs, were discarded. For further comparison with in vivo data only the categories were used, combined with the p-value of the annotation, which was the highest.
The data obtained from targeted protein and transcriptomics analyses were compared with known in vivo observations from Draft Assessment Reports (DARs) of the pesticide active substances required for pesticide legislation. To facilitate the comparison of the data, the in vitro data was transformed into a more comprehensible form by applying evaluation matrices as shown in Table 3 .
The in vivo effects attributed to the pesticide active substances were taken from the publication by Nielsen et al. ( 2012 ). Additionally, the DARs of the two substances not reported in Nielsen et al . were analyzed and assigned accordingly. All in vivo effects identified by the authors for liver and kidneys can be found in Online Resource 1. Based on expert knowledge, descriptions of in vitro outcomes were combined with in vivo observations (see Tables 4 and 5 ).
Based on the combination of the in vitro and the in vivo data, it was possible to draw conclusions on the concordance of the predictions. In order to establish optimized thresholds for regarding an effect as in vitro positive, the analyses were performed by considering at least medium effects, strong and very strong effects, or very strong effects only (see Table 3 ) and comparing these to the corresponding in vivo effect. In case multiple in vitro predictors were connected to the same in vivo observation, a positive prediction from one was sufficient to be considered in vitro positive. For protein analyses, the comparison was performed for the data from HepaRG cells and RPTEC individually, as well as combined, where a positive prediction from one of the cell lines was considered sufficient and compared to hepatotoxic and nephrotoxic in vivo effects. For the gene transcription analysis, the categories obtained by IPA were compared to in vivo observations from DARs. A further evaluation integrating protein and transcriptional data was conducted, wherein a positive result from either data type was sufficient to classify a sample as in vitro positive. Online Resource 1 shows the combination of the results in detail. The percentage of concordance between in vitro prediction and in vivo observation was calculated. Indicative concordance was defined as percentage of in vivo positive observations that were predicted to be positive by the in vitro test system.
Statistical analysis was performed using R 4.2.1 and RStudio 2023.09.1 + 494. Data evaluation was done with Microsoft Excel 2021.
All experiments were performed in at least three independent biological replicates. Technical replicates, when applicable, were averaged and subsequently mean and standard deviation values were calculated from biological replicates. For targeted protein analysis, statistical significance was calculated with bootstrap technique using R package boot (Canty and Ripley 2016 ; Davidson and Hinkley 1997 ) to account for the high variability that results when the protein expression is affected. Data visualization was done using ggplot2 package (Wickham 2016 ). Calculation of statistical significance of altered gene transcription was performed using Student’s t -test, and R package ComplexHeatmaps was used for data visualization (Gu 2022 ). All R scripts can be found using the link provided in the Data availability section.
Each substance was tested for its effect on the viability of HepaRG cells and RPTEC. Based on these results, the highest non-cytotoxic concentration was determined and employed in further experiments together with a second concentration (i.e., 0.33 × highest non-cytotoxic concentration). For HepaRG cells, published data were used as a starting point for cytotoxicity testing and confirmed with WST-1 and NR uptake assays. The highest non-cytotoxic concentration, defined as the concentration determining a cell viability greater than 80%, is shown in Table 6 .
For RPTEC, a relatively new cell line, little data was available. At least 3 biological replicates were performed in technical triplicates to determine the highest non-cytotoxic concentrations (Table 6 ). The bar graphs in Online Resource 4 depict the concentration-dependent course of all tested concentrations per substance limited by solubility. Online Resource 1 provides a table with calculated approximations of substance concentrations in the target organ at LOAEL or NOEAL level based on in vivo toxicokinetic results from DARs. These approximations can be compared with the selected in vitro concentrations based on cytotoxicity experiments.
The result from multiplex microsphere-based sandwich immunoassays of treated HepaRG cells and RPTEC are shown in Figs. 1 and 2 , respectively. In HepaRG cells, incubation with the highest non-cytotoxic concentrations of Azoxystrobin, Chlorotoluron and Thiabendazole increased the expression of total LC3B, an indicator of autophagy, after 36 h (all three compounds) and 72 h (Chlorotoluron and Thiabendazole). Strong effects were observed on cleaved PARP, an indicator of apoptosis, after 36 h of incubation with 120 µM Cyproconazole (247 ± 147%) and 300 µM Thiabendazole (359 ± 204%). However, after 72 h incubation with 120 µM Cyproconazole, the level of cleaved PARP was strongly reduced. Expression of HIF 1-alpha, an indicator of hypoxia, was significantly increased after 36 h incubation with 45 µM Azoxystrobin (214 ± 24%). Fluxapyroxad and 2-Phenylphenol did not significantly increase the expression of any of the protein analytes.
Effects on protein abundance and protein modification of key proteins observed in HepaRG cells after 36 and 72 h of incubation with the test substances using a multiplexed microsphere-based sandwich immunoassay panel. Results are shown as means of 3 independent experiments, normalized to solvent controls. Statistical differences to the solvent control were calculated with bootstrapping (* p < 0.05)
Effects on protein abundance and protein modification of key proteins in RPTEC after 36 and 72 h of incubation with the test substances using a multiplexed microsphere-based sandwich immunoassay panel. Results are shown as means of 3 independent experiments, normalized to solvent controls. Statistical differences to the solvent control were calculated with bootstrapping (* p < 0.05)
In RPTEC, the abundance of p-elF4B, involved in eukaryotic translation initiation, was increased after 36 and 72 h incubation with 300 µM Cyproconazole (165 ± 45% and 201 ± 51%, respectively), all conditions of Fluxapyroxad, incubation with 3 µM Azoxystrobin for 36 h (166 ± 56%) and incubation with 900 µM Chlorotoluron for 36 and 72 h (238 ± 59% and 170 ± 44%, respectively). Thiabendazole exposure for 36 h resulted in an increase of cleaved PARP at both tested concentrations. Due to the high standard deviation, these results were not statistically significant.
Comparing the results from HepaRG cells and RPTEC, fewer effects were observed in RPTEC than in HepaRG cells. Effects of Azoxystrobin and Chlorotoluron on p-elF4B were observed in both cell lines, as well as increased levels of cleaved PARP after Thiabendazole exposure; yet these results were only significant in HepaRG cells. 2-Phenylphenol did not increase the expression of any of the tested proteins in either cell line, while Fluxapyroxad only affected p-elF4B in RPTEC.
A graphical representation of all data points from HepaRG and RPTEC including means and standard deviations can be found in Online Resource 4.
Changes at the protein level are often preceded by changes at the gene expression level. These were analyzed by RT 2 Profiler™ PCR arrays. Figures 3 and 4 show the results from HepaRG cells and RPTEC, respectively. The genes included in the array were assigned to certain pathways according to the information provided on the manufacturer’s web page. For data interpretation, the percentage of DEG was calculated. In HepaRG cells, most DEG were observed following the exposure to Chlorotoluron. Overall, genes categorized as CYPs and phase I were predominantly affected. Cyproconazole and Chlorotoluron exerted effects on genes associated with fatty acid metabolism (10 and 55%, respectively). Of all steatosis-associated genes, 47% were altered by Chlorotoluron. With regards to individual genes, the strongest increase was observed for CYP1A1 and CYP1A2 , both in the group of CYPs and phase I, after exposure to Chlorotoluron (479-fold and 57-fold, respectively) and Thiabendazole (330-fold and 215-fold, respectively).
Relative quantities of mRNA transcript levels observed after 36 h exposure of HepaRG cells to non-cytotoxic concentrations of the test substances using the Human Molecular Toxicology Pathway Finder RT 2 Profiler™ PCR Array. Data evaluation was performed using the 2 −∆∆ Ct method, according to Livak and Schmittgen ( 2001 ). All target genes were normalized to 5 housekeeping genes. Results are shown as mean of 3 biological replicates and statistical analysis was performed by one sample Student’s t -test (* p < 0.05)
Relative quantities of mRNA transcript levels observed after 36 h exposure of RPTEC to non-cytotoxic concentrations of the test substances using the Human Nephrotoxicity RT 2 Profiler™ PCR Array. Data evaluation was performed using the 2 −∆∆ Ct method, according to Livak and Schmittgen ( 2001 ). All target genes were normalized to 5 housekeeping genes. Results are shown as mean of 3 biological replicates and statistical analysis was performed by one sample Student’s t -test (* p < 0.05)
In RPTEC, the cluster encompassing most of the DEG was that associated with regulation of the cell cycle. Here, Cyproconazole, Fluxapyroxad, Azoxystrobin, and Chlorotoluron affected the expression of over 40% of the associated genes. Genes associated with apoptosis were altered following the exposure to all substances, particularly Cyproconazole and Chlorotoluron (47 and 37%, respectively). Cyproconazole additionally showed pronounced effects on genes encoding for extracellular matrix and tissue remodeling molecules (27 and 40%, respectively). All substances affected about 20% of all genes contained in the group of genes related to cell proliferation. Cyproconazole, Chlorotoluron and 2-Phenylphenol affected 25% of all oxidative stress-associated genes. In comparison to HepaRG cells, where CYPs and phase I was the most impacted group, in RPTEC only one of the DEG established for any of the substances belonged to the group of xenobiotic metabolism. At the level of individual genes, HMOX1, a nephrotoxicity marker, was induced over twofold after incubation with all substances, but highest for Cyproconazole (eightfold). Of all genes, the strongest induction was observed for IGFBP1 , a member of the insulin-like growth factor-binding protein family, which was increased 53-fold by incubation with Cyproconazole and over 52-fold after incubation with Chlorotoluron.
A graphical representation of all data points including means and standard deviations can be found in Online Resource 4 for HepaRG and RPTEC results.
Gene expression results were analyzed with GO enrichment and KEGG analysis. All effects obtained in the analyses can be found in Online Resource 3.
The GO enrichment analysis of HepaRG DEG from the incubation with Cyproconazole pointed at changes in secondary and xenobiotic metabolic processes , and the combined analysis additionally resulted in significant enrichment of response to estrogen . DEG modulated by the exposure to Chlorotoluron were involved in 16 ontologies including metabolic, biosynthetic, and catabolic processes , with lipid metabolic process and organic hydroxyl compound metabolic process being the most statistically supported (i.e., p-value: 9.2 × 10 –8 and 7.7 × 10 –7 , respectively). In RPTEC, nucleic acid metabolic process was the only significantly enriched GO term for Chlorotoluron, while the combined analysis revealed a total of 23. Analysis of DEG from incubation with Thiabendazole resulted, among others, in hits for xenobiotic, terpenoid, and isoprenoid metabolic process in HepaRG and combined results. Although analysis of DEG from incubation with 2-Phenylphenol did not result in significantly enriched GO terms from the HepaRG or the RPTEC data; the combined data set showed 5 enriched terms with NADP metabolic process and myeloid leukocyte migration having the lowest p-values (6.9 × 10 –4 , both).
For KEGG analysis, the HepaRG data set for Fluxapyroxad and Chlorotoluron showed enrichment of drug metabolism-cytochrome P450 , as well as taurine and hypotaurine metabolism (Fluxapyroxad) and metabolic pathways (Chlorotoluron). Thiabendazole data revealed enrichment of steroid hormone biosynthesis , metabolism of xenobiotics by cytochrome P450 and chemical carcinogenesis-DNA adducts . RPTEC data set for Azoxystrobin and Chlorotoluron showed multiple cancer-related pathways. The combined data set only resulted in few pathways: hepatocellular carcinoma for Azoxystrobin, metabolic pathways for Chlorotoluron and mineral absorption for 2-Phenylphenol. All other analyses did not result in any significant enrichment.
Gene expression data were further analyzed with the IPA software. In total 32 different categories of diseases or functions were predicted. Figure 5 shows the ten most frequently resulting categories. Liver Hyperplasia/Hyperproliferation is the only common category across all cell lines and substances. The statistical confidence of the pathway analysis was strongest for Chlorotoluron, which also induced most DEG. Comparing the three methodologies of input data, lower p-values were observed for HepaRG and combined analysis and most categories of diseases or functions were predicted by the combined analysis. Evidently, effects on the kidney were predicted from the input data from liver cells and vice versa.
Results obtained by analysis of transcriptomics data with Qiagen Ingenuity Pathway Analysis. The 10 categories most affected are represented. The x-axis shows the -log 10 value of the p-value obtained for the respective effect
In a final step, the data acquired from targeted protein and transcriptomics analyses were compared with known in vivo observations. Given that the comparison focused on aligning the responses from human cell lines with whole animal data, the analysis focused on the extent to which the omics-responses were indicative of the respective biological response in vivo (indicative concordance). To establish an optimized threshold for the evaluation of in vitro predictions, the in vitro data were transformed by applying evaluation matrices as shown in Table 3 . Based on that, activated key proteins and thus cellular functions were identified for each substance from targeted protein analyses. For the evaluation of gene transcripts, the p-values for the categories obtained by IPA were considered. Indicative concordance with known in vivo results is shown in Table 7 .
For the protein analysis, the indicative concordance ranged from 18 to 47% for the single cell lines and their combination, respectively. In contrast to the results from targeted protein analyses, the indicative concordance for the transcriptomic response was much stronger with greatest values of 55, 63 and 76% for the single cell lines and their combination, respectively. Likewise, for those cases where no effect was seen in vivo, no adverse indications were seen in vitro in 80, 91 and 78% of cases, respectively. For protein analysis, this value ranged from 78 to 86% and was 50% for the combined analysis of protein and transcriptional data. It should be noted, however, that these values decreased when the evaluation criteria were less strict (medium or strong instead of very strong).
In the present study, the pathways triggered by non-cytotoxic concentrations of six pesticide active substances were examined, employing targeted protein and transcriptomics analyses in the liver cell line HepaRG and the kidney cell line RPTEC. Utilizing evaluation matrices and prediction software tools, the observed cellular responses were interpreted and compared with outcomes from established in vivo experiments, in order to assess the relevance of our in vitro model systems in predicting the impact of pesticide exposure on human hepatic and renal cellular function. The primary emphasis of this investigation did not lie in delineating discrete effects attributable to individual substances; rather, it centered on discerning the predictive capacity of the system and serving as a case study to highlight the current challenges in the regulatory adoption of NAMs.
When targeted protein data were used to predict in vivo impacts in rodents, the best result was achieved by the combined analysis and setting the evaluation criteria to medium effects (47%). Regarding the indicative concordance based on transcriptional data, medium effects in HepaRG cells seemed the most promising resulting in a 55% match. This is notable given the systemic as well as species differences between the corresponding test systems. It also highlights that the “gold standard”, i.e., the reference standard used for comparison, is in fact not necessarily indisputable (Trevethan 2017 ). Various studies pointed at the shortcomings of traditional animal studies, such as interspecies concordance, poor reproducibility and unsatisfactory extrapolation to humans (Goodman 2018 ; Karmaus et al. 2022 ; Luijten et al. 2020 ; Ly Pham et al. 2020; Smirnova et al. 2018 ; Wang and Gray 2015 ). One example illustrating the difficulties in extrapolating data from rodents to humans is the question whether Cyproconazole causes neoplasms in the liver. Here, animal studies with CD-1 mice showed statistically significant positive trends for hepatocellular adenomas and combined tumors in male mice (EFSA 2010 ; Hester et al. 2012 ). Ensuing studies identified CAR activation by Cyproconazole as the underlying Mode of Action (MoA) (Peffer et al. 2007 ). Marx-Stoelting et al. ( 2017 ) investigated effects of Cyproconazole in mice with humanized CAR and PXR and demonstrated increased sensitivity of rodents to CAR agonist-induced effects, compared to humanized mice. In line with these observations the Joint FAO/WHO Meeting on Pesticide Residues (JMPR) concluded that Cyproconazole is unlikely to pose a carcinogenic risk to humans (JMPR 2010 ). Likewise, Cyproconazole was not considered to cause neoplasms in the liver when analyzed for this study. However, such detailed analysis of a substance’s MoA is scarce.
Another important factor impeding the comparison of in vitro and in vivo data are the different ontologies. The need for harmonized ontologies and reporting formats of in vivo data has been expressed by many researchers in the field of in silico toxicology and has been addressed in multiple projects (Hardy et al. 2012 ; Sanz et al. 2017 ). For example, uncertainty arises as to the reason if and why an effect for a particular organ is possibly not reported. Depending on the case and study in question, this might be because absent effects were simply not explicitly reported as negative, or because other organ toxicities occurred at lower doses and hence data for the remaining organs were omitted or not assessed, or because the focus of the study was another organ (Smirnova et al. 2018 ). While this does not pose a problem for when such studies are used for risk assessment, it does affect the comparison with in vitro results. Another major obstacle is the retrospective conclusive combination of large and comprehensive sets of mechanistic data in vitro with systemic and histopathological observations in vivo. This issue has recently been picked up by on-going European ONTOX project Footnote 5 (“ontology-driven and artificial intelligence-based repeated dose toxicity testing of chemicals for next generation risk assessment “) and has led the consortium to reverse the strategy and build NAMs to predict systemic repeated dose toxicity effects to enable human risk assessment when combined with exposure assessment (Vinken et al. 2021 ). A recent publication by Jiang et al. ( 2023 ) as part of the ONTOX project identified transcriptomic signatures of drug-induced intrahepatic cholestasis with potential future use as prediction model. However, not all pathologies have been analyzed so far, and those that have were often only studied for a limited number of chemicals, limiting their transferability. Hence, this study relied on the use of computational tools such as IPA, GO enrichment and KEGG analysis, to draw functional conclusions from transcriptomics data. While IPA results in categorized diseases or functions annotations, KEGG and GO analyses display enriched ontologies. Therefore, while KEGG and GO results were too ambiguous to be related to distinct in vivo observations, it was feasible to combine IPA results with in vivo observations. It is noteworthy that even though GO enrichment and KEGG analysis seem fairly similar, the results varied widely between the predictions from the various software tools. Soh et al. ( 2010 ) analyzed consistency, comprehensiveness, and compatibility of pathway databases and made several crucial findings such as the inconsistency of associated genes across different databases pertaining to the same biological pathway. Furthermore, common biological pathways shared across different databases were frequently labeled with names that provided limited indication of their interrelationships. Chen et al. ( 2023 ) demonstrated that using the same gene list with different analysis methods may result in non-concordant overrepresented, enriched or perturbed pathways. Taken together, these considerations may explain the divergent findings from the different transcriptomics analyses in the present study. Additionally, these findings underscore the challenges associated with integrating pathway data from diverse sources and emphasize the need for standardized and cohesive representation of biological pathways in databases.
Compared to the transcriptomic data, protein analyses from HepaRG cells and RPTEC cells resulted in a comparatively low indicative concordance. This challenges the notion that protein analysis may be superior in prediction (Wu et al. 2023 ). One likely explanation is that proteins often reflect molecular functions and adverse effects more accurately, and diseases frequently involve dysregulated post-translational modifications, which are challenging to detect and may be poorly correlated with mRNA levels (Kannaiyan and Mahadevan 2018 ; Kelly et al. 2010 ; Zhao et al. 2020 ). However, due to the relatively low number of protein markers as compared to the number of mRNA markers, the targeted transcriptomics analysis is associated with a higher likelihood of finding a match. In the gene transcription analysis with ensuing IPA evaluation, 370 genes were analysed for HepaRG. In contrast, the protein analysis conducted in this study focussed on 8 proteins or modifications, each indicative of a particular cellular function, that were analysed at two time points after incubation of cells with two concentrations of the test substances. Consequently, a cellular response to a stressor over time can be observed, such as the different levels of cleaved PARP after 36 h and 72 h of incubation with Cyproconazole in HepaRG cells. While elevated levels of this apoptosis indicator were noted after 36 h, reduced levels were observed after 72 h. Possible explanations for this include a cellular feedback mechanism or an advanced stage of apoptosis.
Another central observation is that combination of cell lines and methods significantly increases indicative concordance (up to 88%). In the case of targeted protein analysis, combination of results led to an overall value of 47%, compared to approximately 20% for each cell line. Similar trends were observed for transcriptomic data with 76% indicative concordance for combined results, albeit decreasing the cases where an in vivo negative effect corresponded to no adverse indication seen in vitro , as the total number of positive in vitro effects was increased. Nonetheless, the idea that including omics data in regulatory process will unreasonably increase positive findings and lead to overprotectiveness can be challenged as strengthening the evaluation criteria lead to a reversion of this trend. The shortcomings of stand-alone in vitro tests to replace animal experiments have long been known. For example, single tests do not cover all possible outcomes of interest or all modes of action possibly causing a toxicological effect (Hartung et al. 2013 ; Rovida et al. 2015 ). In the present study, reported in vivo effects such as lesions of biliary epithelium or inflammation of the liver may not be fully represented by a single hepatic cell line. Hence, regulatory toxicologists strive to implement so-called integrated testing strategies (ITS) (Caloni et al. 2022 ). Results from projects in the fields of embryonic, developmental and reproductive, or acute oral toxicity have shown that test batteries increase the predictive value over individual assays (Piersma et al. 2013 ; Prieto et al. 2013 ; Sogorb et al. 2014 ). To share these novel methodologies in ITS for safety evaluations in the regulatory context, the OECD Integrated Approaches for Testing and Assessment (IATA) Case Studies Project offers a platform where comprehensive information on case studies, such as consideration documents capturing learnings and lessons from the review experience, can be found. Footnote 6
While this publication’s scope did not extend to establishing a conclusive ITS for liver and kidney toxicity, it serves as a valuable starting point for future analyses in this direction and offers ongoing assistance and insights. Moving forward, it could prove beneficial when exploring testing protocols that integrate protein and transcriptomics analyses, enhancing the comprehensiveness of safety evaluations in this domain.
The data sets generated during the current study are available in the Jochum-et-al-2024 GitHub repository, https://github.com/KristinaJochum/Jochum-et-al-2024 .
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Department of Pesticides Safety, German Federal Institute for Risk Assessment, Berlin, Germany
Kristina Jochum, Andrea Miccoli, Tewes Tralau & Philip Marx-Stoelting
Institute for Marine Biological Resources and Biotechnology (IRBIM), National Research Council, Ancona, Italy
Andrea Miccoli
Signatope GmbH, Tübingen, Germany
Cornelia Sommersdorf & Oliver Poetz
NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
Oliver Poetz
Department of Food Safety, German Federal Institute for Risk Assessment, Berlin, Germany
Andrea Miccoli & Albert Braeuning
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Conceptualization: Oliver Poetz, Albert Braeuning, Philip Marx-Stoelting, Tewes Tralau; methodology: Kristina Jochum, Philip Marx-Stoelting, Oliver Poetz; formal analysis and investigation: Kristina Jochum, Andrea Miccoli, Cornelia Sommersdorf; writing—original draft preparation: Kristina Jochum, Philip Marx-Stoelting; writing—review and editing: Andrea Miccoli, Cornelia Sommersdorf, Oliver Poetz, Albert Braeuning, Tewes Tralau, Philip Marx-Stoelting; funding acquisition: Tewes Tralau, Philip Marx-Stoelting; resources: Tewes Tralau, Philip Marx-Stoelting, Oliver Poetz.
Correspondence to Philip Marx-Stoelting .
Conflict of interest.
Oliver Poetz is a shareholder of SIGNATOPE GmbH. Cornelia Sommersdorf is an employee at SIGNATOPE GmbH. SIGNATOPE offers assay development and service using immunoassay technology.
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Jochum, K., Miccoli, A., Sommersdorf, C. et al. Comparative case study on NAMs: towards enhancing specific target organ toxicity analysis. Arch Toxicol (2024). https://doi.org/10.1007/s00204-024-03839-7
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Received : 03 July 2024
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Published : 29 August 2024
DOI : https://doi.org/10.1007/s00204-024-03839-7
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A critique of a case analysis must first delineate the details of the case study for readability and clarity. This includes all of the factual data produced by the original case study, such as the dates the study was conducted, significant statistical data and the impact of variables. The case overview may also need to address whether the case ...
A case study analysis requires you to investigate a business problem, examine the alternative solutions, and propose the most effective solution using supporting evidence. Preparing the Case. Before you begin writing, follow these guidelines to help you prepare and understand the case study: Read and Examine the Case Thoroughly
Case study is a method of in-depth research and rigorous inquiry; case analysis is a reliable method of teaching and learning. A case study is a modality of research that investigates a phenomenon for the purpose of creating new knowledge, solving a problem, or testing a hypothesis using empirical evidence derived from the case being studied.
Defnition: A case study is a research method that involves an in-depth examination and analysis of a particular phenomenon or case, such as an individual, organization, community, event, or situation. It is a qualitative research approach that aims to provide a detailed and comprehensive understanding of the case being studied.
Case study protocol is a formal document capturing the entire set of procedures involved in the collection of empirical material . It extends direction to researchers for gathering evidences, empirical material analysis, and case study reporting . This section includes a step-by-step guide that is used for the execution of the actual study.
A case study is a detailed study of a specific subject, such as a person, group, place, event, organization, or phenomenon. Case studies are commonly used in social, educational, clinical, and business research. ... Case studies tend to focus on qualitative data using methods such as interviews, observations, and analysis of primary and ...
A case study research paper examines a person, place, event, condition, phenomenon, or other type of subject of analysis in order to extrapolate key themes and results that help predict future trends, illuminate previously hidden issues that can be applied to practice, and/or provide a means for understanding an important research problem with greater clarity.
A case study is one of the most commonly used methodologies of social research. This article attempts to look into the various dimensions of a case study research strategy, the different epistemological strands which determine the particular case study type and approach adopted in the field, discusses the factors which can enhance the effectiveness of a case study research, and the debate ...
The purpose of case study research is twofold: (1) to provide descriptive information and (2) to suggest theoretical relevance. Rich description enables an in-depth or sharpened understanding of the case. It is unique given one characteristic: case studies draw from more than one data source. Case studies are inherently multimodal or mixed ...
What the Case Study Method Really Teaches. Summary. It's been 100 years since Harvard Business School began using the case study method. Beyond teaching specific subject matter, the case study ...
A Case study is: An in-depth research design that primarily uses a qualitative methodology but sometimes includes quantitative methodology. Used to examine an identifiable problem confirmed through research. Used to investigate an individual, group of people, organization, or event. Used to mostly answer "how" and "why" questions.
Step 4: Analyze Your Findings. Using the information in steps 2 and 3, create an evaluation for this portion of your case study analysis. Compare the strengths and weaknesses within the company to the external threats and opportunities. Determine if the company is in a strong competitive position, and decide if it can continue at its current ...
In case study research, the unit of analysis can be an individual, a group, an organization, a decision, an event, or even a time period. It's crucial to clearly define the unit of analysis, as it shapes the qualitative data analysis process by allowing the researcher to analyze a particular case and synthesize analysis across multiple case ...
A case study is a research approach that is used to generate an in-depth, multi-faceted understanding of a complex issue in its real-life context. It is an established research design that is used extensively in a wide variety of disciplines, particularly in the social sciences. A case study can be defined in a variety of ways (Table 5 ), the ...
Definitions of qualitative case study research. Case study research is an investigation and analysis of a single or collective case, intended to capture the complexity of the object of study (Stake, 1995).Qualitative case study research, as described by Stake (), draws together "naturalistic, holistic, ethnographic, phenomenological, and biographic research methods" in a bricoleur design ...
Case Study Analysis is a widely used research method that examines in-depth information about a particular individual, group, organization, or event. It is a comprehensive investigative approach that aims to understand the intricacies and complexities of the subject under study. Through the analysis of real-life scenarios and inquiry into ...
Drafting the Case. A draft of your analysis should include these sections: Introduction. Identify the key problems and issues in the case study. • Formulate and include a thesis statement, summarizing the outcome of your analysis in 1â€"2 sentences. Background. Set the scene: background information, relevant facts, and the most ...
A case study analysis is a typical assignment in business management courses. The task aims to show high school and college students how to analyze a current situation, determine what problems exist, and develop the best possible strategy to achieve the desired outcome.
1. Examine and describe the business environment relevant to the case study. Describe the nature of the organization under consideration and its competitors. Provide general information about the market and customer base. Indicate any significant changes in the business environment or any new endeavors upon which the business is embarking. 2.
10 steps to develop a case study. Creating a comprehensive case study involves a systematic process of investigation, analysis, and presentation. Below are the key steps to follow when developing a case study: 1. Define the objective. The first step in developing a case study is to clearly define its objective. What are you trying to achieve ...
Case-study methodology is a common and appropriate research tool used in studies of sustainability in higher education. We argue that the decision to publish case studies for a broad audience suggests that others have something to learn from the case study. Therefore, the study should provide a critical analysis of practice and
Give students an opportunity to practice the case analysis methodology via an ungraded sample case study. Designate groups of five to seven students to discuss the case and the six steps in breakout sessions (in class or via Zoom). Ensure case analyses are weighted heavily as a grading component. We suggest 30-50 percent of the overall course ...
How to write a critique. Before you start writing, it is important to have a thorough understanding of the work that will be critiqued. Study the work under discussion. Make notes on key parts of the work. Develop an understanding of the main argument or purpose being expressed in the work. Consider how the work relates to a broader issue or ...
In 7 studies, a within-case analysis was performed. 15-20,22 Six studies used qualitative data for the within-case analysis, and 1 study employed qualitative and quantitative data. Data were analyzed separately, consecutively, or in parallel. The themes generated from qualitative data were compared and then summarized.
Traffic analysis tools include methodologies such as sketch planning, travel demand modeling, traffic signal optimization, and traffic simulation. The purpose of this addendum is to give the reader a summary of real-world case studies that demonstrate the benefits of using traffic analysis tools for the project.
Presented here are three patients who have a common chief complaint. All three cases have discussions on presentation, the differential diagnosis, and management that collectively serve as a Review article. Following the three cases, an expert weighs in in a short commentary with 5 questions for CME credit.A 14-year-old boy presents to the emergency department after developing an acute ...
PDF | On Feb 1, 2004, Kim E. Walker and others published Case studies, make-your-case studies, and case stories: A critique of case-study methodology in sustainability in higher education | Find ...
3.2. Analysis of the Compression Strength of Soil in the Unconsolidated Layer. ... China, was selected for the case study in this paper to investigate the surface subsidence laws and validate the results from numerical modeling analyses. Based on the field data, the thickness of the unconsolidated layer is in the range 644.8 to 655 m with an ...
This paper presents an artificial classification and atomic energy correlation analysis of the chemical components. The choice of data mining is due to its robustness, which can explore intrinsic or hidden relationships between chemical components and their properties. The Mendeleev table is conceivably the earliest example of the data analysis technique in materials science.
In the case of targeted protein analysis, combination of results led to an overall value of 47%, compared to approximately 20% for each cell line. ... Case Studies Project offers a platform where comprehensive information on case studies, such as consideration documents capturing learnings and lessons from the review experience, can be found. ...