The scientific evidence required to make policy decisions that protect human health can be challenging to organize. Primary research is often silo-ed between different agency repositories, the pace of publication is unflagging and wide-spread interdisciplinary collaboration can be logistically difficult. Since 2012, the Organisation for Economic Co-operation and Development (OECD) adverse outcome pathway (AOP) framework has provided solutions for some of the challenges of supplying relevant and accessible scientific data for evidence-based decision-making. Development of AOPs is guided by a crowd-sourced approach in which progressions of adverse outcomes (AO) are distilled into pathways containing only the essential key events (KEs) and the causal key event relationships (KERs) that connect them. The framework has widely been adopted in the toxicology community and more recently projects have applied it to the radiation safety field. Presently, a collaborative effort aims to further expand the use of AOPs through creating a network linking exposure to the space exposome with resulting human health outcomes. The network contains four adverse non-cancer outcomes for which participants of future long-range space missions will be at risk. The work of this thesis has contributed to the construction of the space-health AOP network by accomplishing two main objectives. The first was the creation of a novel protocol for collecting a weight of evidence (WOE) that included the benefits of scoping review and artificial intelligence (AI) tools for literature screening. The scoping review WOE collection strategy was then deployed for collecting data across all four outcomes in the space-health network. The second objective was to identify KEs and KERs and summarize the WOE linking space exposure to one of the four AOs: vascular remodeling. In addition to summarizing the pathway, we have also highlighted important modulating factors and knowledge gaps in the WOE. This thesis work contributes to the future of the AOP framework by formulating a new development protocol and employing it in a novel regulatory context. Using the new protocol, this thesis has furthered biological understanding of the effects of space exposure on the cardiovascular system by collating mechanistic information across scientific disciplines to identify KEs and KERs in occurrence of vascular remodeling.

Adverse outcome pathways (AOPs) provide a framework to organize and weigh the evidence linking a toxicant’s initial interactions with molecules in the cell to adverse outcomes of regulatory concern. AOPs are constructed in modules that include key events (KEs) and key event relationships (KERs). Quantitative understanding of the KERs is critical for the development of predictive toxicological models. The objective of this project was to investigate the ability to define the quantitative associations of the KERs upstream, and contained in, an existing AOP (#296): “Oxidative DNA Damage Leading to Chromosomal Aberrations and Mutations”. The data supporting quantitative associations between these KERs was gathered through literature review and experimental methods. I first used systematic literature review tools to develop and apply a pragmatic and transparent method to search the literature for AOP evidence. A broad search, covering all of the KERs of interest, was initially conducted. This search, which retrieved more than 230 thousand articles, demonstrates the data-rich nature of the AOP. An artificial intelligence informed prioritization of the top 100 articles were then examined in detail. This approach identified 39 articles containing qualitative empirical support for the AOP, but limited quantitative evidence of the KERs. A second search was conducted to address the need for quantitative evidence as well as the lack of evidence for the KER between and increase in reactive oxygen species (ROS) and oxidative DNA damage. The second search retrieved 12 articles that could be used to define a quantitative relationship between cellular ROS and oxidative DNA damage. To begin to address gaps in quantitative understanding, I then conducted experiments in the laboratory to measure oxidative DNA damage, DNA strand breaks, chromosomal aberrations, and mutations in TK6 cells after exposure to a range of concentrations of 4-Nitroquinoline 1-oxide (4NQO: a prototype ROS producing agent). An increase in both oxidative DNA damage and DNA strand breaks was observed after 2, 4, and 6 h exposures with the high throughput comet assay (CometChip). An increase in the incidence of micronuclei was observed after a 24 h exposure to a low concentration of 4NQO, as measured with the flow cytometry micronucleus assay, while high cytotoxicity was found at higher concentrations. Lastly an increase in mutation frequency was observed with Duplex Sequencing, an error-corrected sequencing technology. Additionally, an increase in the proportion of C>A transversions was observed, consistent with the expected mutations following oxidative DNA lesions. Overall, my work contributes to the quantitative understanding of AOP #296 and this project serves as a key example of AOP-informed study design, highlighting notable challenges in characterizing quantitative relationships.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24222号 / 工博第5050号 / 新制||工||1788(附属図書館) / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 米田 稔, 教授 松井 康人, 准教授 松田 知成 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Avec les nouvelles avancées en biologie et toxicologie, on constate de plus en plus la complexité des mécanismes et le grand nombre de voies de toxicité. Les concepts de ‘biologie systémique’ (SB) et de ‘voies des effets indésirables’ (adverse outcome pathway, AOP) pourraient être des outils appropriés pour l’étude de la toxicologie à ces niveaux de complexité élevés. Le point central du travail de cette thèse est le développement d’un modèle de SB du rôle de la voie de signalisation Nrf2 dans le contrôle du stress oxydant. Pour la calibration de ce modèle avec des données expérimentales (exposition des cellules rénales RPTEC/TERT1 à différentes doses de bromate de potassium), plusieurs cycles de proposition/vérification d’hypothèses ont progressivement contribué à l’ajout de nouvelles réactions. Ces nouvelles hypothèses (par exemple : action directe du bromate de potassium sur le DCF, atténuation de la fluorescence du DCF avec le temps, etc.) devraient être confirmées par de futures expérimentations. Ce modèle de SB a été ensuite utilisé pour la quantification d’un AOP de l’insuffisance rénale chronique et comparé à deux autres approches: l’utilisation de modèles statistiques empiriques et celle d’un réseau Bayésien dynamique. Les calibrations des paramètres ont été effectuées par chaînes de Markov simulées MCMC avec le logiciel GNU MCSim avec une quantification des incertitudes associées aux prédictions. Même si la mise au point du modèle SB a été une tâche complexe, la compréhension de la biologie qu’offre ce modèle n’est pas accessible aux deux autres approches. Nous avons aussi évalué les interactions entre Nrf2 et deux autres voies de toxicité, AhR et ATF4, dans le cadre d’une analyse utilisant des données de toxico-génomique provenant de trois projets différents. Les résultats de cette dernière analyse suggèrent d’ajouter au modèle SB de Nrf2 la co-activation par AhR de plusieurs gènes (par exemple, HMOX1, SRXN1 et GCLM) ainsi que d’associer (au moins partiellement) à ce modèle la voie ATF4. Malgré leur complexité, les modèles SB constituent un investissement intéressant pour le développement de la toxicologie prédictive. / New understanding of biology shows more and more that the mechanisms that underlie toxicity are complex and involve multiple biological processes and pathways. Adverse outcome pathways (AOPs) and systems biology (SB) can be appropriate tools for studying toxicology at this level of complexity. This PhD thesis focuses on the elaboration of a SB model of the role of the Nrf2 pathway in the control of oxidative stress. The model’s calibration with experimental data (obtained with RPTEC/TERT1 renal cells exposed to various doses of potassium bromate) comprised several rounds of hypotheses stating/verification, through which new reactions were progressively added to the model. Some of these new hypotheses (e.g., direct action of potassium bromate on DCF, bleaching of DCF with time, etc.) could be confirmed by future experiments. Considered in a wider framework, this SB model was then evaluated and compared to two other computational models (i.e., an empirical dose-response statistical model and a dynamic Bayesian model) for the quantification of a ‘chronic kidney disease’ AOP. All parameter calibrations were done by MCMC simulations with the GNU MCSim software with a quantification of uncertainties associated with predictions. Even though the SB model was indeed complex to conceive, it offers insight in biology that the other approaches could not afford. In addition, using multiple toxicogenomic databases; interactions and cross-talks of the Nrf2 pathway with two other toxicity pathways (i.e., AhR and ATF4) were examined. The results of this last analysis suggest adding new AhR contribution to the control of some of the Nrf2 genes in our SB model (e.g., HMOX1, SRXN1 and GCLM), and integrating in it description of the ATF4 pathway (partially at least). Despites their complexity, precise SB models are precious investments for future developments in predictive toxicology.

Groin hernia is common, and each year 200 repairs per 100 000 adult inhabitants are performed in Sweden. Groin hernias are either inguinal or femoral (2-4%). Elective repair is not associated with an excess mortality, but adverse outcomes include recurrence and long-term pain. Emergency procedures have a 4% mortality rate with an increased risk for bowel resection and postoperative complications. The aim of this thesis was to identify risk factors for adverse outcomes and to propose measures to improve groin hernia treatment. Twenty-three per cent of female hernias were femoral. Thirty-six per cent of femoral hernias, and 5% of inguinal hernias, have emergency procedures. Females (OR 1.47) and patients above 65 years-of-age (OR 2.24) were at higher risk for emergency repair. Bowel resection was performed in 23% of emergency femoral repairs, and the 30-day mortality was 10 times that of an age- and gender-matched population. The majority of emergency patients were unaware of their hernia, and one third had previously had no groin symptoms. Femoral repairs were at larger risk for recurrence than inguinal repairs. The surgical techniques with least risk for recurrence were preperitoneal mesh repairs (open HR 0.28, and laparoscopic HR 0.31). Long-term pain was present in 24% of femoral hernia patients, of whom 5.5% described pain interfering with daily activities. The only factor predicting the risk for long-term pain was pain preoperatively. Pain decreased with time. In a randomized study on inguinal hernia, TEP resulted in less pain six weeks after surgery than Lichtenstein repair performed under local anesthesia (LLA). TEP patients were to a larger extent able to perform sporting activities. No difference was seen in intra-operative complications. Femoral hernias should be given high priority for repair and preperitoneal techniques should be used. Earlier diagnosis, in the elective setting, is probably difficult to attain. Heightened awareness in the emergency department is required. TEP is safe, and results in less pain than LLA six weeks after surgery. A widening of indications for TEP in primary inguinal hernia repair is justifiable.

Introduction: Only 3 types of coronavirus cause aggressive respiratory disease in humans (MERS-Cov, SARS-Cov-1, and SARS-Cov-2). It has been reported higher infection rates and severe manifestations (ICU admission, need for mechanical ventilation, and death) in patients with comorbidities such as diabetes mellitus (DM). For this reason, this study aimed to determine the prevalence of diabetes comorbidity and its associated unfavorable health outcomes in patients with acute respiratory syndromes for coronavirus disease according to virus types. Methods: Systematic review of literature in Pubmed/Medline, Scopus, Web of Science, Cochrane, and Scielo until April of 2020. We included cohort and cross-sectional studies with no restriction by language or geographical zone. The selection and extraction were undertaken by 2 reviewers, independently. The study quality was evaluated with Loney’s instrument and data were synthesized by random effects model meta-analysis. The heterogeneity was quantified using an I2 statistic. Funnel plot, Egger, and Begg tests were used to evaluate publication biases, and subgroups and sensitivity analyses were performed. Finally, we used the GRADE approach to assess the evidence certainty (PROSPERO: CRD42020178049). Results: We conducted the pooled analysis of 28 studies (n = 5960). The prevalence analysis according to virus type were 451.9 diabetes cases per 1000 infected patients (95% CI: 356.74-548.78; I2 = 89.71%) in MERS-Cov; 90.38 per 1000 (95% CI: 67.17-118.38) in SARS-Cov-1; and 100.42 per 1000 (95% CI: 77.85, 125.26 I2 = 67.94%) in SARS-Cov-2. The mortality rate were 36%, 6%, 10% and for MERS-Cov, SARS-Cov-1, and SARS-Cov-2, respectively. Due to the high risk of bias (75% of studies had very low quality), high heterogeneity (I2 higher than 60%), and publication bias (for MERS-Cov studies), we down rate the certainty to very low. Conclusion: The prevalence of DM in patients with acute respiratory syndrome due to coronaviruses is high, predominantly with MERS-Cov infection. The unfavorable health outcomes are frequent in this subset of patients. Well-powered and population-based studies are needed, including detailed DM clinical profile (such as glycemic control, DM complications, and treatment regimens), comorbidities, and SARS-Cov-2 evolution to reevaluate the worldwide prevalence of this comorbidity and to typify clinical phenotypes with differential risk within the subpopulation of DM patients. / Revisión por pares

Résumé : Depuis l'interdiction en 2013 des tests sur les animaux par le Règlement cosmétique n°1223/2009, différentes méthodes in vitro ont été développées. Toutefois, selon un consensus scientifique, aucune méthode ne peut couvrir à elle seule l’ensemble des événements clés (KE) définis pour la sensibilisation cutanée.Après un état de l’art des méthodes alternatives relatives à la sensibilisation cutanée, nous avons sélectionné et comparé 3 tests pour ensuite déterminer la meilleure stratégie à suivre. Dans le but de proposer un nouveau test intégré, nous avons adressé l’ensemble des KEs au sein d’un même type cellulaire. La cellule dendritique (DC) jouant un rôle clé dans le développement de la dermatite de contact allergique (DCA), notre choix s’est porté sur la lignée humaine pro-monocytaire THP-1. Nous avons étudié comme événements initiaux (KE1) les formes réactives à l’oxygène (FRO) et le glutathion (GSH), la voie Nrf2-Keap1 (voie centrale de détoxication) et l’expression génique pour le KE2, ainsi que les modifications phénotypiques pour le KE3.Nous avons montré que les allergisants forts induisent une production précoce des FRO associée à une réduction du GSH. Ils activent également la voie Nrf2-Keap1 et induisent l’expression des marqueurs de surface cellulaire CD54 et CD86, ainsi qu’une production de cytokines spécifiques (IL-8, IL-18,...).Pour conclure, ce travail a permis de proposer un test intégrant l’ensemble des mesures biologiques comme différents KE au sein d’un même type cellulaire. / Abstract : Since the animal testing ban in 2013 by Cosmetics Regulation n°1223/2009, various in vitro methods have been developed. However, according to a scientific consensus, no single method can stand-alone to cover the different key events (KE) defined for skin sensitization.After a state of the art of alternative methods relating to skin sensitization, we selected and compared 3 tests to determine the best strategy to follow. In order to propose a new integrated test, we wanted to address all KE within the same cell line. Because dendritic cell (DC) plays a key role in the development of allergic contact dermatitis (ACD), we have chosen the pro-monocytic human line THP-1. We have studied as initial events (KE1), reactive oxygen species (ROS) and glutathione (GSH), Nrf2-Keap1 pathway (central detoxification pathway) and gene expression for KE2 as well as phenotypic modifications for KE3.We have shown that strong allergens are correlated with early production of FRO associated with GSH reduction. They also activate the Nrf2-Keap1 pathway and induce the expression of CD54 and CD86 cell surface markers as well as production of specific cytokines (IL-8, IL-18, etc.).To conclude, this work propose a new assay integrating all the biological measures as different KEs within the same cell.