Biologie intégrative des réponses au stress et robustesse chez le porc

This PhD thesis is part of the SUSoSTRESS project. This ANR funded project aims at improving the knowledge about molecular and genetic mechanisms underlying inter-individual variability in stress responses. Longitudinal data were collected at several biological levels on a porcine population (Large White). This work is structured in 2 parts. The first part is built around clinical and transcriptomic longitudinal data analyses collected before and after 2 types of stress factors : ACTH and LPS injection. The aim of this contribution is to develop a functional model describing all sources of genetic variation in the HPA axis activity and in stress responses in our study population.More precisely, it aims at defining a model describing the different biological stress responses and the influence of genetic variations in order to identify the most efficient selection levers according to selection goals. This work allowed for the identification of 65 differentially expressed genes during stress responses. Among them, 8 genes were highly linked to cortisol (the main stress hormone) through NR3C1 (glucocorticoid receptor (GR)). These genes are potential biomarkers and can be communicated to breeders as selection levers for a better trade-off between production and robustness traits in farmanimals. The second part is built around the development of a statistical tool suited for the data integration of repeated omicmeasurements with a real target variable.We introduce the "multiway-SIR" approach which extends the dual-STATIS (an approach to study 3-way datasets) method to the SIR framework (a semi-parametric regression model that can be used in an exploratory way). This method is illustrated on clinical data from the ACTH experiment. It allows for the exploration of the link between clinical variable response over time and inter-individual variability in the cortisol response to an ACTH injection.Le travail de cette thèse s’inscrit dans le cadre du projet ANR SUSoSTRESS qui a pour objectif la compréhension des mécanismes moléculaires et génétiques sous-jacents à la variabilité individuelle de réponses de stress et a collecté des données longitudinales à plusieurs niveaux biologiques sur une population d’étude porcine (race Large White). La thèse est organisé en deux partie. La première partie s’articule autour de l’analyse de données cliniques et transcriptomiques collectées à plusieurs pas de temps avant et après application de deux types de stress : injection d’ACTH et de LPS. Dans cette partie, on cherche à développer d’un modèle fonctionnel permettant de décrire et d’intégrer au mieux l’ensemble des sources de variation génétique du fonctionnement de l’axe corticotrope et plus généralement des réponses de stress dans notre population d’étude. Plus précisément, il s’agit d’élaborer un modèle (au sens biologique du terme) décrivant les différentes réponses biologiques de stress et l’influence des variations génétiques (simples et en interaction), dans le but de prédire les leviers les plus efficaces en fonction de l’objectif de sélection. Ce travail a mis en évidence une liste de 65 gènes différentiellement exprimé au cours des réponses au stress, dont un ensemble de 8 gènes liés au au cortisol (l’hormone principale du stress) par NR3C1, le récepteur aux glucocorticoides. Ces gènes sont des biomarqueurs potentiels pouvant être fournis aux éleveurs en tant que leviers de sélection permettant un meilleur équilibre entre amélioration des caractères de production et des caractères de robustesse. La deuxième partie de ce travail s’articule autour du développement d’un outil d’analyse statistiques adapté à l’intégration de données ’omiques longitudinales avec une variable cible d’intérêt.Nous proposons la «multiway-SIR », qui étend la méthode dual-STATIS, une méthode d’analyse de données cubiques non supervisée, au cadre de la SIR, une méthode de régression semi-paramétrique pouvant être utilisée à des fins exploratoires. Cette méthode est appliquée sur les données cliniques de l’expérience d’ACTHet permet d’y explorer l’influence de la variabilité de la réponse du cortisol à une injection d’ACTH

Multiway SIR for biological data integration

National audienc

Multiway-SIR for longitudinal multi-table data integration

International audienceAn extension of DUAL-STATIS to the sliced-inverse regression (SIR) framework is proposed to analyze multi-table datasets with respect to a numeric variable of interest. The method is designed to analyze the case where a data set $\mathbf{X}$, which corresponds to a set of $p$ variables measured $T$ times on the same $n$ subjects is related to a real target variable $\mathbf{y}$, measured on the same $n$ subjects. The approach is an exploratory method which aims at understanding the evolution of the relation between $\mathbf{X}$ and $\mathbf{y}$ through time. The method proceeds in two steps: 1) an inter-structure analysis studies the resemblance between the different time steps by computing similarities between estimates of the covariance of the mean of $\mathbf{X}_{..t}$ conditional to $\mathbf{y}$. Similarly to SIR, the conditional expectation is estimated by slicing the range of $\mathbf{y}$. The result of this analysis is a compromise covariance matrix $\Gamma^c$, which captures a compromise correlation structure of $\mathbb{E}(\mathbf{X}_{..t}|y)$ over $t$; 2) an intra-structure analysis which is a generalized PCA of the compromise. This second step results in graphical outputs which can be used to explore the covariance structure between variables and time steps conditional to $\mathbf{y}$. The method is illustrated on a real problem related to the consequences of a low calorie diet on obese persons in which the target variable of interest is the weight gain/loss

Validity of a questionnaire measuring motives for choosing foods including sustainable concerns

Since the 1990s, sustainability of diet has become an increasingly important concern for consumers. However, there is no validated multidimensional measurement of motivation in the choice of foods including a concern for sustainability currently available. In the present study, we developed a questionnaire that measures food choice motives during purchasing, and we tested its psychometric properties. The questionnaire included 104 items divided into four predefined dimensions (environmental, health and well-being, economic and miscellaneous). It was administered to 1000 randomly selected subjects participating in the Nutrinet-Santé cohort study. Among 637 responders, one-third found the questionnaire complex or too long, while one-quarter found it difficult to fill in. Its underlying structure was determined by exploratory factor analysis and then internally validated by confirmatory factor analysis. Reliability was also assessed by internal consistency of selected dimensions and test–retest repeatability. After selecting the most relevant items, first-order analysis highlighted nine main dimensions: labeled ethics and environment, local and traditional production, taste, price, environmental limitations, health, convenience, innovation and absence of contaminants. The model demonstrated excellent internal validity (adjusted goodness of fit index = 0.97; standardized root mean square residuals = 0.07) and satisfactory reliability (internal consistency = 0.96, test–retest repeatability coefficient ranged between 0.31 and 0.68 over a mean 4-week period). This study enabled precise identification of the various dimensions in food choice motives and proposed an original, internally valid tool applicable to large populations for assessing consumer food motivation during purchasing, particularly in terms of sustainability

P001: Validation d’un questionnaire mesurant les motivations des consommateurs lors d’achats alimentaires en tenant compte de la durabilité

International audienceDepuis les années 1990, la durabilité de l’alimentation est devenue une préoccupation croissante pour les consommateurs. Cependant, il n’existe à ce jour aucun outil validé permettant de mesurer les motivations des consommateurs lors d’achat alimentaires en tenant compte de la durabilité. Nous avons par conséquent développé un questionnaire évaluant les motivations liées aux choix alimentaires lors de l’achat, et analysé ses propriétés psychométriques

Cross-cultural validity of the Intuitive Eating Scale-2. Psychometric evaluation in a sample of the general rench population

Intuitive eating is an adaptive dietary behavior that emphasizes eating in response to physiological hunger and satiety cues. The Intuitive Eating Scale-2 (IES-2) measures such attitudes and behaviors. The aim of the present study was to adapt the IES-2 to the French context and to test its psychometric properties in 335 women and 297 men participating in the NutriNet-Sante study. We evaluated the construct validity of the IES-2 by testing hypotheses with regard to its factor structure, relationships with scores of the revised 21-item Three Factor Eating Questionnaire and the Center for Epidemiologic Studies Depression scale, and differences between "a priori" relevant subgroups. First, the exploratory factor analysis revealed three main dimensions: Eating for Physical Rather than Emotional Reasons, Reliance on Hunger and Satiety Cues, and Unconditional Permission to Eat. Second-order confirmatory factor analysis upheld the 3-factor solution influenced by a broader intuitive eating dimension. IES-2 total score was negatively related to cognitive restraint (r = -031, P < 0.0001), emotional eating (r =-0.58, P < 0.0001), uncontrolled eating (r = -0.40, P < 0.0001), and depressive symptoms (r = -0.20, P <0.0001). IES-2 subscales showed similar correlations. Women had lower scores than did men for the IES-2 total scale (3.3 in women vs. 3.5 in men, P < 0.0001), Eating for Physical Reasons, and Unconditional Permission to Eat subscales. Current or former dieters had lower scores on the IES-2 total scale and on all subscales than did those who had never dieted (all P < 0.01). Finally, results showed satisfactory reliability for the IES-2 total scores (internal consistency = 0.85 and test-retest reliability = 0.79 over a mean 8-week period) and for its subscales. Thus, the French IES-2 can be considered a useful instrument for assessing adult intuitive eating behaviors in empirical and epidemiological studies in the general population

Time course of the response to ACTH in pig: biological and transcriptomic study

Background: HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have highly favored production traits such as lean growth rate, feed efficiency and prolificacy at the cost of robustness. On the hypothesis that the HPA axis could contribute to the trade-off between robustness and production traits, we have designed this experiment to explore individual variation in the biological response to the main stress hormone, cortisol, in pigs. We used ACTH injections to trigger production of cortisol in 120 juvenile Large White (LW) pigs from 28 litters and the kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data. Results: Cortisol level reached its peak 1 h after ACTH injection. White blood cell composition was modified with a decrease of lymphocytes and monocytes and an increase of granulocytes (FDR < 0.05). Basal level of cortisol was correlated with birth and weaning weights. Microarray analysis identified 65 unique genes of which expression responded to the injection of ACTH (adjusted P < 0.05). These genes were classified into 4 clusters with distinctive kinetics in response to ACTH injection. The first cluster identified genes strongly correlated to cortisol and previously reported as being regulated by glucocorticoids. In particular, DDIT4, DUSP1, FKBP5, IL7R, NFKBIA, PER1, RGS2 and RHOB were shown to be connected to each other by the glucocorticoid receptor NR3C1. Most of the differentially expressed genes that encode transcription factors have not been described yet as being important in transcription networks involved in stress response. Their co-expression may mean co-regulation and they could thus provide new patterns of biomarkers of the individual sensitivity to cortisol. Conclusions: We identified 65 genes as biological markers of HPA axis activation at the gene expression level. These genes might be candidates for a better understanding of the molecular mechanisms of the stress response

Time course study of the response to LPS targeting the pig immune gene networks

Background: Stress is a generic term used to describe non-specific responses of the body to all kinds of challenges. A very large variability in the response can be observed across individuals, depending on numerous conditioning factors like genetics, early influences and life history. As a result, there is a wide range of individual vulnerability and resilience to stress, also called robustness. The importance of robustness-related traits in breeding strategies is increasing progressively towards the production of animals with a high level of production under a wide range of climatic conditions and management systems, together with a lower environmental impact and a high level of animal welfare. The present study aims at describing blood transcriptomic, hormonal, and metabolic responses of pigs to a systemic challenge using lipopolysaccharide (LPS). The objective is to analyze the individual variation of the biological responses in relation to the activity of the HPA axis measured by the levels of plasma cortisol after LPS and ACTH in 120 juvenile Large White (LW) pigs. The kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data. Results: Cortisol level reaches its peak 4 h after LPS injection. The characteristic changes of white blood cell count to LPS were observed, with a decrease of total count, maximal at t = +4 h, and the mirror changes in the respective proportions of lymphocytes and granulocytes. The lymphocytes / granulocytes ratio was maximal at t = +1 h. An integrative statistical approach was used and provided a set of candidate genes for kinetic studies and ongoing complementary studies focused on the LPS-stimulated inflammatory response. Conclusions: The present study demonstrates the specific biomarkers indicative of an inflammation in swine. Furthermore, these stress responses persist for prolonged periods of time and at significant expression levels, making them good candidate markers for evaluating the efficacy of anti-inflammatory drugs

Additional file 4 of Time course of the response to ACTH in pig: biological and transcriptomic study

Complete list of enriched GO (Biological process (BP), Molecular function (MF) and Cellular Component (CC) for 34 genes for which L/G ratio had a significant effect ‘.xls’ file. Features the GO items, the corresponding functions, the class of ontology, the number of genes in the input list (enriching a GO and total number) and in the reference list (enriching a GO and total number), the raw and the 679 adjusted Fisher’s exact test P-value and the list of genes. (XLS 7 kb