Abstract

Thesis summary: Traditional approaches investigate the linear effect of high-fat over-consumption on transcriptomic data. However, many biological processes occur in a nonlinear fashion. The objective of this PhD thesis is to study the response types of dietary fat mediated differentially expressed genes (i.e., linear response; nonlinear response: logarithmic, exponential, quadratic and cubic) along the longitudinal axis of the small intestine. The main goal is to assess the presence of: (1) gene-specific response type, which refers to genes that preserve the same response pattern in the whole small intestine; (2) section-specific response type, which explains how particular genes behave in different ways according to the intestinal section where they are expressed. This thesis presents two genome-wide transcriptome analyses that quantified the effects of two dietary lipid interventions in different sections of the small intestine of C57BL/6J mice. The first study includes the analysis of transcriptomic data collected from three sections of the small intestine (i.e., proximal, middle and distal). Data were collected after four weeks of dietary intervention during which mice were fed with various levels of fat (i.e., fat providing 10%, 20%, 30% or 45% kcal out of the total energy intake). Different intestinal sections were expected to exhibit regionalized functionality and display unique digestive and absorptive capacity. The goal was investigating linear and nonlinear (i.e., logarithmic, exponential, quadratic or cubic) transcriptomic responses as a continuous function of dietary fat intake along the longitudinal axis of small intestine. Middle section was the most responsive to dietary fat, and the majority of the genes showed linear response to fat intake. The highest relative importance of logarithmic (saturated) and exponential (unsaturated) response was in the proximal and in the distal section, respectively. Such pattern is coherent with the progressive absorption that occurs along the longitudinal axis of small intestine, with the hypothesis that when the absorptive capacity of the intestinal epithelia is overloaded the remaining fat will overflow to more distal sections. Processes related to inflammation responded in a gene-specific, linear way in the whole small intestine (mostly with up-regulated genes). Cholesterol transport and efflux exhibited section-specific response (i.e., genes were down-regulated with linear and exponential response in the proximal and middle intestine, respectively). The second analysis was performed on transcriptomic data collected from ten sections of the small intestine. The intervention lasted two weeks and mice were fed with three types of diets (i.e., high-fat, low-fat or chow). Three types of transcriptomic responses (i.e., linear, logarithmic or quadratic) to dietary fat were tested. Dietary fat triggered the over-expression of processes related to metabolism and transport of lipids while the processes related to carbohydrate metabolism were down-regulated. Transport and metabolic processes of lipids were significantly associated to logarithmic and linear response, respectively. Middle and distal sections were the most sensitive to fat whereas the proximal section was not responsive to diet (this is due to the prevalence of digestive functions in the proximal small intestine). Considering the complex physiology of small intestine and the influence of environmental effects such as diet and microbiota, nonlinear modelling of transcriptomic response to fat intake can provide a promising new avenue for research in molecular nutrition. The approach of studying nonlinear gene expression as a continuous function of fat intake allows the dynamic characterization of small intestine functioning. It can be used to illustrate the metabolic capacity of the small intestine or the presence of tipping points beyond which the relationship between fat intake and gene expression either weakens (logarithmic response) or strengthens (exponential response). Illustrating characteristic patterns of the gene- and section-specific response to dietary fat along the longitudinal axis of small intestine can contribute to better understand the relationships linking lipid intake to the development of obesity.