From food to physiology characterization and in vitro digestion of milk products and investigation of postprandial metabolism and inflammation after a high-fat meal intake in a human nutrition intervention study

According to the World Health Organization worldwide obesity has more than doubled since 1980. The World health statistics 2012 report shows that one in six adults is obese, one in ten diabetic and one in three has a raised blood pressure. Overweight and obesity are major risk factors for cardiovascular diseases,According to the World Health Organization worldwide obesity has more than doubled since 1980. The World health statistics 2012 report shows that one in six adults is obese, one in ten diabetic and one in three has a raised blood pressure. Overweight and obesity are major risk factors for cardiovascular diseases, diabetes and some cancers. The causes of overweight and obesity are mainly a decrease in physical activity and an increased intake of energy-dense foods leading to a positive energy balance. Not only dietary patterns play a major role in the development of obesity. Food composition also directly impacts on postprandial metabolism and inflammation and, in long term, may contribute to systemic low-grade inflammation, a characteristic associated with the obese state. Thus it is not surprising that there is a growing interest in better understanding the effect of different foods and food compounds on human metabolism and health. The aim of the NutriChip project is to develop a microfluidic chip device to screen foods and their compounds for health promoting, e.g. immune-modulatory, properties. Milk products have been chosen as a food model because their consumption has been shown to be associated with decreased levels of inflammatory markers (1), and also because technological and microbiological transformations allow the realization of various products, such as yoghurt and cheese, having potentially different physiological effects. This thesis covers the biochemical (products characterization and in vitro digestion) and physiological (human nutrition study) aspects of the NutriChip project. Initially, differently heat-treated and fermented milk products were characterized by a proteomic approach. Various fractionation methods were used for selectively enriching minor milk and bacterial proteins in different dairy products. Proteins were separated and identified by two dimensional (2D) gel-electrophoresis and liquid chromatography coupled to mass spectrometry (LC-MS/MS) analysis. All data are collected in an interactive platform, called protein atlas, which is now publicly available on http://www.foodle.ch/de/proteinstart. Currently, the database contains more than 200 different milk proteins and about 250 bacterial proteins. For a better in depth characterization of fermented products, a method for the enrichment of living bacterial cells has been developed. This method allows the investigation of bacterial proteomes under different fermentation conditions. The method was used to monitor the adaption of the yoghurt bacteria Lactobacillus bulgaricus and Streptococcus thermophilus during milk fermentation. Some well-known stress response proteins (chaperone proteins GroEL and DnaK) and various enzymes involved in the glycolysis pathway have been identified as a proof of concept. Another experiment aimed to investigate the bacterial proteome during cheese production with special regards towards the identification of enzymes involved in the formation of the cheese flavor compound 3-methylbutanal. An aminotransferase that catalyzes the first step in the conversion pathway from the amino acid leucine to the flavor compound 3-methylbutanal could be identified. A prerequisite for screening foods for health-modulating activity was the development of a static, three-step in vitro digestion model. The aim was to keep the model as physiological as possible and ideally perform the digestion on a small scale (volume < 15 mL). The digestion model has been thoroughly validated using pasteurized whole milk. The degradation of fat, carbohydrates and proteins into their basic constituents was consistent with human physiological values found in the literature. The system has been used to digest various milk products. With the two proteins α-s1-casein and β-lactoglobulin, a representative of the caseins and whey proteins, respectively, the influence of the fat content, heat treatment and fermentation of the products on their digestibility has been monitored. Particularly we also looked at the generation of bioactive peptides during the digestion process. Towards this aim, the identified peptides in the digestion experiments were compared with bioactive peptide sequences from the literature using the statistic program R. Over 50 milk protein-derived peptides containing bioactive peptide sequences, with e.g. antihypertensive, immune- and cyto-modulatory, opioid functions, could be identified. The next step in simulating the human digestive system is the intestinal transport. Therefore, a cell culture model mimicking the last step of digestion and final absorption of the nutrients, both steps being mediated by intestinal enterocytes, was established. For this aim, Caco-2 cells were used in a Transwell system with an upper and lower compartment containing cell culture medium. Digested milk products were added on top of the Caco-2 cell monolayer and medium was collected from the basolateral chamber for identification of transported, potential bioactive peptides. The final validation of the in vitro models needs the comparison with a human nutrition intervention study. We designed and conducted a dose-response intervention study to determine the caloric dose (500 kcal, 1’000 kcal, 1’500 kcal) of a high-fat meal needed to induce a postprandial metabolic and inflammatory response in normal weight and obese subjects. In our study, we investigated postprandial metabolism and inflammation by measuring classical clinical parameters such as glucose, insulin and triglycerides, as well as the inflammation markers C-reactive protein (CRP), interleukine-6 (IL-6) and endotoxin before and at various time points after the test meals consumption. Our study provided valuable clinical, mechanistic, and methodological insights into the metabolic response of subjects, varying in their metabolic health status, to increasing doses of a high-fat meal. This represents the basis for future studies aiming to investigate health-promoting properties of foods in general, as also their capability in lowering postprandial inflammation, a normal response mechanism after food ingestion. v diabetes and some cancers. The causes of overweight and obesity are mainly a decrease in physical activity and an increased intake of energy-dense foods leading to a positive energy balance. Not only dietary patterns play a major role in the development of obesity. Food composition also directly impacts on postprandial metabolism and inflammation and, in long term, may contribute to systemic low-grade inflammation, a characteristic associated with the obese state. Thus it is not surprising that there is a growing interest in better understanding the effect of different foods and food compounds on human metabolism and health. The aim of the NutriChip project is to develop a microfluidic chip device to screen foods and their compounds for health promoting, e.g. immune-modulatory, properties. Milk products have been chosen as a food model because their consumption has been shown to be associated with decreased levels of inflammatory markers (1), and also because technological and microbiological transformations allow the realization of various products, such as yoghurt and cheese, having potentially different physiological effects. This thesis covers the biochemical (products characterization and in vitro digestion) and physiological (human nutrition study) aspects of the NutriChip project. Initially, differently heat-treated and fermented milk products were characterized by a proteomic approach. Various fractionation methods were used for selectively enriching minor milk and bacterial proteins in different dairy products. Proteins were separated and identified by two dimensional (2D) gel-electrophoresis and liquid chromatography coupled to mass spectrometry (LC-MS/MS) analysis. All data are collected in an interactive platform, called protein atlas, which is now publicly available on http://www.foodle.ch/de/proteinstart. Currently, the database contains more than 200 different milk proteins and about 250 bacterial proteins. For a better in depth characterization of fermented products, a method for the enrichment of living bacterial cells has been developed. This method allows the investigation of bacterial proteomes under different fermentation conditions. The method was used to monitor the adaption of the yoghurt bacteria Lactobacillus bulgaricus and Streptococcus thermophilus during milk fermentation. Some well- known stress response proteins (chaperone proteins GroEL and DnaK) and various enzymes involved in the glycolysis pathway have been identified as a proof of concept. Another experiment aimed to investigate the bacterial proteome during cheese production with special regards towards the identification of enzymes involved in the formation of the cheese flavor compound 3-methylbutanal. An aminotransferase that catalyzes the first step in the conversion pathway from the amino acid leucine to the flavor compound 3-methylbutanal could be identified. v A prerequisite for screening foods for health-modulating activity was the development of a static, three-step in vitro digestion model. The aim was to keep the model as physiological as possible and ideally perform the digestion on a small scale (volume < 15 mL). The digestion model has been thoroughly validated using pasteurized whole milk. The degradation of fat, carbohydrates and proteins into their basic constituents was consistent with human physiological values found in the literature. The system has been used to digest various milk products. With the two proteins α-s1-casein and β-lactoglobulin, a representative of the caseins and whey proteins, respectively, the influence of the fat content, heat treatment and fermentation of the products on their digestibility has been monitored. Particularly we also looked at the generation of bioactive peptides during the digestion process. Towards this aim, the identified peptides in the digestion experiments were compared with bioactive peptide sequences from the literature using the statistic program R. Over 50 milk protein-derived peptides containing bioactive peptide sequences, with e.g. antihypertensive, immune- and cyto-modulatory, opioid functions, could be identified. The next step in simulating the human digestive system is the intestinal transport. Therefore, a cell culture model mimicking the last step of digestion and final absorption of the nutrients, both steps being mediated by intestinal enterocytes, was established. For this aim, Caco-2 cells were used in a Transwell system with an upper and lower compartment containing cell culture medium. Digested milk products were added on top of the Caco-2 cell monolayer and medium was collected from the basolateral chamber for identification of transported, potential bioactive peptides. The final validation of the in vitro models needs the comparison with a human nutrition intervention study. We designed and conducted a dose-response intervention study to determine the caloric dose (500 kcal, 1’000 kcal, 1’500 kcal) of a high-fat meal needed to induce a postprandial metabolic and inflammatory response in normal weight and obese subjects. In our study, we investigated postprandial metabolism and inflammation by measuring classical clinical parameters such as glucose, insulin and triglycerides, as well as the inflammation markers C-reactive protein (CRP), interleukine-6 (IL-6) and endotoxin before and at various time points after the test meals consumption. Our study provided valuable clinical, mechanistic, and methodological insights into the metabolic response of subjects, varying in their metabolic health status, to increasing doses of a high-fat meal. This represents the basis for future studies aiming to investigate health- promoting properties of foods in general, as also their capability in lowering postprandial inflammation, a normal response mechanism after food ingestion.

The Phosphate Specific Transport (Pst) System in Fast- and Slow-Growing Mycobacteria

Cyntia De Piano

Although mycobacteria are known to accumulate polyphosphate (PolyP), a linear polymer of orthophosphate, when subjected to stresses, the exact roles of this molecule are not yet clearly understood. We found that deletion of the pstA gene encoding for a transmembrane domain of the high-affinity phosphate-specific ABC transporter system (Pst system) resulted in accumulation of high amounts of PolyP during growth in phosphate (Pi)-replete conditions in Mycobacterium tuberculosis and Mycobacterium smegmatis. These PolyP stores were gradually used during Pi starvation by the ApstA mutants in order to sustain growth and this allowed the mutant strains to reach a higher cell density than the wild-type (WT) parental strain. Neither the mRNA nor the protein levels of polyphosphate kinase 1 (PPK1) could explain the PolyP accumulation observed in the mutant, suggesting that another regulatory mechanism is involved. The ApstA mutant of M. smegmatis was hypersensitive to several in vitro stresses, including detergent, oxidative stress, and cell wall targeting antibiotics. Deletion of the main enzyme involved in PolyP synthesis, PPK1, in the ApstA mutant background of M. smegmatis completely reversed the PolyP accumulation and partially reversed the stress sensitivity as well as the derepression of PHO regulon genes observed in the ApstA mutant. The mechanism of PolyP accumulation in M. smegmatis was investigated using a genetic approach. We found that this mechanism differs from the (p)ppGpp-mediated PolyP accumulation observed in Escherichia coli, since deletion of the RelA enzyme in a ApstA mutant background did not prevent PolyP accumulation. The mechanism of PolyP degradation during Pi starvation in the M. smegmatis ApstA mutant was also analyzed. Deletion of both polyphosphatase enzymes (PPX1 and PPX2) as well as the polyphosphate kinase 2 (PPK2) enzyme did not have any impact on PolyP degradation. PPK1 is a bifunctional enzyme that can either synthesize or degrade PolyP. Our current hypothesis is that PPK1 might perform the reverse reaction (PolyP degradation) during Pi starvation. The aim of the second part of my project was to make a comparative study of the expression and regulation of the phosphate specific transporter (pst) operon in fast-growing [M. smegmatis] and slow-growing [M. tuberculosis] mycobacteria. To achieve this goal, pst reporter strains of M. smegmatis and M. tuberculosis were constructed by precise insertion of a modified dest_gfp gene (provided by Giulia Manina) encoding a destabilized green fluorescent protein (dest_GFP) into the corresponding pst locus as transcriptional ) fusions. The transcriptional reporter construct [p) was introduced in both the WT and the ApstA mutant backgrounds. The kinetics of induction of the pst-gfp reporters in WT and ApstA mutant strains in response to Pi starvation was analyzed. Population-averaged measurements were made using qRT-PCR and Western blotting. Single-cell measurements using flow cytometry and timelapse fluorescence microscopy were also performed. For the microscopy experiments, the bacteria were cultured in custom-made microfluidic devices that permit rapid switching of the culture medium, e.g., switching between Pi-replete and Pi-depleted media. Because these studies require precise environmental control and resolution of individual and temporal phenotypes, my principal experimental tool was the integrated microfluidics and timelapse fluorescence microscopy systems that have recently been developed in the laboratory. Although there have been many studies published on the population-averaged behavior of bacteria responding to external stresses such as Pi limitation, we are not aware of any studies addressing the individuality of such responses using a real-time single-cell approach. We observed that the kinetics of induction of the Pst operon upon Pi starvation scaled with the growth rate of the bacteria and peak induction occurred within about two generations for both smegmatis and tuberculosis. Interestingly, we found that the basal level of Pst expression and the steady state level reached upon induction by Pi starvation were similar in tuberculosis and M. smegmatis, although the kinetics of induction were much faster in M. smegmatis. These studies contributed to improve the understanding of the regulation and the kinetics of response of the PHO regulon in fast- and slow-growing mycobacteria. The finding that PolyP plays a role in this process could also apply to other organisms where the PHO regulon is regulated in a similar way.

EPFL2013

NutriChip: Nutrition Analysis meets Microfluidics

Sandro Carrara, Julien Michel Ghaye, Martinus Gijs, Hamideh Jafarpoorchekab, Gözen Köklü, Christine Ruffert, Paolo Silacci, Guy Vergères

This focus article introduces the concept of NutriChip, an integrated microfluidic platform for investigating the potential of the immuno-modulatory function of dairy food. The core component of the NutriChip is a miniaturized artificial human gastrointestinal tract (GIT), which consists of a confluent layer of epithelial cells separated from a co-culture of immune cells by a permeable membrane. This setting creates conditions mimicking the human GIT and allows studying processes that characterize the passage of nutrients though the human GIT, including the activation of immune cells in response to the transfer of nutrients across the epithelial layer. The NutriChip project started by developing a biologically active in vitro cellular system in a commercial Transwell co-culture system. This Transwell system serves as a reference for the micro-scale device which is being developed. The microfluidic setup of NutriChip allows monitoring of the response of immune cells to pro-inflammatory stimuli, such as lipid polysaccharide (LPS), and to the application of potentially anti-inflammatory dairy food. This differential response will be quantified by measuring the variation in expression of pro-inflammatory cytokines, including interleukin 1 (IL-1) and interleukin 6 (IL-6), secreted by the immune cells, and this is achieved by using a dedicated optical imager. A series of dairy products will be screened for their anti-inflammatory properties using the NutriChip system and, finally, the outcome of the NutriChip will be validated by a human nutrition trial. Therefore, the NutriChip platform offers a new option to evaluate the influence of food quality on health, by monitoring the expression of relevant immune cell biomarkers.

Royal Society of Chemistry2013

The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity

Flavia Aurelia Shoko Hodel

Contemporary genomic approaches allow us to seek answers to biological questions that were previously out of reach. Genome-wide association studies (GWAS) have identified numerous genetic polymorphisms associated with human diseases, providing new insight into the genes and pathways involved in pathogenesis. The work presented in this thesis aimed to harness the power of large-scale genomics, statistical methods and bioinformatic tools to explore the interactions between persistent infections, chronic low-grade inflammation, and coronary heart disease (CHD). To achieve this, we used data collected from large population-based studies of individuals of European ancestry.To identify human genetic determinants of the humoral immune response against persistent or frequently recurring infections, with a special focus on human polyomaviruses, we performed GWAS and meta-analyses of serostatus and quantitative immunoglobulin G responses. We identified NFKB1 as a common locus associated with antibody response to multiple pathogens. For polyomaviruses, we found strong associations of HLA class II, FUT2, STING1, and MUC1 genetic variants with the intensity of the humoral response. Together, these results demonstrate the modulating contribution of host genetic variation to the individual response against some of the most prevalent human viruses.Even when they are latent, chronic infections can trigger some degree of local or systemic immune response, resulting in low-grade inflammation. In an effort to better understand the variability of humoral immune response and inflammation patterns in response to pathogen exposure, we found evidence for an association between Chlamydia trachomatis and Helicobacter pylori seropositivity, and higher plasma levels of C-reactive protein (CRP), a sensitive indicator of inflammation. High polygenic risk was also significantly associated with CRP levels, confirming that human genetic variation plays a modulating role in systemic inflammation. These results improve our understanding of the relationship between persistent infections and chronic inflammation, an important determinant of long-term morbidity in humans.Finally, we developed statistical models to explore the influences of genetic variation, persistent infections and low-grade inflammation on incident CHD. We identified high polygenic risk and Fusobacterium nucleatum infection as associated with an increased risk of developing CHD, in addition to conventional risk factors. These results confirm that CHD is a multicomponent disease that is caused by demographic, genetic and environmental factors. Moreover, they might allow for better identification of individuals at high risk for CHD and provide a rationale for future anti-infective prevention trials.Together, this research demonstrates that current genomic and serological technology, bioinformatic analysis and functional follow-up studies have the potential to provide new insight into the molecular basis of host-pathogen interactions, and their role in chronic diseases. From a translational perspective, the results of this project include new targets for diagnosis and therapeutic development, new disease biomarkers, and better predictive models. Every advance in the understanding of complex disease has the potential to improve genomic and clinical medicine, and I am pleased to have had the opportunity to act at different levels to participate in this much needed transition to precision medicine.