Network-Based Selection of Candidate Markers and Assays to Assess the Impact of Oral Immune Interventions on Gut Functions

To assess the safety and efficacy of oral immune interventions, it is important and required by regulation to assess the impact of those interventions not only on the immune system, but also on other organs such as the gut as the porte d'entrée. Despite clear indications that the immune system interacts with several physiological functions of the gut, it is still unknown which pathways and molecules are crucial to assessing the impact of nutritional immune interventions on gut functioning. Here we used a network-based systems biology approach to clarify the molecular relationships between immune system and gut functioning and to identify crucial biomarkers to assess effects on gut functions upon nutritional immune interventions. First, the different gut functionalities were categorized based on literature and EFSA guidance documents. Moreover, an overview of the current assays and methods to measure gut function was generated. Secondly, gut-function related biological processes and adverse events were selected and subsequently linked to the physiological functions of the GI tract. Thirdly, database terms and annotations from the Gene ontology database and the Comparative Toxicogenomics Database (CTD) related to the previously selected gut-function related processes were selected. Next, database terms and annotations were used to identify the pathways and genes involved in those gut functionalities. In parallel, information from CTD was used to identify immune disease related genes. The resulting lists of both gut and immune function genes showed an overlap of 753 genes out of 1,296 gut-function related genes indicating the close gut-immune relationship. Using bioinformatics enrichment tools DAVID and Panther, the identified gut-immune markers were predicted to be involved in motility, barrier function, the digestion and absorption of vitamins and fat, regulation of the digestive system and gastric acid, and protection from injurious or allergenic material. Concluding, here we provide a promising systems biology approach to identify genes that help to clarify the relationships between immune system and gut functioning, with the aim to identify candidate biomarkers to monitor nutritional immune intervention assays for safety and efficacy in the general population. This knowledge helps to optimize future study designs to predict effects of nutritional immune intervention on gut functionalities.