21 1 General Introduction of the liver, amino-acid deprivation leads to hypoalbuminemia and hepatic steatosis, while the effect on the intestine is characterized by increased barrier permeability. Both organs show a clear reduction in peroxisomal protein markers and dysfunctional mitochondria which are thought to be responsible for the hepatic steatosis and disruption of the intestinal barrier permeability. Moreover, as a proof of principle, I demonstrate how these in vitro models can be used as a pre-screening tool to test potential treatments to prevent both peroxisomal and mitochondrial loss. Fenofibrate and rapamycin are used to prevent peroxisomal loss and mitochondrial loss in the liver and the intestine respectively. In chapter 3 I make use of the opportunities offered by the embedding of my PhD project in the European Perico training network, aimed at deciphering the role of peroxisomes in cellular interaction and signaling. In this chapter one of my Perico colleagues develops and implements a deep learning computational model to measure and track organoid size and growth. Together, we apply this tool to detect and measure different types of cystic organoids in brightfield microscopy images. It can be used for a wide range of purposes in different aspects of organoid research. In order to illustrate the potential of this tool we use it to measure the size of organoids under control and amino-acid deprived conditions, and we compare the results with manually annotated data from chapter 2. Part II- Applications of the new malnutrition models In chapter 4, I study the mechanisms underlying peroxisomal loss and potential treatments to prevent such loss. To do so, I make use of the hepatic in vitro malnutrition model described in chapter 2. Together with a colleague from the pediatrics department at the UMCG I demonstrate that amino-acid deprivation in hepatic organoids is accompanied by a clear induction of the autophagic flux, which we measure using a novel autophagic probe. Furthermore, I apply this model to identify different therapeutic compounds. Finally, I show that longchain poly-unsaturated fatty acids (LCPUFA) are more effective than synthetic PPAR-α agonists and demonstrate that docosahexaenoic acid (DHA) prevents peroxisomal and mitochondrial loss during amino-acid deficiency. In chapter 5, I develop a kinetic model of the peroxisomal β-oxidation based on kinetic studies described in the literature. Doing so, I review the kinetics of the enzymes involved in the pathway. Then I use the model to predict the effects of amino acid deficiency in the pathway. For that purpose, I combine targeted proteomics data from amino-acid deprived organoids and the above-
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