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Podocytes are highly specialized kidney cells that are attached to the outer aspect of the glomerular capillaries and are damaged in more than 75% of patients with an impaired renal function. This specific cell type is characterized by a complex 3D morphology which is essential for proper filtration of the blood. Any changes of this unique morphology are directly associated with a deterioration of the size-selectivity of the filtration barrier. Since podocytes are postmitotic, there is no regenerative potential and the loss of these cells is permanent. Therefore, identification of small molecules that are able to protect podocytes is highly important. The aim of this work was to establish an in vivo high-content drug screening in zebrafish larvae. At first, we looked for a reliable podocyte injury model which is fast, reproducible and easy to induce. Since adriamycin is commonly used in rodents to damage podocytes, we administered it to the larvae and analyzed the phenotype by in vivo microscopy, (immuno-) histology and RT-(q)PCR. However, adriamycin did not result in a podocyte-specific injury in zebrafish larvae. Subsequently, we decided to use a genetic ablation model which specifically damages podocytes in zebrafish larvae. Treatment of transgenic zebrafish larvae with 80 µM metronidazole for 48 hours generated an injury resembling focal and segmental glomerulosclerosis which is characterized by podocyte foot process effacement, cell depletion and proteinuria. Following this, we established an in vivo high-content screening system by the use of a specific screening zebrafish strain. This screening strain expresses a circulating 78 kDa eGFP-labeled Vitamin D-binding fusion protein, which passes the filtration barrier only after glomerular injury. Therefore, we had an excellent readout to follow podocyte injury in vivo. We generated a custom image analysis software that measures the fluorescence intensity of podocytes and the vasculature automatically on a large scale. Furthermore, we screened a specific drug library consisting of 138 compounds for protective effects on larval podocytes using this in vivo high-content system. The analysis identified several initial hits and the subsequent validation experiments identified belinostat as a reliable and significant protective agent for podocytes. These results led to a patent request and belinostat is a promising candidate for a clinical use and will be tested in mammalian podocyte injury models.