Tuning the 3D microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease

Embedding cells in 3D environments can enhance their physiological properties and tissue architecture can be controlled using bioprinting approaches. One cellular source for in vitro reconstituted kidney tubules are directly reprogrammed induced renal tubular epithelial cells (iRECs). Here, we investigated the compatibility of iRECs with different biomaterials as self assembly or bioprinting dependent guided growth approaches. We assess cell viability, morphology, their transcriptional changes and protein expression properties. iRECs showed high viability and biocompatibility with dispensing methods and bioinks. However, the morphology of multicellular aggregates was dramatically influenced by the microenvironment. Transcriptomic analyses revealed differentially expressed gene-signatures specific to each of the used biomaterials and to bioprinted tubule-like structures. In conclusion, we find that the 3D environment elicits a strong influence on the morphology and expression profiles of iRECs that unmasks disease phenotypes and can be harnessed for and tailored to experimental demands. Combining directly reprogrammed cells with the appropriate biomaterials will facilitate optimal construction of biomimetic kidney tubule and disease models at scale. iRECs were 2D cultured and at 3 timepoints (passage p35, p48 and p53) the experiment was performed as biological replicates. Experiment: harvest 2D iRECs and prepare 2D culture, 3D cultures (in Matrigel, Collagen I and Fibrin) and bioprinted (Collagen I, Fibrin) samples, in parallel from the same pool of cells. Renal Epithelial Growth Medium (REGM) was changed 3 times per week, until harvesting for RNA extraction and sequencing at day 7 in culture. Transcriptomic data analysis was performed to detect primary influences of the four microenvironments with respect to the control (2D plates iRECs).