Hypoxic injury triggers maladaptive repair in human kidney organoids [scRNA-seq]

Reduction in blood supply to the kidneys occurs to certain extent during acute kidney injury (AKI). Individuals who suffered AKI are at risk of developing chronic kidney disease (CKD) through a maladaptive repair process. Currently, the lack of a reliable research model that allows the characterization of the maladaptive regeneration during such transition, impedes the development of effective therapies. Here, we present the first human kidney organoid model that physiologically and morphologically resembles the AKI and the maladaptive regeneration. Kidney organoids were generated from human induced pluripotent stem cells. After 18 days of grow the organoids were under hypoxic conditions for 2 days to simulate AKI. Organoids were collected at day 20 to assess hypoxic injury, and after a 5-day recovery in normoxic conditions to assess maladaptive repair. The transcriptome, proteome and metabolome were profiled. Gene expression analysis of day 20 hypoxic organoids identified signatures of injury, cell death (necroptosis and ferroptosis), cell cycle arrest and changes in metabolism. The maladaptive repair phenotype was supported by enrichment of pathways associated with inflammatory signals, oxidative stress, and tissue remodelling. Specific genes associated with kidney injury and disease such as GDF15, MMP7, ICAM1, TGFB1, CCN1, C3 and S100A8/9 were upregulated. Single-cell RNA sequencing localized expression of maladaptive repair genes and activation of TNF and JAK-STAT signalling pathways specific to tubular epithelial cells. Dysregulation in metabolic pathways such as glycolysis and gluconeogenesis, amino acid and lipid metabolisms were conserved in this model. Altogether, these results support the use of kidney organoids as a model of AKI and early CKD that can be used for biomarker validation, elucidation of pathological mechanisms, and drug screening. The objective of this study involved evaluating the capacity of human iPSC-derived organoids to model the transition from AKI to CKD, including maladaptive repair. Hypoxia is involved in the pathophysiology of both AKI and CKD, here, we take a holistic approach and analyzed the transcriptome, proteome, and metabolome of organoids cultured under transient hypoxia, with findings validated against patients and animal models. We used three different cell lines to demonstrate reproducibility in different genetic backgrounds. We then used a single cell line as a representative for further investigation. All the experiments were performed using at least three replicates to demonstrate biological reproducibility. We performed quality controls for every differentiation and randomly assigned kidney organoids for experiment and control groups.