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

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

PROVIDER: PRJNA1013406 | ENA |

REPOSITORIES: ENA

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Hypoxic injury triggers maladaptive repair in human kidney organoids

Project description:Hypoxic injury triggers maladaptive repair in human kidney organoids

| PRJNA1013401 | ENA

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

Project description: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.

2025-08-15 | GSE242425 | GEO

Hypoxia Triggers Signatures of Maladaptive Repair in Human Kidney Organoids [bulk RNA-seq]

Project description:Hypoxia Triggers Signatures of Maladaptive Repair in Human Kidney Organoids [bulk RNA-seq]

| PRJNA990729 | ENA

Hypoxic injury triggers maladaptive repair in human kidney organoids

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-08-15 | GSE242426 | GEO

Endothelial Prolyl Hydroxylase 3 Mitigates Maladaptive Inflammation to Promote Post-Ischemic Kidney Repair

Project description:Acute kidney injury (AKI) is a major health concern and well-established risk factor for the development of chronic kidney disease (CKD). Tissue hypoxia is a prominent feature of the injured kidney that shapes the biological behavior of parenchymal and immune cells. Endothelial cells have important immunomodulatory roles, but the impact of dysregulated oxygen sensing on their responses remains poorly understood. By leveraging a combination of conditional mouse strains, single-cell analyses of mouse and human samples, and in vitro experiments, we demonstrate that the oxygen sensor PHD3 in the endothelium suppresses maladaptive inflammatory responses, thereby promoting kidney repair. Specifically, post-ischemic inactivation of endothelial PHD3, but not PHD1, leads to maladaptive kidney repair, characterized by increased fibrosis and inflammation. scRNA-seq analysis of the postischemic endothelial PHD3-haplodeficient kidney shows an endothelial IFN-γ gene signature, mirroring the responses observed in patients with severe AKI. By performing loss- and gain-of-function experiments in vitro, we demonstrate that PHD3 regulates IFN-γ responsive pro-inflammatory signatures in a HIF-dependent manner. Consistent with this, simultaneous deletion of ARNT in endothelial PHD3-deficient mice restored kidney repair. Thus, our findings provide novel mechanistic insights into endothelial oxygen sensing and the AKI-to-CKD transition, highlighting potential therapeutic avenues for mitigating disease progression.

2026-02-18 | GSE294712 | GEO

Hypoxia Triggers Signatures of Maladaptive Repair in Human Kidney Organoids [bulk RNA-seq]

Project description:Chronic kidney disease (CKD) affects over half of all adults over 70 and 13% of the global population. The development of renal fibrosis is strongly correlated with loss of kidney function during CKD and involves cellular injury, excessive production of extracellular matrix proteins and inflammation. Current treatments focus on controlling blood pressure, controlling diabetes, and steroid therapies; however, we have no treatments to suppress renal fibrosis. Because hypoxia plays a key role in the development and progression of CKD, we have developed a new model of induced pluripotent stem cell-derived kidney organoids to study in vitro the development of fibrosis in a human model.

2025-08-15 | GSE236379 | GEO

Endothelial Prolyl Hydroxylase 3 Mitigates Maladaptive Inflammation to Promote Post-Ischemic Kidney Repair

Project description:Endothelial Prolyl Hydroxylase 3 Mitigates Maladaptive Inflammation to Promote Post-Ischemic Kidney Repair

| PRJNA1251356 | ENA

Single cell RNA-seq analyses of kidney repair and how maladaptive repair leads to kidney atrophy following ischemia/reperfusion injury

Project description:Single cell RNA-seq analyses of kidney repair and how maladaptive repair leads to kidney atrophy following ischemia/reperfusion injury

| PRJNA679306 | ENA

Enhancer Regulation in Kidney Repair [RNA-seq]

Project description:The endogenous repair process of the mammalian kidney allows rapid recovery after acute kidney injury (AKI) through robust proliferation of tubular epithelial cells. There is currently limited understanding of which transcriptional regulators activate these repair programs and how transcriptional deregulation leads to maladaptive repair. Here we investigate the existence of enhancer dynamics in the regenerating mouse kidney.

2020-05-27 | GSE114293 | GEO

Enhancer Regulation in Kidney Repair [ChIP-seq]

2020-05-27 | GSE114292 | GEO