Trajectory-resolved human kidney organoid model defines OPFR developmental toxicity linked to adult CKD
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE329346 | GEO | 2026/05/05
REPOSITORIES: GEO
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Project description:Introduction: Low birthweight is a risk factor for chronic kidney disease (CKD), in part due to an associated low nephron number, but the mechanisms leading to increased risk are not well understood. Low birthweight and growth restriction can be modeled in mice using gestational low protein (LP). Using this model, here we sought to 1) identify a potential window for therapeutic intervention to prevent future CKD in LP animals, 2) understand the transcriptional impact of LP on adult kidneys, and 3) clarify the mechanistic connection between low nephron endowment and predisposition to disease in LP animals. We hypothesized that gestational LP-induced growth restriction would lead to shorter nephrogenesis and altered gene expression in adulthood. Methods: At the initiation of pregnancy, CD-1 dams received a normal protein (NP, 18%) or LP (8%) diet. Offspring were euthanized on postnatal days (PN) 2-7 (n=2-7/day). Kidneys were stained with Periodic acid–Schiff (PAS). Immunofluorescence was used to assess SIX2 (progenitor cells), JAG1 (nascent nephron patterning), and LEF1 (Wnt signaling). At 6 weeks, mice underwent transdermal glomerular filtration rate (GFR) measurement. Ex vivo kidneys underwent histologic evaluation, bulk RNA sequencing, and cationic ferritin- enhanced MRI to quantify glomerular number (Nglom). Results: LP mice had protracted nephrogenesis extending to PN5-6, compared to NP mice that had completed nephrogenesis by PN3-5. Adult LP mice had fewer glomeruli, and LP males had lower GFR and more ATG compared to NP males. LP mice did not have evidence of glomerular hypertrophy. In LP males, the following genes were downregulated: Gfr1, Pax8, Fgf10, Dvl1, and Aldh1a1. Foxd1, Hif1an, Egln3, and Fzd7 were upregulated in the LP males. LP females exhibited upregulation of Etv5 and Osr2 and downregulation of Gata3, Mgp, and Trpv6 with no overlap of dysregulated genes between the sexes. Conclusions: LP offspring exhibit prolonged nephrogenesis and a reduced nephron endowment in adulthood. In males, this is characterized by a suppressed retinoic acid–GDNF–Wnt axis, while both sexes show persistent dysregulation of developmental genes. Together, these findings identify the late gestational and early postnatal periods as critical therapeutic windows. Targeting these molecular pathways during active nephrogenesis may offer a strategy to mitigate the programmed risk of CKD in growth-restricted offspring.
2026-03-03 | GSE320330 | GEO
Project description:Nephron endowment is determined by the self-renewal and induction of a nephron progenitor pool established at the onset of kidney development. In the mouse, the related transcriptional regulators Six1 and Six2 play non-overlapping roles in nephron progenitors. Transient Six1 activity prefigures, and is essential for, active nephrogenesis. In contrast, Six2 maintains later progenitor self-renewal from the onset of nephrogenesis. We compared Six2’s regulatory actions in mouse and human nephron progenitors by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Surprisingly, SIX1 was identified as a SIX2 target unique to the human nephron progenitors. Further, RNA-seq and immunostaining revealed overlapping SIX1 and SIX2 progenitor activity in the 16 week human fetal kidney. Human SIX1 ChIP-seq revealed a similar set of targets to SIX2, and predicted both factors bind DNA through an identical recognition site. In contrast to the mouse where Six2 binds its own enhancers but doesn’t interact with DNA around Six1, both human SIX1 and SIX2 bind homologous SIX2 enhancers and putative enhancers positioned around SIX1. Transgenic analysis of a putative human SIX1 enhancer in the mouse revealed a transient, mouse-like, pre-nephrogenic, Six1 regulatory pattern. Together, these data demonstrate a divergence in SIX-factor regulation between mouse and human nephron progenitors. In the human, an auto/cross-regulatory loop drives continued SIX1 and SIX2 expression during active nephrogenesis. In contrast, the mouse establishes only an auto-regulatory Six2 loop. It is tempting to speculate that differential SIX-factor regulation may contribute to species differences in the duration of progenitor programs and nephron output.
2016-01-31 | GSE73866 | GEO
Project description:Nephron endowment is determined by the self-renewal and induction of a nephron progenitor pool established at the onset of kidney development. In the mouse, the related transcriptional regulators Six1 and Six2 play non-overlapping roles in nephron progenitors. Transient Six1 activity prefigures, and is essential for, active nephrogenesis. In contrast, Six2 maintains later progenitor self-renewal from the onset of nephrogenesis. We compared Six2’s regulatory actions in mouse and human nephron progenitors by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Surprisingly, SIX1 was identified as a SIX2 target unique to the human nephron progenitors. Further, RNA-seq and immunostaining revealed overlapping SIX1 and SIX2 progenitor activity in the 16 week human fetal kidney. Human SIX1 ChIP-seq revealed a similar set of targets to SIX2, and predicted both factors bind DNA through an identical recognition site. In contrast to the mouse where Six2 binds its own enhancers but doesn’t interact with DNA around Six1, both human SIX1 and SIX2 bind homologous SIX2 enhancers and putative enhancers positioned around SIX1. Transgenic analysis of a putative human SIX1 enhancer in the mouse revealed a transient, mouse-like, pre-nephrogenic, Six1 regulatory pattern. Together, these data demonstrate a divergence in SIX-factor regulation between mouse and human nephron progenitors. In the human, an auto/cross-regulatory loop drives continued SIX1 and SIX2 expression during active nephrogenesis. In contrast, the mouse establishes only an auto-regulatory Six2 loop. It is tempting to speculate that differential SIX-factor regulation may contribute to species differences in the duration of progenitor programs and nephron output.
2016-01-31 | GSE73865 | GEO
Project description:When assembling a nephron during development a multipotent stem cell pool becomes restricted as differentiation ensues. A faulty differentiation arrest in this process leads to transformation and initiation of a Wilms' tumor. Mapping these transitions with respective surface markers affords accessibility to specific cell subpopulations. NCAM1 and CD133 have been previously suggested to mark human renal progenitor populations. Herein, using cell sorting, RNA sequencing, in vitro studies with serum-free media and in vivo xenotransplantation we demonstrate a sequential map that links human kidney development and tumorigenesis; In nephrogenesis, NCAM1+CD133- marks SIX2+ multipotent renal stem cells transiting to NCAM1+CD133+ differentiating segment-specific SIX2- epithelial progenitors and NCAM1-CD133+ differentiated nephron cells. In tumorigenesis, NCAM1+CD133- marks SIX2+ blastema that includes the ALDH1+ WT cancer stem/initiating cells, while NCAM1+CD133+ and NCAM1-CD133+ specifying early and late epithelial differentiation, are severely restricted in tumor initiation capacity and tumor self-renewal. Thus, negative selection for CD133 is required for defining NCAM1+ nephron stem cells in normal and malignant nephrogenesis. Human fetal kidney mRNA profiles of 3 cell populations (NCAM1+/CD133-, NCAM+/CD133+, NCAM-/CD133+) were generated by deep sequencing using Illumina HiSeq.
2016-04-01 | E-GEOD-78502 | biostudies-arrayexpress
Project description:Human pluripotent stem cell-derived organoids are models for human development and disease. We report a modified human kidney organoid system that generates thousands of similar kidney organoids, each consisting of 1 to 2 nephron-like structures. Single-cell transcriptomic profiling and immunofluorescence validation highlighted patterned nephron-like structures, utilizing similar pathways, with distinct morphogenesis, to human nephrogenesis. To examine this platform for therapeutic screening, the polycystic kidney disease genes PKD1 and PKD2 were inactivated by gene-editing. PKD1 and PKD2 mutant models exhibited efficient and reproducible cyst formation. Cystic outgrowths could be propagated for months to centimeter-sized cysts. To shed new light on cystogenesis, 247 protein kinase inhibitors (PKI) were screened in a live imaging assay identifying novel compounds blocking cyst formation but not overall organoid growth. Scaling and further development of the organoid platform will enable a broader capability for kidney disease modeling and high-throughput drug screens.
2022-06-23 | GSE164564 | GEO
Project description:Maternal ketosis during pregnancy can impact fetal development, yet its effects on kidney development are not well understood. This study investigates the impact of maternal ketosis on offspring nephrogenesis using two mouse models: a ketogenic diet and β-hydroxybutyrate supplementation. Pregnant mice were subjected to either intervention from conception until birth. Offspring kidneys were analyzed at birth and in adulthood for nephron number, glomerular density, and renal function. Nephron progenitor cells (NPCs) were isolated from embryonic kidneys and analyzed using RNA sequencing, immunostaining, and quantitative PCR. Both ketosis models resulted in significantly reduced glomerular density at birth and a 25% decrease in nephron number in adult offspring, accompanied by impaired renal function. RNA sequencing revealed over 1,000 differentially expressed genes in the ketogenic diet group and 164 in the β-hydroxybutyrate group, with 67 overlapping genes. Pathway analysis showed downregulation of cell cycle and Myc target pathways, and upregulation of inflammatory pathways in both models. Immunostaining confirmed a 40% reduction in NPC proliferation and decreased c-Myc expression under ketotic conditions. Additionally, ketosis increased TNFα expression and activated the NFκB pathway in NPCs. These findings provide the first evidence linking maternal ketosis to impaired nephrogenesis, demonstrating a negative impact on offspring kidney development by altering NPC proliferation, Myc signaling, and inflammatory responses. This study highlights potential risks associated with ketogenic diets or other ketosis-inducing conditions during pregnancy.
2024-11-10 | GSE274301 | GEO
Project description:Early human kidney development is poorly documented due to tissue inaccessibility and a lack of genetic tractability. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study the nephron lineage in a human context. We confirm the presence of a SIX2+ population in early kidney organoids with a transcriptional profile akin to human fetal nephron progenitors. Using lineage-tracing analyses, we show that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. Labeling of SIX2+ cells at various time-points during organoid differentiation revealed a markedly reduced capacity for these cells to contribute to nephron formation over time. This suggests human kidney organoids lack a true nephron progenitor niche, as the developing kidney does in vivo, capable of both self-renewal and ongoing nephrogeneis. Nonetheless, human iPSC-derived kidney tissue maintains previously identified lineage relationships, which supports the utility of in vitro organoid models for interrogating the molecular and cellular basis of early human development.
2019-03-12 | GSE119561 | GEO
Project description:Human pluripotent stem cell-derived kidney organoids replicate embryonic nephrogenesis in a 3D-culture system. Recent advances suggest that refining the culture environment to replicate spatiotemporal cues present during embryonic organogenesis improves patterning. Here, this paradigm was applied to FGF signalling, a key regulator of embryonic nephron progenitor maintenance, nephrogenesis and ureteric branching. Both FGF8b and FGF10 signalling is sufficient to support nephrogenesis, with each having distinct effects on nephron patterning. FGF10 enhanced the initial WT1+ mesenchymal population, leading to proximally biased nephrons, while FGF8b biased toward early distal patterning, leading to the formation of cells with connecting segment identity. The addition of both FGF8b and FGF10 together had an additive effect, leading to a balance of proximal and distal patterning. This differential patterning was retained in tissue transplanted under the murine renal capsule, with FGF8b-treated organoids displaying increased distal/connecting segments. These findings highlight plasticity during organoid nephrogenesis that can be modulated by FGF signalling and identify an approach to refine nephrogenesis toward key cell types.
2025-06-12 | GSE299104 | GEO
Project description:Preterm neonates are at high risk for nephron loss under adverse clinical conditions (e.g., cardiocirculatory decompensation, nephrotoxic drugs). Importantly, the onset of renal damage potentially collides with the proceeding nephrogenesis of prematurity prior 36 weeks of gestation. Recent animal studies suggest that early nephron loss within this vulnerable phase is associated with more severe glomerular and tubulointerstitial alterations later in life, irrespective of the occurrence of arterial hypertension. It is known that nephrogenic pathways are reactivated after acute kidney injury supporting renal repair and regeneration. In this study we hypothesized that nephron loss during nephrogenesis leads to an alteration of the kidney developmental program which in turn impairs homeostasis and repair and thus aggravates kidney injury later in life. Preterm infants prior to 36 weeks of gestation show an active nephrogenesis after birth. In rats, nephrogenesis is still active until day 10 of life. Mimicking the human situation of acute nephron loss in preterm neonates with ongoing nephrogenesis, rats were uninephrectomized at day 1 of life (UNXd1). A second group of animals was uninephrectomized at day 14 of life (UNXd14), which resembles a nephron loss after terminated nephrogenesis. Age-matched control groups were sham operated. Three days after uninephrectomy the animals were sacrificed. Transcriptional renal changes were analyzed by RNAseqencing, followed by in silico functional pathway analysis. In UNXd1 animals 1182 genes were differentially regulated compared to the respective control group. The functional groups “renal development” and “kidney injury” were among the most differentially regulated groups and revealed distinctive alterations in UNXd1 animals. Reduced expression levels of candidate genes concerning renal development (Bmp7, Gdnf, Pdgf-B, Wt1) and kidney injury (nephrin, podocin, Tgf-β1) were detected in the kidney of UNXd1 animals. The downregulation of Bmp7 and Gdnf expression in the remaining kidney of UNXd1 animals persisted until day 28 of life. In UNXd14 rats Six2 was upregulated and Pax22 downregulated compared to controls. We conclude that neonatal nephron loss during active nephrogenesis affects renal development and induces persistently reduced expression levels of genes which in turn might hinder tissue repair after kidney injury later in life.
2021-06-09 | GSE176395 | GEO
Project description:Preterm birth-affecting ~10% of live births globally-is associated with a markedly increased lifetime risk of chronic kidney disease (CKD), reportedly up to fivefold higher than in term births. Yet, the mechanisms linking prematurity to impaired renal development remain incompletely understood. Here, we investigated how preterm birth influences nephron endowment, kidney function, and the trajectory of kidney injury in a mifepristone-induced mouse model. We compared renal structure and function between preterm and term-born mice at postnatal day (P) 30 and P180, quantifying nephron number, glomerular morphology, and injury markers. We also performed bulk RNA sequencing on sorted nephron progenitor cells (NPCs) and non-NPC fractions from post-conception (PC) days 19.5–21.5, spanning the final window of nephrogenesis. Preterm mice exhibited up to 17% fewer nephrons at P30 (p < 0.01) and a ~25% lower kidney-to-body-weight ratio at P30 and P180 (both p < 0.05), despite a ~40% increase in body weight by P180. Injury biomarkers were elevated at P30 and P180, with serum creatinine increased by ~50%, NGAL by ~35%, urinary albumin excretion approximately doubled (p < 0.001), and KIM-1 elevated in preterm versus term controls. Glomerular density at P180 was reduced by ~30% in preterm mice; glomeruli were disproportionately localized in the medulla, and increased Bowman’s space area and capsule ratios suggested filtration defects. Transcriptomic profiling around the time of preterm birth revealed acute induction of cellular stress pathways and transiently impaired NPC differentiation that resolved within 24 hours. Concomitantly, we observed a short-lived increase in NPC proliferation and an approximate 24-hour extension of nephrogenesis, consistent with a compensatory response to bolster nephron formation and indicating a potential therapeutic window. In summary, preterm birth perturbs NPC developmental timing and stress responses, leading to reduced nephron endowment and persistent susceptibility to kidney injury.
2026-04-17 | GSE316576 | GEO