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A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE231630 | GEO | 2023/05/04

REPOSITORIES: GEO

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Single-nucleus atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Project description:Kidney stone disease causes significant morbidity and increases health care utilization. In this dataset, we applied a single-nucleus assay to renal papila samples in order to charachterize the cellular and molecular niches in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.

2023-05-04 | GSE231569 | GEO

A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Project description:Kidney stone disease causes significant morbidity and increases health care utilization. The pathogenesis of stone disease is incompletely understood, due in part to the poor characterization of the cellular and molecular makeup of the human papilla and its alteration with disease. In this work, we characterize the human renal papilla in health and calcium oxalate stone disease using single nuclear RNA sequencing, spatial transcriptomics and high-resolution large scale multiplexed 3D and Co-Detection by indexing (CODEX) imaging. We define and localize subtypes of principal cells enriched in the papilla as well as immune and stromal cell populations. We further uncovered an undifferentiated epithelial cell signature in the papilla, particularly during nephrolithiasis.

2023-05-04 | GSE206306 | GEO

A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Project description:A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

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Single-nucleus atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Project description:Single-nucleus atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

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A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Project description:A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

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Kidney Stone Microbiome

Project description:Whole shotgun metagenomic sequencing from stool samples from calcium oxalate kidney stone formers and healthy control participants

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Spatially explicit analysis identifies significant potential for bioenergy with carbon capture and storage in China.

Project description:As China ramped-up coal power capacities rapidly while CO2 emissions need to decline, these capacities would turn into stranded assets. To deal with this risk, a promising option is to retrofit these capacities to co-fire with biomass and eventually upgrade to CCS operation (BECCS), but the feasibility is debated with respect to negative impacts on broader sustainability issues. Here we present a data-rich spatially explicit approach to estimate the marginal cost curve for decarbonizing the power sector in China with BECCS. We identify a potential of 222 GW of power capacities in 2836 counties generated by co-firing 0.9 Gt of biomass from the same county, with half being agricultural residues. Our spatially explicit method helps to reduce uncertainty in the economic costs and emissions of BECCS, identify the best opportunities for bioenergy and show the limitations by logistical challenges to achieve carbon neutrality in the power sector with large-scale BECCS in China.

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High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing

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

2024-01-17 | GSE227046 | GEO

A Comprehensive Immune Cell Atlas of Cystic Kidney Disease Reveals the Involvement of Adaptive Immune Cells in Injury-Mediated Cyst Progression in Mice.

Project description:BackgroundInducible disruption of cilia-related genes in adult mice results in slowly progressive cystic disease, which can be greatly accelerated by renal injury.MethodsTo identify in an unbiased manner modifier cells that may be influencing the differential rate of cyst growth in injured versus non-injured cilia mutant kidneys at a time of similar cyst severity, we generated a single-cell atlas of cystic kidney disease. We conducted RNA-seq on 79,355 cells from control mice and adult-induced conditional Ift88 mice (hereafter referred to as cilia mutant mice) that were harvested approximately 7 months post-induction or 8 weeks post 30-minute unilateral ischemia reperfusion injury.ResultsAnalyses of single-cell RNA-seq data of CD45+ immune cells revealed that adaptive immune cells differed more in cluster composition, cell proportion, and gene expression than cells of myeloid origin when comparing cystic models with one another and with non-cystic controls. Surprisingly, genetic deletion of adaptive immune cells significantly reduced injury-accelerated cystic disease but had no effect on cyst growth in non-injured cilia mutant mice, independent of the rate of cyst growth or underlying genetic mutation. Using NicheNet, we identified a list of candidate cell types and ligands that were enriched in injured cilia mutant mice compared with aged cilia mutant mice and non-cystic controls that may be responsible for the observed dependence on adaptive immune cells during injury-accelerated cystic disease.ConclusionsCollectively, these data highlight the diversity of immune cell involvement in cystic kidney disease.

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A Drosophila model identifies a critical role for zinc in mineralization for kidney stone disease.

Project description:Ectopic calcification is a driving force for a variety of diseases, including kidney stones and atherosclerosis, but initiating factors remain largely unknown. Given its importance in seemingly divergent disease processes, identifying fundamental principal actors for ectopic calcification may have broad translational significance. Here we establish a Drosophila melanogaster model for ectopic calcification by inhibiting xanthine dehydrogenase whose deficiency leads to kidney stones in humans and dogs. Micro X-ray absorption near edge spectroscopy (μXANES) synchrotron analyses revealed high enrichment of zinc in the Drosophila equivalent of kidney stones, which was also observed in human kidney stones and Randall's plaques (early calcifications seen in human kidneys thought to be the precursor for renal stones). To further test the role of zinc in driving mineralization, we inhibited zinc transporter genes in the ZnT family and observed suppression of Drosophila stone formation. Taken together, genetic, dietary, and pharmacologic interventions to lower zinc confirm a critical role for zinc in driving the process of heterogeneous nucleation that eventually leads to stone formation. Our findings open a novel perspective on the etiology of urinary stones and related diseases, which may lead to the identification of new preventive and therapeutic approaches.

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