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

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

PROVIDER: PRJNA849988 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19696058_1.fastq.gz	Fastqsanger.gz
	SRR19696058_2.fastq.gz	Fastqsanger.gz
	SRR19696059_1.fastq.gz	Fastqsanger.gz
	SRR19696059_2.fastq.gz	Fastqsanger.gz
	SRR19696060_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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

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

| PRJNA966977 | ENA

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

| PRJNA967196 | ENA

Gene expression profile difference among renal location in a stone former

Project description:Comparison between renal papilla tissue with and without the presence of calcified Randall’s plaques, and between the papilla, medulla, and cortex regions from within a single recurrent stone forming kidney demonstrated that patterns of gene expression between the papilla, medulla, and cortex that distinguished these three regions from one another. Disease and function analysis of these gene sets demonstrated up-regulation of genes related to urinary/renal disorders, granulocyte response, vascular smooth muscle cell proliferation, dehydration, and renal calcification and down-regulation of genes related to carboxylic acid/ lipid/ fatty acid transport and urine osmolality.

2018-07-11 | GSE116860 | GEO

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

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

2023-05-04 | GSE231630 | GEO

Kidney Stone Induces Developmental Stage-specific Alterations in Gene Expression

Project description:OBJECTIVES: Kidney stone diseases are common in premature infants, but the underlying molecular and cellular mechanisms are not fully defined. We carried out a prospective observational study using microarray analysis to identify factors that may be crucial for the initiation and progression of stone-induced injury in the developing mouse kidney. METHODS: Mice with adenine phosphoribosyltransferase (Aprt) deficiency develop 2,8-dihydroxyadenine (DHA) nephrolithiasis. Gene expression changes between Aprt-/- and Aprt+/+ kidneys from newborn and adult mice were compared using Affymetrix gene chips. RESULTS: We observed that: (i) gene expression changes induced by Aprt deficiency are developmental stage-specific; (ii) maturation-related gene expression changes are delayed in developing Aprt-/- kidneys; and (iii) immature Aprt-deficient kidneys contain large numbers of intercalated cells blocked from terminal differentiation. CONCLUSIONS: This study presents a comprehensive picture of the transcriptional changes induced by stone injury in the developing mouse kidney. Our findings help explain growth impairment in kidneys subject to injury during the early stages of development. Total RNA were extracted from kidneys of 12 newly born and 6 adult mice (half Aprt-/- and half control). Gene expression changes between Aprt-/- and Aprt+/+ kidneys from newborn and adult mice were compared using Affymetrix gene chips.

2010-01-13 | E-GEOD-18160 | biostudies-arrayexpress

Kidney Stone Induces Developmental Stage-specific Alterations in Gene Expression

2010-01-13 | GSE18160 | GEO

Kidney Stone Microbiome

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

| PRJEB39576 | ENA

Oxidative modifications of urinary proteins increase kidney stone risk

Project description:Clinical and animal studies have demonstrated the increasing evidence of oxidative stress in kidney stone disease. Recent findings have shown that the interactions between calcium oxalate (CaOx) crystals and renal tubular cells can promote many cellular events such as cell proliferation, cell death, cellular injury, mitochondrial dysfunction and inflammatory cascade. All of these cellular events are associated with oxidative stress and overproduction of free radicals and reactive oxygen species (ROS) such as superoxide and hydrogen peroxide in renal tubular cells. However, almost all of these references have shown that oxidative stress occurs after the causative crystals have been deposited in the kidney or exposed to renal tubular cells, whereas its primary role as the etiology remained unclear. In this study, we examined effects of oxidative modifications of urinary proteins on CaOx stone formation processes. Urinary proteins were modified by performic oxidation and the presence of oxidatively modified urinary proteins was verified, quantified and characterized by Oxyblot assay and tandem mass spectrometry (nanoLC-ESI-LTQ-Orbitrap-MS/MS). Subsequently, activities of oxidatively modified urinary proteins on CaOx stone formation processes were examined.

2021-11-03 | PXD019360 | Pride

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