Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury

ABSTRACT: Background: The kidney glomerulus is a specialized capillary bed that is involved in urine production and blood pressure control. Glomerular injury is a major cause of chronic kidney disease, a widespread epidemic without therapeutic options. Single-cell transcriptomics have radically improved our ability to characterize complex organs, such as the kidney. Cells of the glomerulus, however, have been largely underrepresented in previous single cell kidney studies due to their paucity and intractability. Methods: We used single-cell RNA sequencing to comprehensively characterize the different types of cells in the glomerulus from healthy mice and from four different disease models (nephrotoxic serum nephritis, diabetes, doxorubicin toxicity, CD2AP deficiency). Results: All cell types in the glomerulus were identified using unsupervised clustering analysis. We identified novel marker genes and gene signatures of mesangial cells, vascular smooth muscle cells of the afferent and efferent arteriole, parietal epithelial cells, and three different types of endothelial cells. Analysis of the disease models revealed cell type-specific and injury type-specific responses in the glomerulus, including acute activation of the Hippo pathway in podocytes after nephrotoxic immune injury. Conclusions: We have generated a comprehensive high-resolution single-cell transcriptomic profile of the kidney glomerulus from healthy and injured mice. The dataset provides a useful resource for identifying novel disease-related genes and pathways.

ORGANISM(S): Mus musculus

PROVIDER: GSE146912 | GEO | 2020/07/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Aging and senescence-associated signatures of aged kidney glomerular cells [bulk RNA-seq]

Project description:The kidney governs many physiological factors of the body, and the glomerulus is its core filtration unit. Glomeruli comprise of less than 1.5% of the kidney’s volume and thus are underrepresented in many analyses of the kidney, and require particular isolation methods. Aging is a major risk factor for kidney disease, yet despite the importance of proper glomerular function, we have limited knowledge of the changes that glomerular cells undergo during aging. Here we interrogate the aged mouse kidney, glomerulus and glomerular cells using various approaches, including single cell RNA sequencing (scRNA-Seq), to identify age and senescence associated changes at the tissue and cellular level. We show that the aged kidney and glomerulus undergo structural changes, including increased fibrosis, glomerulonephritis and expression of injury and senescence-associated markers. Lastly, we utilized our method for high-throughput analysis of mouse glomeruli to characterize cell-specific and age-related changes in glomerular cells. This analysis revealed a senescence-associated phenotype in aged mesangial cells, and emphasized the potential importance of mesangial cells and macrophages in this niche. Our study provides insights into the molecular and cellular changes of the aging glomerulus that suggest therapeutic targets for age-related renal dysfunction.

2024-09-01 | GSE240373 | GEO

Aging and senescence-associated signatures of aged kidney glomerular cells [scRNA-seq]

2024-09-01 | GSE240374 | GEO

Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury

Project description:Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury

| PRJNA612350 | ENA

RNAseq of kidneys from a mice model of chronic leptospirosis infection and induced a secondary nephrotoxic injury by adenine feeding

Project description:Background The mysterious chronic kidney disease is multifactorial causes. One of the risk factors is leptospirosis, a re-emerging infectious disease caused by Leptospira spp., for endemic leptospirosis tend to coincide with high-incidence regions of chronic kidney disease of unknown etiology. This study aims to investigate the role of leptospirosis as an emerging culprit in which chronic subclinical kidney injury, may predispose to progressive kidney disease when superimposed on secondary nephrotoxic injury. Methods Adenine-induced renal injury in chronic leptospira-infected C57/BL6 mice were studied for evaluating the renal function, histology and gene expression changes. We employed RNA sequencing-based renal transcriptome to investigate pathogenic pathways associated with secondary nephrotoxic injury in chronic kidney injury due to leptospirosis. Results The severity of kidney lesions was increased and the expression of immune/inflammation/fibrosis genes were significantly up-regulated in either low-dose (0.1%) and high-dose (0.2%) adenine-induced renal injury superimposed on infected mice. Whole renal transcriptome analysis reveals that the substantial amplification of the tremendous amount of expressed genes and fibrosis-related pathways was found in adenine-induced kidney injury add-on to leptospira-infected mice which correlated with kidney dysfunction and fibrosis compared to infection or adenine itself. A total of 41 differentially expressed genes associated with fibrosis were identified in infected mice fed with adenine, suggesting that these potential genes contributed to aggravated renal progression occurred in adenine-fed chronic leptospira-infected mice. Conclusions In summary, this study indicates that chronic subclinical kidney infection when exposed to different degree of secondary nephrotoxic injury may predispose to exacerbated and progressive chronic kidney disease.

2021-04-05 | GSE150641 | GEO

Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

Project description:Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), were missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we used Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis revealed genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells (MDCs). Importantly, we detected heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observed remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

2020-11-21 | GSE160048 | GEO

Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

| EGAS00001004943 | EGA

Cellular recruitment by podocyte-derived pro-migratory factors in assembly of the human renal filter

Project description:Analysis of monogenic kidney disease-causing genes, and secondary pathology resulting from systemic diseases including diabetes and hypertension, highlight the importance of the kidney’s filtering system, the renal corpuscles. To elucidate the developmental processes that establish the renal corpuscle, we employed single-nucleus droplet-based sequencing to capture single nuclei from the human fetal kidney. This enabled the identification of distinct cell types of the nephron (podocytes), interstitial (mesangial cells) and vascular (glomerulus) lineages that together generate the renal corpuscles. Computational trajectory analysis identified transient gene expression in the development of these cell types, predicting early precursors or mature podocytes express FBLN2, BMP4 or NTN4, in conjunction with recruitment, differentiation, and modeling of vascular and mesangial cell types into a functional filter. In vitro studies provide evidence these factors exhibit angiogenic or mesangial recruiting and inductive properties consistent with a key organizing role for podocyte precursors in kidney development. Together these studies define a spatiotemporal developmental program for the primary filtration unit of the human kidney and provide novel insights into cell interactions regulating co-assembly of constituent cell types.

2019-10-03 | GSE114569 | GEO

Gene expression profile at single cell levels from glomerulus in wild type (WT) and inhibitor of MyoD family A(I-mfa) knock out mice

Project description:Background: Inhibitor of MyoD family A (I-mfa) is a cytosolic protein and its function in kidney is unknown. In this study we used scRNAseq technique to study the diversity at single cell levels in kidney glomerulus from both wild types and I-mfa knockout mice seperately. Translational Project Award from American Heart Association (20TPA35500045, to R. Ma)

2024-10-30 | GSE263869 | GEO

Ischemic vs. nephrotoxic acute renal failure, early time points (2h and 8h)

Project description:Acute renal failure (ARF) has high morbidity and mortality. In animal ARF models, effective treatments must be administered before or shortly after the insult, limiting their clinical potential. We used microarrays to identify early biomarkers that distinguish ischemic from nephrotoxic ARF, or that detect both injury types. We compared rat kidney transcriptomes 2 and 8 hours after ischemia/reperfusion and after mercuric chloride. Quality control and statistical analyses were necessary to normalize inter-experimental groups, eliminate outliers, and exclude unaltered genes. Principal component analysis revealed distinct ischemic and nephrotoxic trajectories, and clear array groupings. Therefore, we used supervised analysis, t-tests and fold changes, to compile gene lists for each group, exclusive or non-exclusive, alone or in combination. Keywords: Disease classification/time course

2006-03-17 | GSE3219 | GEO

Opposing roles of dendritic cells subsets in experimental GN

Project description:Classical dendritic cells (DCs) are key players at the interface between innate and adaptive immunity. In the kidney exist 2 major subsets of cDCs: CD11b+ cDCs and CD103+ cDCs. We investigated their function in the most widely used model of experimental glomerulonephritis (GN) in mice: nephrotoxic nephritis (NTN). Consistent with a role for cDCs in nephrotoxic nephritis, depletion of ZBTB46+ cells (all cDCs) attenuated kidney injury, while deficiency of the CD103+ subset of cDCs accelerated injury via a mechanism that involved increased neutrophils. This RNAseq was performed to analyze transcriptional changes in FACS-sorted renal CD11b+ and CD103+ cDCs under healthy conditions and at day 7 of NTN to reveal why both subsets have different functions in GN.

2017-10-12 | GSE104820 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data