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Human kidney proteomics, glomerular and tubular cellular and matrix fractions

ABSTRACT: Glomerular and tubulointerstitial fractions were enriched from human kidneys samples. Ages of human kidney samples: 15, 29, 37, 61, 67 and 69 years of age. The glomerular and tubulointerstitial samples were processed to enrich for extracellular matrix components and the fractions analysed by mass spectrometry.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: UoC Randles

LAB HEAD: Rachel Lennon

PROVIDER: PXD022219 | Pride | 2022-02-22

REPOSITORIES: Pride

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Kidney organoids recapitulate human basement membrane assembly in health and disease.

Morais Mychel R P T MRPT Tian Pinyuan P Lawless Craig C Murtuza-Baker Syed S Hopkinson Louise L Woods Steven S Mironov Aleksandr A Long David A DA Gale Daniel P DP Zorn Telma M T TMT Kimber Susan J SJ Zent Roy R Lennon Rachel R

eLife 20220125

Basement membranes (BMs) are complex macromolecular networks underlying all continuous layers of cells. Essential components include collagen IV and laminins, which are affected by human genetic variants leading to a range of debilitating conditions including kidney, muscle, and cerebrovascular phenotypes. We investigated the dynamics of BM assembly in human pluripotent stem cell-derived kidney organoids. We resolved their global BM composition and discovered a conserved temporal sequence in BM ...[more]

PMID: 35076391

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Human kidney proteomics, glomerular and tubular cellular and matrix fractions

Project description:kidney samples: 15, 29, 37, 61, 67 and 69 years of age. The glomerular and tubulointerstitial samples were processed to enrich for extracellular matrix components and the fractions analysed by mass spectrometry.

2021-10-13 | PXD026002 | Pride

Col4a1 mouse glomerular datasets

Project description:Glomeruli were isolated from Col4a1+/SVC and Ctrl mice. Samples were enriched for extracellular matrix. Glomerular extracellular matrix and cellular fractions were analysed by mass spectrometry.

2022-08-12 | PXD022363 | Pride

Mouse kidney glomerular extracellular matrix LC-MSMS

Project description:Across the spectrum of human disease there are significant changes in the composition and organisation of extracellular matrix (ECM). Furthermore, disease severity can vary according to race and sex, yet mechanisms for these variations are unclear. Using the kidney glomerulus as a model system, we tested the hypothesis that genetic background and sex influence composition and organisation of ECM. We characterised ECM from healthy mice with different predisposition to glomerular disease using global microarray, discovery proteomics and electron microscopy. Transcriptomic and proteomic analyses revealed unique strain and sex dependent glomerular ECM signatures with novel ECM proteins, which relate to glomerular dysfunction with leakage of macromolecules into the glomerular filtrate. In addition, we found striking structural changes in basement membranes in disease-susceptible mice. These findings were not explained by mutations in known ECM or glomerular genes. Pathway analysis of merged transcriptomic and proteomic datasets identified potential ECM regulatory pathways involving inhibition of matrix metalloproteinases, LXR/RXR, NRF2, notch and CDK5. These pathways may therefore alter ECM and confer susceptibility to disease.

2016-07-09 | PXD000811 | Pride

Expression data from Human Kidney (HK) samples

Project description:Males are 50% more likely to develop end stage kidney failure compared to women. In this study we wanted to find out the molecular mechanism responsible for this increased risk. We collected kidney samples from patients with and without kidney disease and performed a comprehensive gene expression analysis in healthy and diseased male and female kidneys. Interestingly, the set of gender biased genes in healthy kidneys were different from those in diseased kidneys indicating not only baseline gene expression differences but also that the male and female kidney respond differently to disease condition. Our studies indicate that men and women with kidney problems might need to be treated differently. Keywords: Gender difference We collected 42 kidney samples from healthy living transplant donors, nephrectomies and from diagnostic kidney biopsies. Preliminary studies did not show significant gene expression differences in control kidneys based on the collection method (i.e. living kidney biopsy vs. unaffected portion of tumor nephrectomy). We grouped the tissue samples based on the histological readings of the kidney biopsies. Samples with evidence of glomerular and tubulointerstitial fibrosis were assigned into the diseased group. Characteristics of the research participants indicate diverse ethnic and disease groups and mild (StageIII) CKD. The tissue was microdissected into glomerular and tubulointerstitial fractions and expression arrays were performed separately.

2010-04-13 | E-GEOD-12682 | biostudies-arrayexpress

Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis

2018-05-17 | GSE108109 | GEO

Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis

Project description:Glomerular transcriptome from human kidney biopsies in Neptune and ERCB. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. Corresponding tubulointerstitial transcriptome data is submitted under GEO ID: GSE108113. RNA from the glomerular compartment was extracted and processed for hybridization on Affymetrix ST 2.1 microarrays, annotated using Human Entrez Gene ID custom CDF version 19. This dataset is part of the TransQST collection.

2018-05-17 | E-GEOD-108109 | biostudies-arrayexpress

Spatial transcriptome analysis unveils an innate immune activation signature of acute T cell-mediated rejection in kidney transplants

Project description:To unveil the molecular mechanisms underlying TCMR, we utilized spatial transcriptomics on post-transplant TCMR and non-TCMR patients. Contrary to the prevailing T cell-centric view, our findings reveal uniform inflammatory responses across glomerular and tubulointerstitial regions in TCMR.

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Col4a3 mouse glomerular datasets

Project description:Glomeruli were isolated from Col4a3-/- and Ctrl mice. The extracellular matrix was enriched and both cellular and matrix fraction were analysed by mass spectrometry.

2022-08-12 | PXD022392 | Pride

Col4a5 mouse glomerular extracellular matrix

Project description:Alport mouse model (Col4a5) have been submitted for proteomic analysis. Glomeruli have been isolated from mouse kidneys, extracellular matrix has been enriched and analysed by mass spectrometry.

2022-08-12 | PXD022227 | Pride

Kidney VISTA prevents IFNγ-IL-9 axis-mediated tubulointerstitial fibrosis after acute glomerular injury

Project description:Backgrounds: The present study addressed whether V-domain Ig suppressor of T cell activation (VISTA), constitutively expressed in kidney macrophages, has a protective role in tubulointerstitial fibrotic transformation after acute antibody-mediated glomerulonephritis. Methods: Wild-type (WT) and VISTA-deficient (Vsir-/-, KO) mice were treated with nephrotoxic serum to induced acute antibody-mediated glomerulonephritis, and their cytokine and fibrosis profiles were compared. Results: VISTA was highly expressed in kidney macrophages (resident more than infiltrating subset). If VISTA was depleted, tubules suffered further damage after glomerular injury. In damaged Vsir–/– mice, the contact frequency of macrophages with infiltrated T cells increased, and then the immunometabolic characteristics of T cells changed to overproduction of interferon-γ. The Vsir–/– parenchymal tissue cells responded to this altered milieu as more producing interleukin-9, which augmented tubulointerstitial fibrosis and irreversible kidney dysfunction. The blocking antibodies against interferon-γ and interleukin-9 protected above pathological process by VISTA depletion. Conclusions: VISTA is a sentinel protein of kidney macrophages, which prevents tubulointerstitial fibrosis via interferon-γ-interleukin-9 axis after acute antibody-mediated glomerular injury.

2021-08-04 | GSE181163 | GEO

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