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Analysis of the urinary proteome of mice with and without VPS34 knockout

ABSTRACT: We analyzed the effect of tubular VPS34 knockout on the urinary proteome.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Kidney

SUBMITTER: Markus Rinschen

LAB HEAD: Markus Rinschen

PROVIDER: PXD007106 | Pride | 2024-01-26

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20170315_Q1_AWH_ColID_319_ProjID_456_Benzing_sample_01.index	Other
	20170315_Q1_AWH_ColID_319_ProjID_456_Benzing_sample_01.raw	Raw
	20170315_Q1_AWH_ColID_319_ProjID_456_Benzing_sample_02.index	Other
	20170315_Q1_AWH_ColID_319_ProjID_456_Benzing_sample_02.raw	Raw
	20170315_Q1_AWH_ColID_319_ProjID_456_Benzing_sample_03.index	Other

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1 - 5 of 34

Publications

VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney.

Rinschen Markus M MM Harder Jennifer L JL Carter-Timofte Madalina E ME Zanon Rodriguez Luis L Mirabelli Carmen C Demir Fatih F Kurmasheva Naziia N Ramakrishnan Suresh K SK Kunke Madlen M Tan Yifan Y Billing Anja A Dahlke Eileen E Larionov Alexey A AA Bechtel-Walz Wibke W Aukschun Ute U Grabbe Marlen M Nielsen Rikke R Christensen Erik I EI Kretzler Matthias M Huber Tobias B TB Wobus Christiane E CE Olagnier David D Siuzdak Gary G Grahammer Florian F Theilig Franziska F

Science signaling 20221129 762

The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics analyses with functional and superresolution imaging assays of mice with an inducible deficiency in proximal tubular cells, we revealed that VPS34 contr ...[more]

PMID: 36445937

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Proteomic analysis of mousekidney cortices with and without VPS34 knockout

Project description:We analyzed the proteome of mouse with a tubule-specific VPS34 knockout and compared it to control mice.

2024-01-26 | PXD007092 | Pride

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

Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA

Project description:Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.

2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress

Urinary exosomal miRNA signatures in type II diabetic nephropathy patients

Project description:Urinary exosomal miRNA profiling was conducted in urinary exosomes obtained from 8 healthy controls (C), 8 patients with type II diabetes (T2D) and 8 patients with type II diabetic nephropathy (DN) using AgilentÂ´s miRNA microarrays.

2016-11-03 | E-MTAB-4166 | biostudies-arrayexpress

Analysis of the mouse kidney cortex phosphoproteome of VPS34 knockout and control animals

Project description:We generated phosphoproteomics data of renal cortices of mice with and without tubule-specific vps34 knockout.

2024-01-26 | PXD007093 | Pride

The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research [RNAseq]

Project description:Scientific evidence suggests that not only murine scent communication is regulated by major urinary proteins, but that their expression may also vary in response to metabolism via a yet unknown mechanism. Major urinary proteins are expressed mainly in the liver, showing a sexually dimorphic pattern with substantially higher expression in males. Here, we investigate the metabolic implications of a major urinary protein knockout in twelve-week-old male and female C57BL/6N mice during ad libitum feeding. Despite both sexes of major urinary protein knockout mice displayed numerically increased body weight and visceral adipose tissue proportions compared to sex-matched wildtype mice, the main genotype-specific metabolic differences were observed exclusively in males. Male major urinary protein knockout mice exhibited plasma and hepatic lipid accumulation accompanied by a hepatic transcriptome indicating an activation of lipogenesis. These findings match the higher major urinary protein expression in male compared to female wildtype mice, suggesting a more distinct reduction in energy requirements in male compared to female major urinary protein knockout mice. The observed sex-specific anabolic phenotype confirms a role of major urinary protein in metabolism and, since major urinary proteins are not expressed in humans, suggests the major urinary protein knockout mouse as a potential alternative model for translational metabolism research which needs to be further elucidated.

2022-08-01 | GSE188156 | GEO

The major urinary protein gene cluster knockout mouse as a novel model for translational metabolism research [RRBS]

2022-08-01 | GSE188157 | GEO

Quantification of highly homologous Major Urinary Proteins in wild house mice

Project description:Male house mice were housed under semi-natural conditions and their urinary proteins were quantified using MS1 and MS2 based label-free strategies. This dataset consists of 52 raw MS files, comprising 26 DIA (SWATH) and 26 IDA runs on a TripleTOF 5600. The composition of the dataset is described in the manuscript by Enk et al., titled: "Regulation of highly homologous Major Urinary Proteins in house mice quantified with label-free proteomic methods ", Molecular Biosystems, in review.

2016-08-08 | PXD004642 | Pride

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.

Project description:While insulin replacement therapy restores the health and prevents the onset of diabetic complications (DC) for many decades, some T1D patients have elevated hemoglobin A1c values suggesting poor glycemic control, a risk factor of DC. We surveyed the stool microbiome and urinary proteome of a cohort of 220 adolescents and children, half of which had lived with T1D for an average of 7 years and half of which were healthy siblings. Phylogenetic analysis of the 16S rRNA gene did not reveal significant differences in gut microbial alpha-diversity comparing the two cohorts. The urinary proteome of T1D patients revealed increased abundances of several lysosomal proteins that correlated with elevated HbA1c values. In silico protein network analysis linked such proteins to extracellular matrix components and the glycoprotein LRG1. LRG1 is a prominent inflammation and neovascularization biomarker. We hypothesize that these changes implicate aberrant glycation of macromolecules that alter lysosomal function and metabolism in renal tubular epithelial cells, cells that line part of the upper urinary tract.

2019-03-28 | PXD012413 | Pride

Urinary proteomics in youths with and without type 1 diabetes

Project description:Diabetic kidney disease is the leading cause of end-stage renal disease worldwide. Our understanding of the early kidney response to chronic hyperglycemia remains incomplete. In this study, we aimed to uncover the early, dysregulated pathways in the diabetic kidney before the onset of microalbuminuria by analysing the urinary proteomes of otherwise healthy youths with and without type 1 diabetes. Our study population included two cohorts for the discovery (N = 30) and validation (N = 30) of differentially excreted proteins. Of the 2451 proteins identified, 576 were quantified in all samples from the discovery cohort, and 34 comprised the urinary signature for early type 1 diabetes after Benjamini-Hochberg adjustment (Q < 0.05). The top pathways associated with this signature included lysosome, glycosaminoglycan degradation, and innate immune system (Q < 0.01). Notably, all enzymes involved in keratan sulfate degradation were significantly elevated in urines from youths with type 1 diabetes (fold change > 1.6). Increased urinary excretion of monocyte differentiation antigen CD14, hexosaminidase A, and lumican was also observed in the validation cohort (P < 0.05). Our findings draw attention to novel pathways such as keratan sulfate degradation in the early kidney response to hyperglycemia.

2020-06-01 | PXD017213 | Pride

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