Dataset Information

Diagnosing inflammation and infection in the urinary system via proteomics

ABSTRACT: Current methodology for the diagnosis of diseases in the urinary system includes patient symptomology, urine analysis and urine culture. Asymptomatic bacteriuria from urethral colonization or indwelling catheters, sample contamination from perineal or vaginal sources, and non-infectious inflammatory conditions can mimic UTIs, leading to uncertainty on medical treatment decisions. Organisms causing more than 98% of all UTIs and commensal microbes of the urogenital and perineal area were identified from 76 urine sediments with detection sensitivities estimated to be similar to urine culture. Proteomic data permitted a thorough evaluation of inflammatory and antimicrobial immune responses. Hierarchical clustering of the data revealed that high abundances of proteins from activated neutrophils were associated with pathogens in most cases, and correlated well with leukocyte esterase activities and leukocyte counts via microscopy. Proteomic data also allowed assessments of urothelial injury, by quantifying proteins highly expressed in red blood cells and contributing to the acute phase response. Lactobacillus and Gardnerella vaginalis were frequently identified suggesting urethral colonization and/or vaginal contamination of urine.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

SUBMITTER: Yanbao Yu

LAB HEAD: Yanbao Yu

PROVIDER: PXD012414 | Pride | 2019-03-28

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1DLC130819QE_UTI_112_P1-II-1.raw	Raw
	1DLC130819QE_UTI_112_P1-II-2.raw	Raw
	1DLC130819QE_UTI_112_S1-I.raw	Raw
	1DLC130819QE_UTI_112_S1-II.raw	Raw
	1DLC130821QE_UTI_1_rep1.raw	Raw

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Publications

Diagnosing inflammation and infection in the urinary system via proteomics.

Yu Yanbao Y Sikorski Patricia P Bowman-Gholston Cynthia C Cacciabeve Nicolas N Nelson Karen E KE Pieper Rembert R

Journal of translational medicine 20150408

<h4>Background</h4>Current methodology for the diagnosis of diseases in the urinary system includes patient symptomology, urine analysis and urine culture. Asymptomatic bacteriuria from urethral colonization or indwelling catheters, sample contamination from perineal or vaginal sources, and non-infectious inflammatory conditions can mimic UTIs, leading to uncertainty on medical treatment decisions.<h4>Methods</h4>Innovative shotgun metaproteomic methods were used to analyze urine sediments from ...[more]

PMID: 25889401

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Project description:Periurethral human mesenchymal stem cell (hMSC) injections are associated with functional improvement in animal models of post-partum stress urinary incontinence (SUI). However, limited data exists on the role of hMSCs in modulating gene expression in tissue repair after urethral injury. We quantified temporal gene expression modulation in hMSCs, and injured rat urethral tissue, using RNA seq in an animal model of SUI, over a 3-day time period following urethral injury, and local hMSC therapy. We injected PKH fluorescent-labeled human hMSC into the periurethral space of rats, following a 4h vaginal distention (3 rats per time point). Control rats underwent vaginal distention injury only, and were sacrificed at 12h, 24h, 36h, 72h post injury. Rat urethral and vaginal tissues were frozen and sectioned. Fluorescent labeled hMSCs were distinguished from adjacent, unlabeled rat urethral tissue. RNA was prepared from urethral tissue obtained by laser dissection of frozen tissue sections and sequenced on an Illumina HiSeq 2500. Differentially expressed genes (DEGs) over 72h were evaluated using a 2-group t-test (p<0.05). Our transcriptional analyses identified candidate genes involved in tissue injury, that were broadly sorted by injury and exposure to hMSC, throughout the first 72h of acute phase of injury. DEGs in treated urethra, compared with untreated urethra, were functionally associated with tissue repair, angiogenesis, neurogenesis, and oxidative stress suppression. DEGs included a variety of cytokines, extracellular matrix stabilization and regeneration genes, cytokine signaling modification, cell cycle regulation, muscle differentiation and stabilization. Moreover, our results revealed DEGs changes in the hMSCs (PKH-labelled), which were harvested from injured urethra. The expressions are related to DNA damage repair, transcription activation, stem cell regulation, cell survival, apoptosis, self-renewal, cell proliferation, migration and injury response.