MiRNA sequencing revealed differentially expressed exosomes miRNAs in PDE of patients with peritoneal ultrafiltration failure
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE182736 | GEO | 2021/08/27
REPOSITORIES: GEO
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Project description:MiRNA sequencing revealed differentially expressed exosomes miRNAs in PDE of patients with peritoneal ultrafiltration failure
| PRJNA757643 | ENA
Project description:Chronic exposure to biological incompatibility of peritoneal dialysis solution is one of the principal causes of ultrafiltration failure (UF). However, the changes of peritoneal cell composition and molecular mechanism of peritoneal microenvironment after long-term PD are unclear. Single-cell RNA sequencing was performed to profile cell composition and transcriptome characteristics in effluent obtained from patients undergoing PD with short vintage (SV), long vintage without ultrafiltration failure (LV_NOT_UF), and long vintage with ultrafiltration failure (LV_UF). A total of 6 SV patients, 6 LV_NOT_UF patients, and 4 LV_UF patients were enrolled. The median PD duration of the three groups were 5 months (range:1.0–6.0 months), 137 months (range: 92–189 months) and 132 months (range: 120–161 months), with no significant differences in age (38.3 ± 21.5 years, 45.7 ± 10.6 years and 41.0 ± 16.7 years, P>0.05) and gender (male%: 33.3%, 50.0% and 25.0%, P>0.05). scRNA-seq data annotated 8 main cell types including epithelial-like mesothelial cells (E-MCs), mesenchymal-like mesothelial cells (M-MCs), fibroblast, plasma B cells, conventional dendritic cells, plasmacytoid dendritic cells, natural killer T cells, and myeloid cells. LV_UF patients showed higher proportion of E-MCs, which exhibited activated autophagy and had properties of both anti-inflammatory and pro-inflammatory, and neutrophil- and autophagy-related DEGs of E-MCs were upregulated in the LV_UF group. In contrast, the M-MCs and the AQP1 expression in the peritoneal mesenchyme were reduced in the LV_UF group compared to the other groups. The neutrophils in PD effluent were elevated in the LV_UF group, while the M2-like MRC1-macrophages gradually decreased from the SV, LV_NOT_UF to LV_UF group. Compared with the LV_NOT_UF group, the upregulated DEGs of monocytes/macrophages in the LV_UF group not only involved in pro-inflammatory response, but also promoted EMT progress. Additionally, neutrophils and monocytes/macrophages both interacted with MCs. Our study uncovers peritoneal different individual cell populations and cellular functions in different stages of PD which indicates the dynamic changes of microenvironments of peritoneal membrane. These findings provide new insights into the novel roles of mesothelial cells and inflammatory cells in UF.
2023-11-27 | GSE248762 | GEO
Project description:Peritoneal fibrosis is a major complication of long-term peritoneal dialysis (PD), leading to ultrafiltration failure and sometimes life threatening encapsulating peritoneal sclerosis. Fibrosis is driven by activated myofibroblasts that are derived, in part, from mesothelial-to-mesenchymal transition (MMT). We aimed to discover novel mediators of MMT and then experimentally exploit them to prevent peritoneal fibrosis. Using an antibody to HBME-1 and streptavidin nanobead technology, we first pioneered a novel method to purify rat mesothelial cells. After exposing mesothelial cells to transforming growth factor β1 (TGFβ1), we undertook RNAseq whole transcriptome analyses and outlined, the expression profile of sorted mesothelial cells at pre- and post- MMT.
2018-06-18 | E-MTAB-5998 | biostudies-arrayexpress
Project description:Proteomics-based analysis of Peritoneal Dialysis Effluent is a relatively new approach to studying the changes associated with PD. Recent studies have shown altered proteomic profiles in various conditions of PD patients, including uremia, diabetes, peritonitis, abnormal peritoneal transport function and with different peritoneal dialysis modality. However, these studies extracted proteins in PDE by precipitation techniques resulting in high abundant diffusible proteins from blood circulation which interfered with the identification of low abundant, locally secreted, yet important, biomarkers. we hypothesize that EVs are secreted from peritoneal resident cells and contain known biomarkers for PDE-related membrane injury. As a proof of concept, here we identified and characterized EVs from PDE of healthy PD patients using transmission electron microscopy (TEM), dynamic light scattering (DLS), and nanoparticle tracking analysis (NTA). Furthermore, we did proteomics and bioinformatics analyses to determine the number and type of proteins measurable within EVs isolated from the PDE using two methods of vesicle isolation.
2018-08-14 | PXD006371 | Pride
Project description:Peritoneal dialysis (PD) is a successful renal replacement therapy for end-stage renal disease that effectively improves the quality of life. Long-term PD causes epithelial mesenchymal transformation (MMT) of peritoneal mesothelial cells, leading to peritoneal fibrosis which reduces the efficiency of PD. Macrophages are considered players in the onset and perpetuation of peritoneal injury. Yet, the mechanisms employed by macrophage-mesothelial cells communication to regulate peritoneal fibrosis are not fully elucidated resulting in lack of disease-modified drugs. This study analyzes the role of macrophage-mesothelial cell communication by intraperitoneal injection of macrophage derived exosomes in PD model rats. These results show that macrophages secrete exosomal miR-204-5p that directly targets Foxc1, leading to the activation of MMT in mesothelial cells. The data also shows that intraperitoneal injection of dissolved AS-IV can improve MMT by altering macrophage derived exosomal miRNAs. This study indicates that intercellular crosstalk between peritoneal macrophages and mesothelial cells is mediated by macrophage derived miR-204-5p-containing exosomes that control the MMT progression, providing AS-IV for prevention and treatment of PD induced peritoneal fibrosis. Our results demonstrate, for the first time, a novel role of the AS-IV on miR-204-5p/Foxc1/β-catenin axis in improving peritoneal fibrosis in vivo and vitro.
2023-01-01 | GSE165342 | GEO
Project description:Peritoneal dialysis (PD) is a modality of renal replacement therapy in which the high volumes of available PD effluent (PDE) represents a rich source of biomarkers for monitoring disease and therapy. Although this information could help guiding the management of PD patients, little is known about the potential of PDE to define pathomechanism-associated molecular signatures in PD. Here we present the utilization of a high-performance multiplex proteomics approach based on depletion of highly abundant plasma proteins and enrichment of low abundance proteins and quantitation using a combination of label-free and isobaric labeling strategies for PDE samples from PD patients (n=20), who received either standard PD fluid or a novel PD fluid (added alanyl-glutamine (AlaGln)) in an open-label, randomized, two-period, cross-over clinical trial.
2012-12-13 | PXD006863 | Pride
Project description:Peritoneal dialysis (PD) is the worldwide recognized preferred dialysis treatment for children affected by end-stage kidney disease (ESKD). However, due to the unphysiological composition of PD fluids, the peritoneal membrane (PM) of these patients may undergo structural and functional alterations, which may cause fibrosis. Several factors may accelerate this process and primary kidney disease may have a causative role. In particular, patients affected by corticoresistant primary focal segmental glomerulosclerosis), a rare glomerular disease leading to nephrotic syndrome and ESKD, seem more prone to develop peritoneal fibrosis. The mechanism causing this predisposition is still unrecognized. To better define this condition, we carried out, for the first time, a new comprehensive comparative proteomic mass spectrometry analysis of mesothelial exosomes from peritoneal dialysis effluent (PDE) of 6 pediatric patients with focal segmental glomerular sclerosis (FSGS) versus 6 patients affected by other primary renal diseases (No FSGS). Our omic study demonstrated that, despite the high overlap in the protein milieu between the two study groups, machine learning allowed a complete distinction of the whole proteomic exosome mesothelial content of FSGS versus No FSGS (with 100% accuracy). Out of the 2490 identified proteins, 40% (995) were involved in epithelial-mesenchymal transition (EMT)/fibrosis and in the transforming growth factor-β pathway. Additionally, the Weight Gene Co-expression Network Analysis algorithm identified that some of the discriminative proteins (TIMP1, CTHRC1, SPARC, CHMP4B, COL5A2, ANXA13, FNC2 and CENP-E) were also highly correlated to PD vintage, fibrosis, EMT and non-neoplastic PM disease. All together our data demonstrated that mesothelial cells of FSGS patients are more prone to activate a pro-fibrotic machinery with exosomes having a primary role in this process. Moreover, they indicated that identified FSGS-associated elements in mesothelial exosome protein could be employed as potential new biomarkers of mesothelial integrity. Finally, our results highlighted that in FSGS patients particular attention should be paid to use more biocompatible dialysis solution, reduce the length of time on PD and personalize PD regimens to minimize the risk of rapid loss of PM function or development of encapsulating peritoneal sclerosis.
2022-02-17 | PXD024556 | Pride
Project description:Peritoneal macrophages from healthy New Zealand White rabbits were treated with exosomes from Cysticercus pisiforms and treated with PBS were used as control.
2022-04-21 | PXD033317 |
Project description:Loss of ultrafiltration capacity in peritoneal dialysis (PD) patients is often associated with peritoneal vascular changes, manifest as diabetes-like vasculopathy and angiogenesis. The endothelial monolayer lining the vessel lumen controls vessel barrier function and thereby influences peritoneal substrate transport and ultrafiltration. In this study, we first characterized the response to conventional PD fluids of endothelial cells isolated from peritoneal biopsies of children undergoing PD. 9 omental biopsies from the pediatric biopsy biobank (mean age 5.7 years) were included in this study. PD patients were treated with conventional PD fluid (mean PD vintage 12.5 months). Age-matched controls (n=5) with normal renal function undergoing elective surgery were also included. In patients on PD, the biopsy sampling site was at least 5 cm away from the PD catheter entry site. Written informed consent was obtained from parents, and from patients as appropriate. The study was performed according to the Declaration of Helsinki and registered at www.clinicaltrials.gov (NCT01893710). The study was part of the International Pediatric Dialysis Network (IPDN; www.pedpd.org). Patients with a BMI of >35 kg/m2 and with chronic inflammatory diseases were excluded. Specimens obtained during surgery were instantaneously frozen with liquid nitrogen and stored at -80°C. Arterioles macroscopically located within fat tissue and microscopically at least 1mm distant from the peritoneal surface were micro-dissected. Elastica van Gieson stainings of the arteriolar elastic lamina were used as templates for microdissection of arterioles from cresol violet–stained neighboring sections. 100 µm thick tissue slices were cut with a cryotome and 30 deep-frozen arteriolar rings per patient were micro-dissected using a stereo microscope and a microneedle. Arteriolar rings were lysed in 100 µl lysis buffer (30 mM Tris, pH 8.5, 7M urea, 2M thiourea, 4% 3-[(3-Cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS), 1 mM EDTA, 1 tablet of Complete Protease Inhibitor (Roche, Basel, Switzerland) and 1 tablet of phosphatase inhibitor (PhosSTOP, Roche) per 100 ml). The resulting lysates were stored at -80°C until further processing. Total protein concentration was determined with the 2D-Quant kit (GE). Quality control and verification of protein concentrations was performed by SDS-PAGE. We investigated the molecular mechanisms of endothelial cell pathology during in vivo and in vitro PD fluid exposure by proteomic and bioinformatic analysis of the endothelial cell response to hyperglycemic stress, integrating current understanding of PD-related cellular injury and stress responses (Bender et al., Nephrol Dial Transplant, 2011, doi:10.1093/ndt/gfq484; Kratochwill et al., BioMed research international, 2015, doi:10.1155/2015/628158; Kratochwill et al., J Proteome Res, 2009, doi:10.1021/pr800916s; Lechner et al., J Proteome Res, 2010, doi:10.1021/pr9011574).
2021-09-09 | PXD022183 | Pride
Project description:Loss of ultrafiltration capacity in peritoneal dialysis (PD) patients is often associated with peritoneal vascular changes, manifest as diabetes-like vasculopathy and angiogenesis. The endothelial monolayer lining the vessel lumen controls vessel barrier function and thereby influences peritoneal substrate transport and ultrafiltration. The dipeptide alanyl-glutamine (AlaGln) has recently shown cytoprotective effects when added to PD fluid, including preservation of mesothelial cells in vitro (Kratochwill et al., Nephrol Dial Transplant, 2012, doi:10.1093/ndt/gfr459) and attenuation of the exuberant angiogenesis seen in long-term rodent models of PD (Ferrantelli et al., Kidney international, 2016, doi:10.1016/j.kint.2015.12.005). These effects have been reflected in early phase clinical trials as restoration of effluent cell stress responses and improved biomarkers of peritoneal health (Kratochwill et al., PLoS One, 2016, doi:10.1371/journal.pone.0165045; Vychytil et al., Kidney international, 2018, doi:10.1016/j.kint.2018.08.031). In a randomized clinical phase II trial, 8 weeks treatment with AlaGln in PD fluid decreased peritoneal protein loss. This clinically important effect might be explained by preserved peritoneal membrane and vessel integrity, but the role of AlaGln in preservation of peritoneal endothelial cell function remains unclear. In this study, we investigated to what extent in vivo observed biological processes and pathways are replicated by in vitro exposure of human umbilical vein endothelial cells (HUVEC) to conventional PD fluid. HUVECs were exposed to experimental solutions for up to 24 h. All test fluids were sterile-filtered before usage. Each experiment consisted of three independent samples in biological replicates on separate culture plates. For PD fluid incubation, cells were first exposed for 1 h to pure glucose-based PD fluid (Dianeal PD4 3.86% glucose, Baxter, Castlebar, Ireland), or to the same PD fluid supplemented with AlaGln dipeptide (8 mM, Dipeptiven; Fresenius Kabi, Bad Homburg, Germany), or to normal medium without growth factors as control. Cells were subsequently exposed for 24 h to the above solutions diluted 1:1 with culture medium and brought to 2% FCS. Cells were then washed three times (250 mM sucrose, 10 mM Tris/HCl, pH 7) and lysed in 125 µL per well of lysis buffer (30 mM Tris, pH 8.5, 7 M urea, 2 M thiourea, 4% CHAPS, 1 mM EDTA, one tablet of Complete Protease Inhibitor (Roche, Basel; Switzerland) per 100 ml, and one tablet of PhosStop Protease Inhibitor (Roche) per 100 mL). Total protein concentration was determined with the 2D-Quant kit (GE Healthcare, Uppsala, Sweden) per manufacturer’s manual. Lysates were stored at -80°C until further processing. We investigated the molecular mechanisms of endothelial cell pathology during in vivo and in vitro PD fluid exposure by proteomic and bioinformatic analysis of the endothelial cell response to hyperglycemic stress, integrating current understanding of PD-related cellular injury and stress responses (Bender et al., Nephrol Dial Transplant, 2011, doi:10.1093/ndt/gfq484; Kratochwill et al., BioMed research international, 2015, doi:10.1155/2015/628158; Kratochwill et al., J Proteome Res, 2009, doi:10.1021/pr800916s; Lechner et al., J Proteome Res, 2010, doi:10.1021/pr9011574). We then evaluated the effect of AlaGln addition to conventional PD fluid on these parameters in endothelial cells. This strategy allowed characterization of endothelial cell injury and stress responses during exposure to conventional hyperglycemic PD fluid, and their modulation by added AlaGln.
2021-09-09 | PXD022170 | Pride