Combined transcriptome and proteome profiling reveal cell-type-specific functions of Drosophila garland and pericardial nephrocytes
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PROVIDER: PRJNA1051627 | ENA |
REPOSITORIES: ENA
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Project description:Drosophila nephrocytes are specialised cells that share critical functional, morphological, and molecular features with podocytes of the mammalian kidney, including the slit diaphragm, which is a functional filtration barrier. Accordingly, nephrocytes are considered highly suitable invertebrate models for glomerular disease in humans. In this study, we established a method to individually isolate the garland and pericardial nephrocytes from Drosophila of different developmental stages. This allowed us to collect nephrocyte samples that were devoid of any contamination by other cell types. We used a combination of mass spectrometry-based proteomics and RNA-Seq-based transcriptomics to characterise the proteome and transcriptome of the respective cells in an integrated manner. In addition to identifying a set of factors that were expressed exclusively in nephrocytes, we observed characteristic changes in the cellular proteome and transcriptome as a consequence of ageing. Furthermore, functional enrichment analyses suggested that larval and adult nephrocytes fulfil distinct physiological functions, which was also indicated for garland and pericardial nephrocytes in adult animals. In addition, the latter cells were characterised by transcriptomic and proteomic profiles that were suggestive of a cell-type-specific energy metabolism. Finally, both types of nephrocytes displayed transcriptomic signatures that indicated elevated immune signalling, implying that nephrocytes are immune competent. The data generated in this study may represent a valuable basis for a more specific application of the Drosophila model system in the analysis of renal cell function in health and disease.
2024-10-09 | GSE250029 | GEO
Project description:Drosophila nephrocytes are specialised cells that share critical functional, morphological, and molecular features with podocytes of the mammalian kidney, including the slit diaphragm, which is a functional filtration barrier. Accordingly, nephrocytes are considered highly suitable invertebrate models for glomerular disease in humans. In this study, we established a method to individually isolate the garland and pericardial nephrocytes from Drosophila of different developmental stages. This allowed us to collect nephrocyte samples that were uncontaminated by other cell types. We used a combination of mass spectrometry-based proteomics and RNA-Seq-based transcriptomics to characterise the proteome and transcriptome of the respective cells in an integrated manner. In addition to identifying a set of factors that were expressed exclusively in nephrocytes, we observed characteristic changes in the cellular proteome and transcriptome as a consequence of ageing. Furthermore, functional enrichment analyses suggested that larval and adult nephrocytes fulfil distinct physiological functions, which was also indicated for garland and pericardial nephrocytes in adult animals. In addition, the latter cells were characterised by transcriptomic and proteomic profiles that were suggestive of a cell-type-specific energy metabolism. Finally, both types of nephrocytes displayed transcriptomic signatures that indicated elevated immune signalling. The data generated in this study may represent a valuable basis for a more specific application of the Drosophila model system in the analysis of renal cell function in health and disease.
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Project description:To better characterize the role of PCAT in the pathogenesis of disease, we performed a large-scale unbiased analysis of the transcriptional differences between pericardial and subcutaneous adipose tissue, analysing 53 microarrays across 19 individuals. Patients who underwent elective coronary artery bypass grafting and/or cardiac valve replacement surgeries participated in the study. Pericardial adipose tissue and subcutaneous adipose tissue were harvested from patients.
2011-02-01 | E-GEOD-26339 | biostudies-arrayexpress
Project description:Pericardial fluid exosome miRNA profiling
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Project description:Despite the invasive nature of its collection, being in close contact to the heart, the pericardial fluid (PF) proteome reflects the pathophysiological status of this organ. Therefore, whenever it is available, e.g. on occasion of open-heart surgery, PF proteomic analysis can give important clues of the molecular mechanisms underlying heart disease and it may help uncover new diagnostic/prognostic markers as well as new therapeutic targets. Still, the characterization of its protein fraction is challenged by large amounts of albumin, that can be relatively higher than in plasma/serum. To help expand the PF catalogued to date and to validate the technique for future applications, we have fractionated and characterized the pericardial fluid, using N-(trimethoxysilylpropyl)ethylenediamine triacetic acid (EDTA)-functionalized magnetic nanoparticles (NPs@EDTA) followed by a GeLC-MS/MS approach. As compared to a traditional albumin and IgG-depletion kit, we found this method to be as efficient in removing albumin, with similar inter-individual proteome variability. Furthermore, the NPs@EDTA-based fractionation approach could expand the protein dynamic range and displayed good proteome reproducibility. Overall, 565 proteins were identified, with more than half being new assignments to PF proteome.
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