Susceptibility of mice to primary Echinostoma caproni infections is associated with metabolic and structural changes
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Bacillus Phage Phi3t-spbeta Hybrid Mus Musculus (mouse)
TISSUE(S): Ileum Smooth Muscle
SUBMITTER: 
Luz Valero
LAB HEAD: Rafael Toledo
PROVIDER: PXD068954 | Pride | 2026-04-22
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 220210_CM_L1.wiff | Wiff | |||
| 220210_CM_L1.wiff.scan | Wiff | |||
| 220210_CM_L2.wiff | Wiff | |||
| 220210_CM_L2.wiff.scan | Wiff | |||
| 220210_CM_L3.wiff | Wiff |
Items per page: 5 1 - 5 of 30 |
Similar Datasets
Project description:Chronic myelogenous leukemia (CML) is a myeloproliferative disorder caused by expression of the chimeric BCR-ABL tyrosine kinase oncogene, resulting from the t(9;22) chromosomal translocation. Imatinib (gleevec, STI-571) is a selective inhibitor of Bcr-Abl activity highly effective in the treatment of CML. However, even though almost all CML patients respond to treatment with imatinib or third generation inhibitors. These drugs are not curative and need to be taken indefinitely or until patients become resistant. Therefore, to get a definitive eradication of leukemic cells, it is necessary to find novel therapeutic combinations, for achieving greater efficacy and fewer side effects. Nutraceuticals play an increasingly important role in the treatment of cancer. Curcumin is an Indian spice with several therapeutic properties: anti-oxidant, analgesic, anti-inflammatory, antiseptic and anti-cancer. In cancer disease, it acts by blocking cell transformation, proliferation, and invasion and by inducing cell apoptosis. In the present study, byapplying a quantitative proteomic SWATH-MS strategy we evaluated the effect of curcumin onK562 cells. Our findings revealed that the most relevant effect induced by curcumin was a consistent decrease of several proteins involved in glucose metabolism, most of which were HIF-1α targets, concomitant with the up-regulation of functional and structural mitochondrial proteins. The mechanism by which curcumin affects metabolic enzyme profile was associated with the reduction of HIF-1α activity, due to the miR-22-mediated down-regulation of importin 7 (IPO7) expression. Finally, the ability of curcumin to enhance in vitro the efficiency of imatinib was reported. In summary, our data indicates that the miR-22/IPO7/HIF-1α axis may be considered as a novel molecular target of curcumin adding new insights for better defining therapeutic activity and anticancer properties of this natural compound.
2018-07-30 | PXD007771 | Pride
Project description:Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.
2021-02-08 | PXD011330 | Pride
Project description:Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in saliva samples, contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to study the periodontal proteome in saliva in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 85 subjects, 44 periodontally healthy and 41 with generalised untreated periodontitis in stages III-IV, were included, and saliva samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 36 individuals showed significant clinical improvement in the mean full-mouth probing pocket depth (PPD) value, and saliva samples were collected from them.
2025-04-23 | PXD043491 | Pride
Project description:Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in gingival crevicular fluid (GCF) samples contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to investigate the periodontal proteome in GCF in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 84 subjects, 44 periodontally healthy and 40 with generalised untreated periodontitis in stages III-IV, were included, and GCF samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 25 individuals showed significant clinical improvement in probing pocket depth (PPD) at the selected sites, and GCF samples were collected from them.
2024-10-17 | PXD043474 | Pride
Project description:Macrophages are involved in the immunological response to inflammatory and infectious agents, including Human Immunodeficiency Virus type 1 (HIV-1) infection. They are a primary targets of the virus and facilitate transfer across the blood brain barrier into the central nervous system. In the presence of toxic substances, such as methamphetamine (Meth), the protective functions of macrophages are further impaired. It has been shown that both HIV-1 infection and Meth induce changes in the proteome of macrophages. Therefore, in the presented study we employed a nano-liquid chromatography (nanoLC)-SWATH mass spectrometry (MS) approach to detect and quantify changes on proteome level that are induced in human monocyte derived macrophages (hMDM) that were exposed to Meth before or after HIV infection. As we focused in this study on actin and a cluster of Ras-related proteins (Rab), we selected the following proteins: actin (UniProt P60709), Ras-related protein Rab-1A (UniProt P62820), Ras-related protein Rab-2A (UniProt P61019), Ras-related protein Rab-4B (UniProt P61018), Ras-related protein Rab-7A (UniProt P51149), Ras-related protein Rab-9A (UniProt P51151), Ras-related protein Rab-11 (UniProt P62491), Ras-related protein Rab-14 (UniProt P61106), Ras-related protein Rab-22A (UniProt Q9UL26), Ras-related protein Rab-24 (UniProt Q969Q5), Ras-related protein Rab-37 (UniProt Q96AX2) for further validation, which we performed using liquid chromatography-multiple reaction monitoring (LC-MRM) MS technique. The MRM data from this study, along with LC-MRM analysis and data processing parameters, were separately described and deposited in PASSEL repository with accession number PASS01591.
2022-05-19 | PXD023291 | Pride
Project description:Schwanniomyces etchellsii is an unconventional, halotolerant microorganism. Like some other yeasts, it can efficiently perform various biocatalytic transformations of organic compounds in seawater more effectively than in freshwater. In seawater, conversion rates are higher, by-product production is minimized, greater substrate loading is possible, and cells can be recycled for further use. To identify the molecular features that explain this behavior, comparative proteomic and lipidomic studies were conducted on cells grown in seawater and freshwater at various growth stages. The results showed higher expression of proteins involved in the stress response, such as glycerol-3-phosphate dehydrogenase, the glycerol transporter Stl1 and the P-type ATPase sodium pump Ena1, and several phospholipid biosynthesis proteins, including inositol-3-phosphate synthase and phosphatidate cytidylyltransferase, in seawater. Changes in metabolic enzymes and other proteins involved in responding to stimuli were also observed between the two conditions. Overall, cells grown in a freshwater medium exhibited higher levels of enzymes involved in biosynthetic processes. Differences in lipid profiles were also observed between cells grown in the two media. Higher levels of monoacyl and diacylglycerols were found in seawater, while higher levels of phospholipids containing serine and ethanolamine were found in freshwater. Consistent with more permeable membranes, cells grown in seawater exhibited lower levels of ergosterol.
2026-01-19 | PXD070596 | Pride
Project description:Schwanniomyces etchellsii is an unconventional, halotolerant microorganism. Like some other yeasts, it can efficiently perform various biocatalytic transformations of organic compounds in seawater more effectively than in freshwater. In seawater, conversion rates are higher, by-product production is minimized, greater substrate loading is possible, and cells can be recycled for further use. To identify the molecular features that explain this behavior, comparative proteomic and lipidomic studies were conducted on cells grown in seawater and freshwater at various growth stages. The results showed higher expression of proteins involved in the stress response, such as glycerol-3-phosphate dehydrogenase, the glycerol transporter Stl1 and the P-type ATPase sodium pump Ena1, and several phospholipid biosynthesis proteins, including inositol-3-phosphate synthase and phosphatidate cytidylyltransferase, in seawater. Changes in metabolic enzymes and other proteins involved in responding to stimuli were also observed between the two conditions. Overall, cells grown in a freshwater medium exhibited higher levels of enzymes involved in biosynthetic processes. Differences in lipid profiles were also observed between cells grown in the two media. Higher levels of monoacyl and diacylglycerols were found in seawater, while higher levels of phospholipids containing serine and ethanolamine were found in freshwater. Consistent with more permeable membranes, cells grown in seawater exhibited lower levels of ergosterol.
2026-01-19 | PXD070554 | Pride
Project description:Schwanniomyces etchellsii is an unconventional, halotolerant microorganism. Like some other yeasts, it can efficiently perform various biocatalytic transformations of organic compounds in seawater more effectively than in freshwater. In seawater, conversion rates are higher, by-product production is minimized, greater substrate loading is possible, and cells can be recycled for further use. To identify the molecular features that explain this behavior, comparative proteomic and lipidomic studies were conducted on cells grown in seawater and freshwater at various growth stages. The results showed higher expression of proteins involved in the stress response, such as glycerol-3-phosphate dehydrogenase, the glycerol transporter Stl1 and the P-type ATPase sodium pump Ena1, and several phospholipid biosynthesis proteins, including inositol-3-phosphate synthase and phosphatidate cytidylyltransferase, in seawater. Changes in metabolic enzymes and other proteins involved in responding to stimuli were also observed between the two conditions. Overall, cells grown in a freshwater medium exhibited higher levels of enzymes involved in biosynthetic processes. Differences in lipid profiles were also observed between cells grown in the two media. Higher levels of monoacyl and diacylglycerols were found in seawater, while higher levels of phospholipids containing serine and ethanolamine were found in freshwater. Consistent with more permeable membranes, cells grown in seawater exhibited lower levels of ergosterol.
2026-01-19 | PXD070465 | Pride
Project description:The ubiquitin-directed AAA-ATPase VCP/p97 facilitates degradation of misfolded proteins in diverse cellular stress response pathways. Resolving the complexity of dynamic interactions with hosts of accessory proteins and substrates has therefore been a major challenge. Here, we used affinity-purification SWATH mass spectrometry (AP-SWATH) to identify proteins that specifically interact with a p97 substrate-trapping mutant, p97-E578Q. AP-SWATH identified differential interactions over a large detection range from abundant cofactors to pathway-specific partners and individual ligases such as RNF185 and MUL1 that were trapped in p97-E578Q complexes. In addition, we identified substrate candidates including the PP1 regulator CReP/PPP1R15B that dephosphorylates eIF2α and thus counteracts attenuation of translation by stress-kinases. We demonstrate here that p97 with its Ufd1-Npl4 adapter ensures rapid turnover and balanced levels of CReP in unperturbed cells. Moreover, we show that p97 is essential for the quantitative stress-induced degradation of CReP and, consequently, robust eIF2α phosphorylation to enforce the stress response. Thus, p97 not only facilitates bulk degradation of misfolded proteins upon stress, but also has an unanticipated function in directly modulating the integrated stress response at the level of signalling.
2018-04-04 | PXD007876 | Pride
Project description:Endometriosis is a gynaecological disease facing significant diagnostic challenges, contributing to an extensive diagnostic delay. Non-invasive diagnostic biomarkers of endometriosis could expedite diagnosis and minimise the reliance on surgery to confirm endometriosis. This pilot study aimed to identify candidate protein biomarkers of endometriosis from cervicovaginal fluid i) collected from consenting people having surgery for suspected endometriosis and ii) sampled via low vaginal swab. Samples from people with (n=20) and without (n=19) endometriosis across were analysed by data independent acquisition mass spectrometry using the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH)-MS approach. Samples were measured and analysed in two experimental runs (E1 and E2) based on time periods of sample collection. ELISA was performed to validate SWATH-MS findings.
2026-04-06 | PXD065951 | Pride