Carbonic Anhydrase 3 Overexpression Modulates Signal-ling Pathways Associated with Cellular Stress Resilience and Proteostasis
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Early Embryonic Cell
DISEASE(S): Breast Cancer
SUBMITTER: 
Merrina Anugraham
LAB HEAD: Daniel Kolarich
PROVIDER: PXD071770 | Pride | 2025-12-15
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Frank_MA_1_1_08082025_20250808212846.mzML | Mzml | |||
| Frank_MA_1_1_08082025_20250808212846.mzid | Mzid | |||
| Frank_MA_1_2_08082025.mzML | Mzml | |||
| Frank_MA_1_2_08082025.mzid | Mzid | |||
| Frank_MA_1_3_08082025.mzML | Mzml |
Items per page: 5 1 - 5 of 41 |
Similar Datasets
Project description:Size exclusion chromatography (SEC) is a well-established method for the isolation of extracellular vesicles (EVs), but the large elution volumes necessitate a concentration step prior to proteomics analysis. This concentration step can lead to significant EV loss. Here we report an EV proteomics approach that enables the isolation of EVs into just 80 µL, which is directly compatible with proteomics analysis without the need for prior concentration. EVs were characterized by transmission electron microscopy, Western blot, and nanoparticle tracking analysis, all of which confirmed the presence of small EVs. Proteomics analysis of the EVs was performed and benchmarked against those isolated using an automated UHPLC-SEC platform. The novel workflow identified more proteins and more EV markers, including 96 of the 100 top exosomal proteins from the ExoCarta database, compared to 91 identified using EV samples isolated by UHPLC-SEC. When applied to EVs isolated from pancreatic cancer cell lines the workflow demonstrated higher sensitivity for previously reported EV markers of pancreatic cancer.
2025-05-03 | PXD060798 | Pride
Project description:Proteomics part of multi-omic analyses of the citramalate fermentation were undertaken to uncover the reasons for remarkable citramalate productivity in an engineered strain of E. coli.
2019-06-05 | PXD013088 | Pride
Project description:Objective: Roux-Y gastric bypass (RYGB) surgery is a last treatment resort to induce substantial and sustained weight loss in severe obesity. The anatomical rearrangement affects the intestinal microbiota but so far, little information is available how it interferes with microbial functionality and microbial-host interaction independent from weight loss. Design: A RYGB rat model was utilized and compared to sham-operated controls which were kept at matched body weight as RYGB animals by food restriction. We assessed microbial taxonomy by 16S rRNA gene sequencing and functional activity by metaproteomics and metabolomics on microbiota samples collected separately from the ileum, the cecum as well as the colon and separately analysed the lumen and mucus associated microbiota. Results: Altered gut architecture in RYGB strongly affected the occurrence of Actinobacteria, especially Bifidobacteriaceae and Proteobacteria which were increased, whereas Firmicutes were decreased, although Streptococcaceae and Clostridium perfringens were observed at higher abundances. A decrease of conjugated as well as secondary bile acids was observed in the RYGB-gut lumen. In addition the arginine biosynthesis pathway in the microbiota was altered, indicated by the changes in abundance of upstream metabolites and enzymes, resulting in lower levels of arginine and higher levels of aspartate in the colon after RYGB. Conclusion: The anatomical rearrangement in RYGB affects microbiota composition and functionality by changes in amino acid and bile acid metabolism, independent of weight loss. The shift in microbiota taxonomic structure after RYGB may be mediated by the resulting change in composition of the bile acid pool in the gut lumen.
2020-03-17 | PXD013337 | Pride
Project description:Cholesterol import in mammalian cells is mediated by the LDL receptor pathway. Here, we perform a genome-wide CRISPR screen using an endogenous cholesterol reporter and identify >100 genes involved in LDL-cholesterol import. We characterise C18orf8 as a core subunit of the mammalian Mon1-Ccz1 guanidine exchange factor (GEF) for Rab7, required for complex stability and function. C18orf8-deficient cells lack Rab7 activation and show severe defects in late endosome morphology and endosomal LDL trafficking, resulting in cellular cholesterol deficiency. Unexpectedly, free cholesterol accumulates within swollen lysosomes, suggesting a critical defect in lysosomal cholesterol export. We find that active Rab7 interacts with the NPC1 cholesterol transporter and licenses lysosomal cholesterol export. This process is abolished in C18orf8-, Ccz1- and Mon1A/B-deficient cells and restored by a constitutively active Rab7. The trimeric Mon1-Ccz1-C18orf8 (MCC) GEF therefore plays a central role in cellular cholesterol homeostasis coordinating Rab7 activation, endosomal LDL trafficking and NPC1-dependent lysosomal cholesterol export.
2020-10-29 | PXD021444 | Pride
Project description:Ovarian cancer (OC) ranks as the third most common gynecological cancer. Like other cancers, there still a need for effective biomarkers. To explore if plasma proteolytic products could serve as biomarkers, we devised a platform incorporating CyDye labeling, macroporous reversed-phase liquid chromatography, reducing/non-reducing SDS-PAGE, and fluorescence imaging. With paired preoperative and postoperative plasma samples, our analyses revealed a circulating complement C3 derivative present only at the disease state. This 145-kDa species under non-reducing condition split into 72-, 39-, and 29-kDa fragments upon reduction, reminiscent of the C3c structure. Mass spectrometric analyses showed multiple C-terminal ends in the C3c α’1 fragment, which were used differently among OC patients. The variety of ends were also observed in serum samples prepared using various complement activators, redefining C3c as a mix of multiple molecular entities. A commercialized ELISA assay targeting only the canonical C3c showed a strong correlation between increased plasma levels and the OC occurrence and pro-gression. Our results suggest that plasma proteolysis in complement deactivation is involved in ovarian tumorigenesis, and the resulting protein changes may help develop next-generation cancer biomarker.
2025-05-26 | PXD057890 | Pride
Project description:Corneal wound healing involves complex cellular processes, including keratocyte cell death, which plays a pivotal role in initiating tissue repair. Recent studies suggest that pyroptosis, characterized by the release of pro-inflammatory factors, occurs during tissue repair which may also contribute to the inflammatory phase of corneal wound healing. In this study, we investigated the nature of cell death in human keratocytes treated with nigericin, a known pyroptosis inducer. Surprisingly, nigericin triggered a unique form of non-inflammatory cell death marked by extensive vacuolation, resembling paraptosis. Proteomic analysis revealed that our human keratocytes lack key components of the canonical pyroptosis pathway, including NLRP3, ASC, and caspase-1, potentially explaining the absence of pyroptosis in these cells. This process was further confirmed by the absence of caspase-3 activation and lack of ER stress, alongside increased autophagic marker LC3-II accumulation. These findings suggest that nigericin triggers a paraptosis-like cell death in keratocytes, rather than pyroptosis, highlighting an alternative mechanism of cell death in corneal wound healing that warrants further exploration.
2025-06-30 | PXD058468 | Pride
Project description:Secreted proteins found in the supernatant of different mutants were analyzed by mass spectrometry employing In source-CID. After analysis of intact N-glycopeptides on MS1 level, N-glycan compositions found were compared between two strains, consequently unraveling the molecular function of enzymes knocked down. Hereby, the role of a putative fucosyltransferase and the identity of a second core- xylosyltransferase could be confirmed.
2019-11-19 | PXD012107 | Pride
Project description:The AMPA glutamate receptor (AMPAR) is the major type of synaptic excitatory ionotropic receptor in the brain. The most abundant AMPAR subtypes in the hippocampus are GluA1/2 and GluA2/3 heterotetramers. Each subtype contributes differentially to mechanisms of synaptic plasticity, which may be in part caused by how these receptors are regulated by specific associated proteins. A broad range of AMPAR interacting proteins have been identified and several were shown to affect biogenesis, AMPAR trafficking, and channel properties, alone or in distinct assemblies, and several revealed preferred binding to specific AMPAR subunits. To date, a systematic separate interactome analysis of the major GluA1/2 and GluA2/3 AMPAR subtypes is lacking. To reveal interactors belonging to specific AMPAR sub-complexes, we performed both quantitative and interaction proteomics on hippocampi of wildtype and GluA1- or GluA3 knock-out mice. Whereas GluA1/2 receptors co-purified TARP-γ8, PRRT1 and CNIH2 with highest abundances, GluA2/3 receptors revealed strongest co-purification of CNIH2, TARP-γ2, and OLFM1. Further analysis revealed that TARP-γ8-PRRT1 can interact directly, and co-assemble into an AMPAR subcomplex especially near the synapse.
2022-12-12 | PXD031603 | Pride
Project description:Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced cross-links, fixated tissue proteins are difficult to extract hampering the performance of mass spectrometry (MS)-proteomic analysis on formaldehyde-fixated tissue. Recent years saw the use of different combinations of high-temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixated paraffin-embedded tissue proteomes. However, in order to achieve protein extraction yields similar to fresh-frozen tissue high-temperature heating is necessary. Such harsh extraction conditions may affect, labile post-translational modifications such as phosphorylations resulting in the loss of important protein information. The objective of the present work is to assess cleavable fixative reagents that allow tissue preservation as well as efficient protein extraction from fixated tissue for MS-proteomics under mild conditions. To this regard, we investigated disuccinimidyl tartrate (DST) and dithiobis[succinimidylpropionate] (DSP) as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups leading to amide bond formation. Linkers can be cleaved with sodium metaperiodate (cis-diols) or reducing agents (disulfide bonds), respectively. Our results show that reversible protein crosslinking allows tissue fixation with morphology preservation comparable to formalin. In addition, cleavage of DSP improves protein recovery from fixated tissue by a factor of 18 and increases the number of identified proteins by approximately 20% under mild extraction conditions avoiding the need for sample boiling, which could affect labile post-translational modifications. A major advantage of DSP over formaldehyde is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by periodic cleavage, while effective, resulted in side reactions that prevented effective protein extraction and subsequent protein identification. Protein crosslinkers, which can be cleaved under mild conditions, are thus viable alternatives to formaldehyde as tissue fixatives facilitating protein analysis from paraffin embedded, fixated tissue.
2018-01-29 | PXD002169 | Pride
Project description:Burkholderia mallei and Burkholderia pseudomallei are both potential biological threats agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. Analyzing the expressed proteomes of B. mallei and B. pseudomallei revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Expression of multiple virulence factors and proteins of several PKS/NRPS clusters was demonstrated. Proteome analysis can be used not only to identify bacteria but also to characterize the expression of important factors that putatively contribute to pathogenesis of B. mallei and B. pseudomallei.
2022-12-15 | PXD028126 | Pride