Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subcellular Relocalization of Proteins in Response to Cisplatin-Induced DNA Damage

ABSTRACT: Cells regulate the intracellular localization of proteins to adapt to different environmental conditions including DNA damage, but this form of regulation has not been analyzed systematically. The aim of this study was to investigate the protein distribution between nucleus and cytoplasm in response to cisplatin treatment. SKOV3 cells were treated or untreated with cisplatin in concentration 40 µM for 24 h followed by mass spectrometry-based proteomic analysis of extracts of cytoplasmic and nuclear fractions. To validate the quality of separation of the nuclear and cytoplasmic fractions, abundance of proteins, which are often used as markers of nuclear fraction (lamin B1 and RPA194), was evaluated using mass spectrometry. A total of 4,085 proteins were identified. Among them, 442 proteins were up-regulated, and 578 proteins were down-regulated in the nuclear fraction after cisplatin treatment. Interestingly, according to our data, after treatment of cells with cisplatin, spliceosomal proteins significantly increased in the cytoplasmic fraction. This indicates the relocalization of spliceosomal proteins from the nucleus into the cytoplasm under the influence of therapeutic stress.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Malignant Neoplasm Of Ovary

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Arapidi

PROVIDER: PXD019642 | Pride | 2024-05-29

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	V341_01_MGFPeaklist.dat	Other
	V341_01_MGFPeaklist.mgf	Mgf
	V341_01_MGFPeaklist.mzid.gz	Mzid
	V341_01_MGFPeaklist.mzid_V341_01_MGFPeaklist.MGF	Mzid
	V341_01_MGFPeaklist.xml	Xml

Items per page:

1 - 5 of 85

Similar Datasets

Cisplatin-Induced Changes in Proteomic Profiles of Ovarian Cancer Cell and Fibroblast Secretomes

Project description:Exogenous signals from drug-stressed cancer cells promote acquisition of a more aggressive phenotype of neighboring tumor cells. To identify extracellular signaling molecules that potentially contribute to the development of therapy resistance, we examined how cancer cell secretome changes in response to chemotherapy. We performed LC-MS/MS analysis of conditioned media (CM) from ovarian cancer cells SKOV3 before and 48 hours after cisplatin treatment. We identified 1,820 and 784 proteins in secretomes of cancer cells treated or untreated with cisplatin, respectively. Functional annotation of proteins which secretion increased after cisplatin showed that these proteins were mainly associated with cluster of spliceosome. To investigate whether secretion of spliceosomal proteins during induction of apoptosis is a specific property of tumor cells, we compared proteomes of CM from primary culture of normal human skin fibroblasts before and 48 hours after exposure to cisplatin (IC50). A LC-MS/MS analysis revealed that most of the proteins in the CM of fibroblasts and cancer cells under normal conditions overlap, while the secretomes after therapy demonstrate much more pronounced differences. GO and KEGG enrichment analysis revealed higher abundance of cell adhesion and extracellular matrix proteins in CM of fibroblasts before chemotherapy; while lysosomal proteins and growth factors, associated with wound healing were increased after cisplatin treatment. Spliceosomal proteins were only slightly present in fibroblast CM and did not show any changes in a response to chemotherapy. We suggest that the acquisition of ovarian cancer chemoresistance might be partially mediated by extracellular spliceosomal components.

2024-05-29 | PXD019096 | Pride

SILAC Strategy for Analysis of Proteins Released To the Extracellular Medium and Penetrated

Project description:Exogenous signals from drug-stressed cancer cells accelerate the proliferation of neighboring tumor cells and promote them to acquire a more aggressive phenotype. We have recently found an exciting phenomenon: drug-stressed cancer cells secrete various spliceosomal proteins. We have observed this phenomenon both in vitro (culture media from cancer cell lines [Pavluykov M. et al.//Cancer Cell, 2018]) and in vivo (ovarian cancer ascites after chemotherapy [Shender V. et al//Mol. Сell. Proteomics, 2014]). The aim of this study was to elucidate which proteins from the extracellular vesicles can penetrate into recipient cells. SKOV3 donor cells were cultured on special medium containing isotope labeled lysine and arginine. When label inclusion was more than 98%, the cells were treated or untreated (control) with cisplatin. After 48 h, extracellular vesicles containing labeled proteins were isolated. These vesicles were added to unlabeled SKOV3 recipient cells and, after 10 or 48 h, the cells were lysed and subjected to LC-MS/MS to identify labeled proteins. We found that at least 189 heavy-labeled proteins entered recipient cells from the vesicles at 10-hour of incubation. Among them, 101 proteins were present at a higher level in cells incubated with apoptotic vesicles, and 29 proteins were present at a higher level in cells incubated with vesicles from non-apoptotic cells. Functional annotation of heavy-labeled proteins elevated in samples incubated with apoptotic vesicles revealed the highest enrichment in a cluster of spliceosome-related proteins. We suggest that the acquisition of a more aggressive phenotype of recipient cancer cells might be partially mediated by extracellular spliceosomal components.

2024-05-29 | PXD027948 | Pride

The Role of Extracellular Spliceosomal snRNAs in Communication of Ovarian Cancer Cells

Project description:Exogenous signals from drug-stressed cancer cells accelerate the proliferation of neighboring tumor cells and promote them to acquire a more aggressive phenotype. We have recently found an exciting phenomenon: drug-stressed cancer cells secrete various components of the spliceosome: proteins and a number of snRNAs. We have observed this phenomenon both in vitro (culture media from cancer cell lines [Pavluykov M. et al.//Cancer Cell, 2018]) and in vivo (ovarian cancer ascites after chemotherapy [Shender V. et al//Mol. Сell. Proteomics, 2014]). The aim of this study was to elucidate the role of secreted spliceosomal snRNAs in intercellular communication. We constructed synthetic U12 and U6atac snRNAs close to the natural structure, including some non-canonical nucleotides imitating post-transcriptional RNA modification. Proteomic analysis of SKOV3 cells transfected with U6atac or U12 snRNA analogs has shown that both exogenous snRNAs lead to an increase of abundance of proteins related to cell cycle regulation and M phase. It has been recently shown that a number of spliceosomal proteins affect regulation of the cell cycle, in particular the M phase (Maslon et al., 2014). Here we demonstrated that not only spliceosomal proteins but also spliceosomal snRNAs (U12 and U6atac) affect activation of mitotic cell cycle genes. This study reveals previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.

2024-05-29 | PXD027950 | Pride

Cisplatin-induced proteome changes in ovatian cancer cells

Project description:Tumors easily acquire resistance to individual drugs and drug combinations thereby limiting the treatment effectiveness. Drug-stressed tumor cells secrete components that promote the survival of recipient cells and repopulation of damaged tumors. We have previously found that therapy-induced secretomes are enriched with spliceosomal proteins. The behavior of splicing-associated genes in response to chemotherapeutic drugs is poorly understood. We show that a severely stressed cell dramatically down-regulates spliceosomal proteins by secreting them into the extracellular space, reducing the expression of the respective genes, and disrupting the splicing. Our meta-analysis indicates that drugs with different action mechanisms cause a correlated decrease in the transcription of genes involved in spliceosome and mitotic cell cycle pathways and induce similar intron retention patterns in these genes. The key transcription factors regulating the concerted change in transcription are MYC, E2F1, TP53, and WT1. Based on the correlation analysis with siRNA data, we conclude that a decrease in the representation of intracellular spliceosomal proteins in response to stress is aimed at the cell cycle arrest. At the expression and processing levels, we demonstrate that a strong interplay between splicing-associated and cell cycle genes develops in stressed cancer cells.

2018-05-22 | PXD007615 | Pride

psiCLIP of SmB, Prp16 and Prp22 in C, C* and P spliceosomal complexes

Project description:Despite the major progress made into spliceosome mechanisms through CryoEM, a major obstacle of this approach is its inability to map the positioning of helicases on the RNA substrate. Here we present a method ‘psiCLIP’ which probes protein-RNA interactions in specific spliceosomal states. The method is based on iCLIP, but is different to previous iCLIP studies in that it is performed on step-specific spliceosomes that are prepared from in vitro splicing extracts, similarly to those prepared for CryoEM. We applied psiCLIP to SmB (C complex), Prp16 (C complex) and Prp22 (C* and P complexes), using pre-mRNA substrates based on UBC4 and ACT1. We also used ATPase deficient dominant negative (dn) mutants of Prp16 and Prp22 to determine the contribution of ATPase activity to binding patterns.

2020-03-15 | E-MTAB-8895 | biostudies-arrayexpress

Global analysis of pre-mRNA subcellular localization upon splicing inhibition by spliceostatin A

Project description:RNA-Seq analysis of SSA treated cells HeLa cells, nuclear and cytoplasmic fractions, treated with SSA or MeOH

2016-02-17 | E-GEOD-72156 | biostudies-arrayexpress

MS2-affinity purification coupled with RNAseq (MAPS) revealed functional tRNA-derived RNA fragments

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-16 | E-GEOD-66520 | biostudies-arrayexpress

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore

Project description:Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the g-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs.

2018-05-22 | PXD008334 | Pride

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RyhB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RyhB in a rne131 ?ryhB strain. RyhB (without MS2) was used as control

2015-04-16 | E-GEOD-66519 | biostudies-arrayexpress

Transcriptome of ovarian cancer cells overexpressing SYNCRIP or SNU13

Project description:We showed that in response to chemotherapy, dying cancer cells can secrete spliceosomal components into the extracellular space. These therapy-induced secretomes enriched with spliceosomal components promote the chemoresistance of recipient tumor cells. We demonstrated that spliceosomal proteins SNU13 and SYNCRIP can relocalize from dying tumor cells to recipient tumor cells via extracellular vesicles. To investigate whether the increased abundance of splicing factors could be the reason for the acquisition of a more aggressive phenotype by tumor cells, we got SKOV3 cell lines stably overexpressing SYNCRIP or SNU13. These cell lines were more resistant to cisplatin compared to control cell line expressing empty vector. Next, to investigate how the therapy response is formed in tumor cells with and without overexpression of spliceosomal proteins SNU13 or SYNCRIP, we performed RNAseq analysis of these cells before and 24 hours after cisplatin treatment. Enrichement analyses showed that in response to cisplatin, genes associated with DNA repair and cell cycle regulation were upregulated in cancer cell lines overexpressing SYNCRIP or SNU13 compared with control cells. This study revealed previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.

2024-04-24 | GSE241913 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data