Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Host and Bacterial Urine Proteomics Might Predict Treatment Outcomes for Immunotherapy in Advanced NSCLC

ABSTRACT: Urine extracellular vesicles from NSCLC patients were analyzed via LC-MS/MS to identify host and microbial proteins associated with progression-free survival. The study included 33 baseline urine samples and follow-up data. Samples were processed using EVtrap and analyzed on a Q-Exactive HF-X using a 60-minute gradient.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Non-small Cell Lung Carcinoma

SUBMITTER: David Dora

LAB HEAD: Dr. David Dora

PROVIDER: PXD062630 | Pride | 2025-04-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	011321-Koranyi-NSCLC-urine-EVs-1.raw	Raw
	011321-Koranyi-NSCLC-urine-EVs-10.raw	Raw
	011321-Koranyi-NSCLC-urine-EVs-11.raw	Raw
	011321-Koranyi-NSCLC-urine-EVs-12.raw	Raw
	011321-Koranyi-NSCLC-urine-EVs-13.raw	Raw

Items per page:

1 - 5 of 54

Similar Datasets

Plasma-derived EV Phosphoproteomics through Chemical Affinity Purification

Project description:Invasive nature and pain caused to patients inhibit the routine use of tissue biopsy-based procedures for cancer diagnosis and surveillance. The analysis of extracellular vesicles (EVs) from biofluids have recently gained significant traction in the liquid biopsy field. EVs offer an essential “snapshot” of their precursor cells in real time and contain information-rich collection of nucleic acids, proteins, lipids, etc. The analysis of protein phosphorylation, as a direct marker of cellular signaling and disease progression, could be an important stepstone to successful liquid biopsy applications. Here, we introduce a rapid EV isolation method based on chemical affinity called EVtrap (Extracellular Vesicles Total Recovery and Purification) for EV phosphoproteomics analysis of human plasma. Incorporating EVtrap with high performance mass spectrometry (MS), we were able to identify over 16,000 unique peptides representing 2,238 unique EV proteins from just 5 μL plasma sample, including most known EV markers, with substantially higher recovery levels compared to ultracentrifugation. Most importantly, more than 5,500 unique phosphopeptides representing almost 1,600 phosphoproteins in EVs were identified using only 1 mL of plasma. Finally, we carried out quantitative EV phosphoproteomics analysis of plasma samples from patients diagnosed with chronic kidney disease or kidney cancer (RCC), identifying dozens of phosphoproteins capable of distinguishing disease states from healthy controls. The study demonstrates the potential feasibility of our robust analytical pipeline for cancer signaling monitoring by tracking plasma EV phosphorylation.

2020-06-15 | PXD017994 | Pride

NSCLC Lung Adenocarcinoma Proteomics

Project description:Alterations in cellular antigen processing and presenting machinery has gained increased interest as a hallmark of cancer-related inflammation. Growing evidence suggest that proteasome composition and immunoproteasome expression can influence the efficacy of cancer therapies. By applying proteasome foot-printing to clinical samples of Non Small Cell lung Cancer (NSCLC), we found tumor specific alterations in degradation products and increased expression of the proteasome regulator, PA200. We show that increased levels of PA200 alter the cleavage specificities of proteasomal-cleaved peptides and reduce antigenicity. We found that smoking-induced expression of PA200 abrogated immunoproteasome activity and is associated with poor survival. As immunotherapy is becoming a common treatment of NSCLC, we hypothesized that PA200 expression may contribute to resistance mechanism to immunotherapy. Consistent with this possibility, we found that the ratio between PA200 and the immunoproteasome subunit PSMB10, and not their absolute levels, were significantly associated with poor response to Durvalamab. Induced reduction in PA200 in vivo was associated with increased immune infiltration and attenuated tumor growth.

2023-03-30 | PXD019573 | Pride

Prognosis for Stage I/II NSCLC

Project description:Eighty-four completely resected stage I/II non-small cell lung cancer (NSCLC) without adjuvant therapy were profiled using whole genome expression microarrys in order to identify novel classifications associated with RFS. Association with relapse-free survival (RFS) and clinicopathological parameters was assessed. An external cohort of 162 tumors was used to validate results.

2014-07-29 | E-MTAB-1790 | biostudies-arrayexpress

Identification of proteome changes in apoptotic NSCLC cells

Project description:Here, we used an unbiased, functional target-discovery platform to identify immunogenic proteins from primary non-small cell lung cancer (NSCLC) cells that had been induced to apoptosis by cisplatin (CDDP) treatment in vitro, as compared with their live counterparts. Among the multitude of proteins identified, some of them were represented as fragmented proteins in apoptotic tumor cells, and acted as non-mutated neoantigens. Only the fragmented proteins elicited effective multi-specific T cell responses, upon a chemotherapy protocol including CDDP. Importantly, these responses further increased significantly upon anti-PD-1 therapy, and correlated with patients’ survival and decreased PD-1 expression.

2020-05-27 | PXD016997 | Pride

Quantitative phosphoproteomics reveals the temporal phosphorylation network regulated via mesenchymal stem cells in the tumor microenvironment

Project description:The tumor microenvironment (TME), which comprises cellular and noncellular components, is involved in the complex process of cancer development. Emerging evidence suggests that mesenchymal stem cells (MSCs), one of the vital regulators of the TME, foster tumor progression through paracrine secretion. However, the comprehensive phospho-signaling pathways that are mediated by MSCs-secreting factors have not yet been fully established. In this study, we attempt to dissect the MSCs-triggered mechanism in lung cancer using quantitative phosphoproteomics. A total of 1958 phosphorylation sites are identified in lung cancer cells stimulated with MSCs-conditioned medium (MSC-CM). Integrative analysis of the identified phosphoproteins and predicted kinases demonstrates that MSC-CM functionally promotes the proliferation and migration of lung cancer via the ERK/phospho-c-Fos-S374 pathway. Recent studies have reported that extracellular ATP accumulates in the tumor microenvironment and stimulates the P2X7 receptor on the cancer cell membrane via purinergic signaling. We observe that ectopic ATP synthase is located on the surface of MSCs and excreted extracellular ATP into the lung cancer microenvironment to trigger the ERK/phospho-c-Fos-Ser374 pathway, which is consistent with these previous findings. Our results suggest that ectopic ATP synthase on the surface of MSCs releases extracellular ATP into the tumor microenvironment, which promotes cancer progression via activation of the ERK/phospho-c-Fos-Ser374 pathway.

2022-06-09 | PXD029288 | Pride

Effects of urinary extracellular vesicles from prostate cancer patients on the transcriptomes of cancer-associated and normal fibroblasts

Project description:Patient-derived prostate fibroblast primary cultures PCF-54 and PCF-55 were established from two specimens of PC tissues. EVs were isolated from urine samples of 3 patients with PC and 2 healthy males and used for the treatment of prostate fibroblast primary cultures and normal foreskin fibroblasts. The EV-treated fibroblasts were subjected to RNA sequencing analysis.

2023-04-01 | E-MTAB-11022 | biostudies-arrayexpress

A pipeline for discovery and verification of glycoproteins from plasma-derived extracellular vesicles as breast cancer biomarkers

Project description:Glycoproteins comprise more than half of current FDA-approved protein cancer markers but the development of new glycoproteins as disease biomarkers has been stagnant. Here we present a pipeline to develop glycoproteins from extracellular vesicles (EVs) through integrating quantitative glycoproteomics with a novel reverse phase glycoprotein array, and then apply it to identify novel biomarkers of breast cancer. EV glycoproteomics show promise in circumventing the problems plaguing current serum glycoproteomics and allowed us to identify hundreds of glycoproteins that have not been identified in serum. We identified 1,453 unique glycopeptides representing 556 glycoproteins in EVs, among which 20 are significantly higher in breast cancer patients. We further applied a novel glyco-specific reverse phase protein array to quantify a subset of the candidates. Together, this study demonstrates the great potential of this integrated pipeline for biomarker discovery.

2018-04-26 | PXD007572 | Pride

Proteomic Profile of Urinary Extracellular Vesicles Unravelled Biomarkers for Prostate Cancer Recognition

Project description:Proteomic profiling of extracellular vesicles (EVs) represents a promising approach for early detection and therapeutic monitoring of diseases such as cancer, which was aimed for identifying novel biomarkers for prostate cancer diagnosis in this study. The focus of this study was to develop a robust data independent acquisition (DIA) using mass spectrometry to analyse urinary EV proteomics for prostate cancer and prostate inflammation screening. We combined three library-based analysis (direct-DIA, GPF-DIA, and fractionated DDA) to improve the stability and comprehensiveness of biomarkers. By applying this innovative DIA strategy in conjunction with stable automatic EVs extraction technology, we assessed the levels of urinary EV-associated proteins based on 40 samples consisting of 20 cases and 20 controls, where 18 EV proteins were identified to be differentiated in prostate cancer outcome, of which 3 (i.e., SERPINA3, LRG1, SCGB3A1) were shown to be consistently up regulated. We also observed 6 out of the 18 (33%) EV proteins that had been developed as drug targets, while some of them showed interactions. Moreover, the potential mechanistic pathways of significantly different EV proteins, were enriched in metabolic, immune, and inflammatory activities. These results showed consistent in an independent cohort consist of 20 participants. Based on random forest algorithm, we found that SERPINA3, LRG1, SCGB3A1 add predictable value in addition to age, prostate size, body mass index (BMI) and prostate-specific antigen (PSA). In summary, the current study revealed the EV proteomic landscape and biomarkers for prostate cancer, which has shown to provide promising insights of urine EV proteome in clinical implication.

2023-03-11 | PXD037506 | Pride

Effects of prostate cancer patient urinary extracellular vesicles and hypoxic extracellular vesicles from prostate cancer cell lines on the transcriptomes of cancer-associated and normal fibroblasts

Project description:Patient-derived prostate fibroblast primary cultures PCF-54 and PCF-55 were established from two specimens of PC tissues. Urinary EVs were isolated from urine samples of 3 patients with PC and 2 healthy males and used for the treatment of prostate fibroblast primary cultures and normal foreskin fibroblasts. Normoxic and hypoxic EVs were isolated from cell culture medium of PC3 and LNCaP prostate cancer cell lines, cultivated in normoxic and hypoxic conditions respectively. The EV-treated fibroblasts were subjected to RNA sequencing analysis.

2023-04-01 | E-MTAB-11317 | biostudies-arrayexpress

Baseline NSCLC cell lines compared to a reference mix consisting of 45 NSCLC cell lines

Project description:34 NSCLC cell lines were transcriptionally profiled against a reference mix of 45 NSCLC cell lines to look subtype specific differential gene expression 34 individual cell lines were compared to a reference mix consiting of 45 NSCLC cell lines

2013-01-18 | E-GEOD-43567 | biostudies-arrayexpress

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