Browse
Submit Data
Databases
API
Help

Dataset Information

185 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic Investigation of EVLP Tissue Lung Lobes

ABSTRACT: The aim of this work concerns the development of a proteomics workflow based on LC-MS/MS useful for a comprehensive study of molecular mechanisms related to the effect on the lung subjected to EVLP

INSTRUMENT(S):

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Lung

SUBMITTER: Valentina Roffia

LAB HEAD: Pierluigi Mauri

PROVIDER: PXD006692 | Pride | 2018-11-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	native_IIIM21_frozen_I.rar	Other
	native_IIIM21_frozen_I.raw	Raw
	native_IIIM21_frozen_II.rar	Other
	native_IIIM21_frozen_II.raw	Raw
	native_IIIN23_frozen_I.rar	Other

Items per page:

1 - 5 of 72

Publications

Proteome Investigation of Rat Lungs subjected to Ex Vivo Perfusion (EVLP).

Roffia Valentina V De Palma Antonella A Lonati Caterina C Di Silvestre Dario D Rossi Rossana R Mantero Marco M Gatti Stefano S Dondossola Daniele D Valenza Franco F Mauri Pierluigi P Blasi Francesco F

Molecules (Basel, Switzerland) 20181122 12

Ex vivo lung perfusion (EVLP) is an emerging procedure that allows organ preservation, assessment and reconditioning, increasing the number of marginal donor lungs for transplantation. However, physiological and airflow measurements are unable to unveil the molecular mechanisms responsible of EVLP beneficial effects on lung graft and monitor the proper course of the treatment. Thus, it is urgent to find specific biomarkers that possess these requirements but also accurate and reliable techniques ...[more]

PMID: 30467300

Similar Datasets

Proteomics of TAS-102 plus surufatinib in metastatic pancreatic cancer

Project description:Metastatic pancreatic cancer (mPC) has a dismal prognosis, with first line systemic therapy relying primarily on FOLFIRINOX (5FU/irinotecan/oxaliplatin) or AG (Gemcitabine/Nab-Paclitaxel). Therapeutic options for mPC refractory to these regimens remain poorly-defined, and data on later lines options are scare. This prospective, single-arm study (NCT05481463) evaluated the safety and preliminary efficacy of combining the anti-angiogenic agent surufatinib with the cytotoxic drug TAS-102 (Trifluridine/Tipiracil) in mPC patients who had progressed on ≥ 2 prior lines of therapy. Primary and secondary endpoints included progression-free survival (PFS), overall survival (OS), objective response rate (ORR), disease control rate (DCR), and safety. Among 20 patients analyzed for efficacy, median PFS was 2.35 months (95% CI: 1.91-3.94) and median OS was 6.34 months (95% CI: 3.81-10.09). The ORR and DCR were 20% (4/20; all partial response) and 30% (6/20), respectively. All patients experienced treatment emergent adverse events (TEAEs), with anemia (59.1%), neutropenia (54.6%), leukopenia (50.0%), and lymphopenia (45.5%) as the most common any-grade events. Grade ≥3 TEAEs including neutropenia (31.8%), lymphopenia (13.6%), and anemia (9.1%), were observed in 50.0% (11/22) of patients. Subgroup analysis identified metastases involving > 2 organs or hepatic sites as potential predicative biomarkers for inferior efficacy. Proteomic screening revealed that overexpressed OCIAD2 correlated with poor prognosis, a finding validated in two publicly available external cohorts (CPTAC database and RuiJin cohort). In conclusion, combination of TAS-102 and surufatinib demonstrates clinically meaningful efficacy and manageable toxicity as a later line therapeutic option for refractory mPC. The biomarkers identified in this study may hold the potential to guide patient stratification and warrant further investigation to optimize precision application of this regimen.

2025-10-02 | PXD064308 | Pride

Clinicopathologic and Proteomic Characteristics of Low-Grade Undifferentiated Spindle Cell SarcomaClinicopathologic and Proteomic Characteristics of Low-Grade Undifferentiated Spindle Cell Sarcoma

Project description:We collected 14 low-grade paired Undifferentiated spindle cell sarcoma (USCS) to conduct a comprehensive mass spectrometry (MS) proteomic analysis on USCSs, while also comparing the clinicopathologic characteristics of low-grade USCSs and UPSs. More than 5600 proteins could be identified. Low-grade USCSs had 353 up-regulated and 500 down-regulated proteins compared to corresponding normal tissue.

2025-06-28 | PXD061644 | Pride

Mycobacterium tuberculosis under nitric oxide stress

Project description:To study the entire transcriptional and translational M. tuberculosis response from initial survival to eventual escape from nitric oxide (NO) stress, we exposed exponentially growing M. tuberculosis to 1 mM diethylenetriamine/nitric oxide (DETA/NO) and followed the adaptive response over 48 hours. Samples were obtained from two independent experiments performed in triplicate and we sampled aliquots for transcriptome profiling by RNA sequencing at 20 min, 2 h and 24 h and for mass spectrometry-based shotgun proteomics at 20 min, 40 min, 1 h, 2 h, 4 h, 8 h, 12 h, 24 h and 48 h post NO exposure.

2017-08-17 | PXD006039 | Pride

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations

Project description:High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation, and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu-stress was down-regulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu-stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.

2017-10-27 | PXD007728 | Pride

Differential gene expression in adrenal medulla after cardiac pressure overload

Project description:Transcriptom analysis of microdissect adrenal medulla after 8 weeks of cardiac pressure overload caused by transverse aortic constriction. Comparative transcriptome analysis was determined using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA). Six microarrays from microdissected adrenal medulla of mice were performed 8 weeks after transverse aortic constriction or sham operation.

2011-05-03 | E-GEOD-21829 | biostudies-arrayexpress

Comparative microRNA profiling of sporadic and BRCA1 associated basal-like breast cancers

Project description:Analysis of miRNA expression in grade 3 luminal, sporadic and BRCA1 associated basal-like breast cancers 44 primary grade III breast cancer (11 BRCA1 basal, 16 sporadic basal, 17 luminal) and 13 normal breast FFPE (formalin fixed, paraffin embedded) specimens, plus 7 controls and 5 cell lines were analysed. The aim of the study was to derive grade-specific miRNA signatures for sporadic and BRCA1 basal-like breast cancers, and to ascertain an immunohistochemical profile regulated by BRCA1 specific miRNAs for potential diagnostic uses.

2014-09-16 | E-GEOD-61438 | biostudies-arrayexpress

Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors

Project description:Purpose: To identify proteins and (molecular/biological) pathways associated with differences between benign and malignant epithelial ovarian tumors. Experimental procedures: Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe) to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore. Results: In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity.

2014-10-13 | PXD001084 | Pride

Label-free proteome analysis of pancreatic cancer cells exposed to 2DG

Project description:The glycolytic inhibitor 2-deoxy-d-glucose (2DG) causes energy starvation, affecting cell viability in a wide range of cancer cell lines. To determine the action of 2DG in pancreatic cancer, we performed proteomic analysis of pancreatic cancer cell line after 2DG treatment. Up-regulation of glutamine: fructose 6-phosphate aminotransferase 1 (GFAT1), which belongs to the hexosamine biosynthesis pathway (HBP) that produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) to maintain glycoprotein, was validated by evaluation of mRNA and protein levels.

2025-11-17 | PXD070833 | Pride

Proteomic profiling of kidney biopsies in nephrotic syndrome

Project description:Minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) are patterns of kidney injury observed in the filtering units of the kidney known as glomeruli. From the NURTuRE cohort of individuals with nephrotic syndrome (NS), we performed laser microdissection and mass spectrometry analysis of kidney biopsy samples to identify proteomic patterns of disease. 56 individuals with idiopathic NS segregated by histological pattern (37 MCD and 19 FSGS) across three age groups: early childhood (0-6 years), late childhood (6-18 years) and adult (>18 years). We identified global differences in glomerular cell and extracellular matrix composition related to both histological pattern and age.

2024-07-15 | PXD053362 | Pride

Proteome resource allocation in bacteria

Project description:A central aim of cell biology is to understand the strategy of gene expression in response to the environment. Here we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector’s total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth-rate dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource-allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse-graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.

2015-02-12 | PXD001467 | Pride

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