Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discrimination of tumor and normal tissues in renal cell carcinoma

ABSTRACT: Uncovering a protein abundance-based gene panel specific to clear cell Renal Cell Carcinoma (ccRCC) could provide support for the everyday clinical decision-making process. We used proteomic data to differentiate between normal kidney and ccRCC tissues. By using datasets of patients with paired normal tissue samples from gene array cohorts, we uncovered the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens at Semmelweis University to validate the strongest genes. Differential expression was evaluated at the protein level using targeted mass spectrometry (MS).

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

DISEASE(S): Renal Clear Cell Carcinoma

SUBMITTER: Aron Bartha

LAB HEAD: Balazs Gyorffy

PROVIDER: PXD033709 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	L_201207_104.raw	Raw
	L_201207_106.raw	Raw
	L_201207_108.raw	Raw
	L_201207_110.raw	Raw
	L_201207_112.raw	Raw

Items per page:

1 - 5 of 164

Publications

Proteotranscriptomic Discrimination of Tumor and Normal Tissues in Renal Cell Carcinoma.

Bartha Áron Á Darula Zsuzsanna Z Munkácsy Gyöngyi G Klement Éva É Nyirády Péter P Győrffy Balázs B

International journal of molecular sciences 20230224 5

Clear cell renal carcinoma is the most frequent type of kidney cancer, with an increasing incidence rate worldwide. In this research, we used a proteotranscriptomic approach to differentiate normal and tumor tissues in clear cell renal cell carcinoma (ccRCC). Using transcriptomic data of patients with malignant and paired normal tissue samples from gene array cohorts, we identified the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens to further investigate the ...[more]

PMID: 36901940

Similar Datasets

Proximal proteomics connects NRF2 suppression to ZNF746/PARIS-driven oxidative stress and apoptosis in Parkinson’s disease

Project description:The nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor activates cytoprotective and metabolic gene expression in response to various electrophilic stressors. In disease, constitutive NRF2 activity promotes cancer progression while decreased NRF2 function contributes to neurodegenerative diseases. In contrast to the regulation of NRF2 protein stability in the cytoplasm, co-complexed proteins that govern NRF2 activity on chromatin are less clear. Using biotin proximity proteomics, we report networks for NRF2 and its family members NRF1, NRF3 and the NRF2 heterodimer MAFG. We found that the Parkinson’s disease zinc finger transcription factor ZNF746 (PARIS) physically associated with NRF2 and MAFG, resulting in suppression of NRF2-driven transcription. ZNF746 expression increased oxidative stress and apoptosis, phenotypes that were reversed by chemical and genetic hyperactivation of NRF2. This study presents a functionally annotated proximity network for NRF2 and suggests that ZNF746 overexpression in Parkinson’s disease directly inhibits NRF2-driven neuroprotection.

2023-12-18 | PXD043248 | Pride

Quantitative profiling of proteome extracted from zebrafish embryos exposed to different concentrations of the fungicide difenoconazole against untreated control groups.

Project description:In the present study OMICs analysis was employed to investigate the early molecular responses of zebrafish embryos to exposure to the fungicide difenoconazole. Difenoconazole, a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee (FRAC) classification, may also induce adverse effects on non-target organisms inhabiting the environment. Early molecular responses in terms of transcriptome and proteome analysis were investigated and refined to select potentially substance specific biomarker candidates for early prediction of difenoconazole toxicity in zebrafish embryos.

2024-01-02 | PXD045650 | Pride

Quantitative profiling of proteome extracted from zebrafish embryos exposed to different concentrations of the fungicide metalaxyl against untreated control groups.

Project description:In the present study OMICs analysis was employed to investigate the early molecular responses of zebrafish embryos to exposure to the fungicide metalaxyl. Metalaxyl, a nucleic acid metabolism inhibitor according to Fungicide Resistance Action Committee (FRAC) classification, may also induce adverse effects on non-target organisms inhabiting the environment. Early molecular responses in terms of transcriptome and proteome analysis were investigated and refined to select potentially substance specific biomarker candidates for early prediction of metalaxyl toxicity in zebrafish embryos.

2024-01-02 | PXD045444 | Pride

Proteomic profiling of Lemna minor exposed to Atorvastatin

Project description:Lemna minor a small aquatic plant has been used extensively in ecotoxicolgical testing to elucidate substance-related effects to freshwater plants. They are free-floating freshwater macrophyte, very sensitive towards chemical exposure and easy to cultivate thus makes the plant suitable for laboratory testing. Here we present a rapid and reproducible data dependent proteomics approach for identifying growth related molecular signatures in lemna minor as an alternative to algae testing. For this, we have analyzed the proteome of lemna minor exposed to atorvastatin as a model substances for identifying growth related molecular perturbations. These fingerprints allow for a definition of potential biomarkers as tools in screening approaches and for integration in plant growth inhibition studies (OECD TG 221), for identifying suspect substances.

2022-08-15 | PXD031680 | Pride

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

Project description:Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. We analyzed frequent ccRCC-specific peptides by MS-based HLA ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate target genes with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from the Cancer Genome Atlas (TCGA KIRC, n=452), yielding 113 candidate genes. DNA methylation (TCGA KIRC, n=273), and somatic mutations (TCGA KIRC, n=392), as well as correlations with tumor metabolites (cohort 1, n=30) and immune-oncological markers (cohort 1, n=37) were analyzed to refine regulatory and functional involvements of candidates. Immunogenicity analysis identified candidate epitopes able to activate native CD8+ T cells. Functional analysis of EGLN3, a candidate with frequent ccRCC-specific immunogenic peptides, revealed possible tumor-promoting functions. Integration of HLA ligandomics, transcriptomics, genetic and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is now mandatory to expand the treatment landscape of ccRCC.

2020-04-03 | PXD017149 | Pride

Proteomic profiling of Lemna minor exposed to Bentazon

Project description:Lemna minor a small aquatic plant has been used extensively in ecotoxicolgical testing to elucidate substance-related effects to freshwater plants. They are free-floating freshwater macrophyte, very sensitive towards chemical exposure and easy to cultivate thus makes the plant suitable for laboratory testing. Here we present a rapid and reproducible data dependent proteomics approach for identifying growth related molecular signatures in lemna minor as an alternative to algae testing. For this, we have analyzed the proteome of lemna minor exposed to bentazon as a model substances for identifying growth related molecular perturbations. These fingerprints allow for a definition of potential biomarkers as tools in screening approaches and for integration in plant growth inhibition studies, for identifying suspect substances, such as in the Lemna sp. growth inhibition test (OECD TG 221).

2022-08-15 | PXD031679 | Pride

Quantitative proteomic profiling of anti-estrogenic sexual endocrine perturbation in zebrafish embryos

Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on development and reproduction, regulatory decisions mostly rely on apical endpoints from in vivo testing with adult animals. Here, we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular fingerprints interfering with the sexual endocrine system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed tamoxifen as model substances for anti-estrogenic perturbation in a modified zebrafish embryo toxicity test (zFET). These signatures allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for identifying suspect ED substances, in the fish early life-stage test (OECD TG 210).

2023-02-25 | PXD036869 | Pride

Quantitative proteomic profiling of anti-androgenic sexual endocrine perturbation in zebrafish embryos

Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on development and reproduction, regulatory decisions mostly rely on apical endpoints from in vivo testing with adult animals. Here, we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular fingerprints interfering with the sexual endocrine system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed flutamide as model substances for anti-androgenic perturbation in a modified zebrafish embryo toxicity test (zFET). These signatures allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for identifying suspect ED substances, in the fish early life-stage test (OECD TG 210).

2023-02-25 | PXD036867 | Pride

Quantitative proteomic profiling of estrogenic sexual endocrine perturbation in zebrafish embryos

Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on development and reproduction, regulatory decisions mostly rely on apical endpoints from in vivo testing with adult animals. Here, we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular fingerprints interfering with the sexual endocrine system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed ethinylestradiol as model substances for estrogenic perturbation in a modified zebrafish embryo toxicity test (zFET). These signatures allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for identifying suspect ED substances, in the fish early life-stage test (OECD TG 210).

2023-02-25 | PXD036868 | Pride

Quantitative proteomic profiling of androgenic sexual endocrine perturbation in zebrafish embryos

Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on development and reproduction, regulatory decisions mostly rely on apical endpoints from in vivo testing with adult animals. Here, we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular fingerprints interfering with the sexual endocrine system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed methyltestosterone as model substances for androgenic perturbation in a modified zebrafish embryo toxicity test (zFET). These signatures allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for identifying suspect ED substances, in the fish early life-stage test (OECD TG 210).

2023-02-25 | PXD036875 | 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