Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tryptic peptide imaging of an urothelial cancer tissue cohort

ABSTRACT: Mass spectrometry imaging analysis of a clinical urothelial cancer cohort for their spatial tryptic peptide composition in two different tissue types, tumor and stroma, and two tumor subtypes, muscle-infiltrating and non muscle-infiltrating tumors.

INSTRUMENT(S): 4800 Proteomics Analyzer

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. Oliver Schilling

PROVIDER: MSV000089594 | MassIVE | Fri Jun 03 04:22:00 BST 2022

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tryptic peptide imaging of an urothelial cancer tissue cohort

Project description:Analysis of a clinical urothelial cancer cohort for their spatial tryptic peptide composition in two different tissue types, tumor and stroma, and two tumor subtypes, muscle-infiltrating and non muscle-infiltrating tumors.

2021-06-04 | PXD026459 | Pride

Uncovering tumor-stroma inter-relationships using quantitative MALDI-Mass spectrometry imaging

Project description:To facilitate analysis of protein expression changes in in situ tumors and stroma, we took advantage of a mouse model that permits conditional activation of the Ser-Thr kinase ROCK within mammary tumor cells. In this study, we undertook MALDI-MSI analysis of tissue samples derived from our conditional ROCK mammary tumor model, to quantify in an unbiased manner, the proteomic changes occurring during the progression of mammary cancers in their specific spatial contexts.

2020-09-07 | PXD019255 | Pride

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Project description:Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we introduced mipDVP, an advanced approach integrating highly multiplexed imaging, single-cell laser microdissection, and sensitive mass spectrometry to spatially profile the proteomes of distinct cell populations in a human colorectal and tonsil cancer with high sensitivity. In a colorectal tumor—a representative cold tumor—we uncovered spatial compartmentalization of an immunosuppressive macrophage barrier that potentially impedes T cell infiltration. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In a tonsil cancer sample—a hot tumor—we identified significant proteomic heterogeneity among cells influenced by proximity to cytotoxic T cell subtypes. T cells in the tumor parenchyma exhibited metabolic adaptations to hypoxic regions. Our spatially resolved, highly multiplexed strategy deciphers the complex cellular interplay within the tumor microenvironment, offering valuable insights for identifying immunotherapy targets and predictive signatures.

2024-12-19 | PXD057118 | Pride

Microdissected tumor epithelium and tumor stroma from patients with breast cancer

Project description:Stratification of breast cancers into subtypes are generally based on immune assays on tumor cells and/or mRNA expression of tumor cell enriched tissues. Here, we have laser microdissected tumor epithelium and tumor stroma from 24 breast cancer biopsies (12 luminal-like and 12 basal-like). We hypothesized that the stromal proteome would separate patients with breast into groups independently of the traditional epithelial based subtypes.

2023-06-23 | PXD027012 | Pride

Multi-omics profiling of non-small cell lung cancer patient-derived xenografts reveals proteome and phosphoproteome remodeling associated with patient outcome

Project description:131 patient-derived xenograft models were generated for non-small cell lung carcinoma and were profiled by analysis of gene copy number variation, whole exome sequence, methylome, transcriptome, proteome, and phospho(Tyr)-proteome. Proteome profiling resolved the known major histology subtypes and revealed 3 proteome subtypes (proteotypes) among adenocarcinoma and 2 in squamous cell carcinoma that were associated with distinct protein-phosphotyrosine signatures and patient survival. Proteomes of human tumor were discernible from murine stroma. Stromal proteomes were similar between histological subtypes, but two adenocarcinoma proteotypes had distinct stromal proteomes. Tumor and stromal proteotypes comprise signatures of targetable biological pathways suggesting that patient stratification by proteome profiling may be an actionable approach to precisely diagnose and treat cancer.

2021-11-24 | PXD016579 | Pride

Multi-omics profiling of non-small cell lung cancer patient-derived xenografts reveals proteome and phosphoproteome remodeling associated with patient outcome

Project description:131 patient-derived xenograft models were generated for non-small cell lung carcinoma and were profiled at the genome, transcriptome and proteome level by analysis of gene copy number variation, whole exome sequencing, DNA methylation, transcriptome, proteome and phospho(Tyr)-proteome. At the proteome level, the human tumor and murine stroma were discernible. Tumor proteome profiling resolved the known major histological subtypes and revealed 3 proteome subtypes (proteotypes) among adenocarcinoma and 2 in squamous cell carcinoma that were associated with distinct protein-phosphotyrosine signatures and patient survival. Stromal proteomes were similar between histological subtypes, but two adenocarcinoma proteotypes had distinct stromal proteomes. Proteotypes comprise tumor and stromal signatures of targetable biological pathways suggesting that patient stratification by proteome profiling may be an actionable approach to precisely diagnose and treat cancer.

2021-11-24 | PXD016674 | Pride

Spatial transcriptomics of TSC angiomyolipoma

Project description:We performed spatial transcriptomics on one IS-dominant tumor and on SLS-dominant tumor. Our goal was to determin different immune infiltration in these two subtypes.

2022-08-09 | GSE210755 | GEO

Schwann cell condition medium MS

Project description:The effects of Schwann cells on the neuro-stroma niche in pancreatic ductal adenocarcinoma (PDAC) remain to be explored. Here, single-cell RNA-sequencing and spatial transcriptome analysis of PDAC tissues reveals that Schwann cells induce malignant subtypes of tumour cells and cancer-associated fibroblasts. Mass Spectrometry (MS) were performed to detected the potential functional factors secreted by Schwann cells.

2023-06-27 | PXD042556 | Pride

Extensive Three-Dimensional Intratumor Proteomic Heterogeneity Revealed by Multiregion Sampling in High-Grade Serous Ovarian Tumor Specimens

Project description:Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOC) and analyzed by mass spectrometry. Unsupervised analyses of protein abundance data revealed independent clustering of enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor “purity”. Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins correlated with the mesenchymal subtype. Protein abundance in tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology, and underscore the need to enrich cellular subpopulations for expression profiling.

2021-07-01 | PXD026570 | Pride

Multiparameter imaging reveals clinically relevant cancer cell – stroma interaction dynamics in head and neck cancer

Project description:Epithelial tumors are characterized by abundant inter- and intra-tumor heterogeneity, which complicates diagnostics and treatment. The contribution of cancer-stroma interactions to this heterogeneity is poorly understood. Here we report a paradigm to quantify phenotypic diversity in head and neck squamous cell carcinoma (HNSCC) with single cell resolution. By combining cell state markers with morphological features, we identify phenotypic signatures that correlate with clinical features, including metastasis and recurrence. Integration of tumor and stromal signatures reveals that partial epithelial-mesenchymal transition (pEMT) renders disease outcome highly sensitive to stromal composition, generating a strong prognostic and predictive signature. Spatial transcriptomics and subsequent analyses of cancer spheroid dynamics identifies cancer-associated fibroblast–pEMT axis as a nexus for intercompartment signaling that reprograms pEMT cells into an invasive phenotype. Taken together, we establish a paradigm to identify clinically relevant tumor phenotypes, and discover a cell state-dependent interplay between stromal and epithelial compartments that drives cancer aggression.

2024-10-28 | GSE252265 | 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