Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma

ABSTRACT: Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In the AS-HN cohort, we observed recurrent somatic mutations in CSMD3 (18%), LRP1B (18%), MUC16 (18%), POT1 (16%) and TP53 (16%). UV-positive AS-HN harbored significantly higher tumor mutation burden (TMB) than UV-negative cases (p=0.0294). NanoString profiling identified three clusters with distinct tumor inflammation signature (TIS) scores (p<0.001). Spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in Ã¢Â€Âœimmune-hotÃ¢Â€Â cases and immune foci even in otherwise Ã¢Â€ÂœcoldÃ¢Â€Â cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.

PROVIDER: EGAS00001007083 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma

Project description:Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In this dataset spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in “immune-hot” cases and immune foci even in otherwise “cold” cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.

2023-03-19 | GSE227469 | GEO

Quantitative and dynamic catalogs of proteins released during apoptotic and necroptotic cell death

Project description:The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase dependent and independent pathways Ã¢â‚¬â€œ apoptosis and necroptosis Ã¢â‚¬â€œ respectively, regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time-course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis- induced membrane permeabilisation and show reduced release of conventionally secreted cytokines.

2020-07-18 | PXD014966 | Pride

Enhanced RNA Interactome capture (eRIC) and total proteome of mouse brain, kidney and liver

Project description:Male mice on a homogenous C57BL6/J genetic background were sacrificed at 11 to 13 weeks of age by cervical dislocation. Brain, kidneys and liver were immediately harvested, flash frozen in liquid nitrogen and stored at -80Ã‚Â°C until use. Animal handling was in accordance with guidelines approved by the European Molecular Biology Laboratory (EMBL). Organ sections (thickness 30 Ã‚Âµm) were prepared in a Cryostat (Leica Biosystems, Leica CM3050 S) set to -20 Ã‚Â°C and deposited onto SuperFrost glass slides (Carl Roth, H880); the glass slides were pre-cooled to -20Ã‚Â°C in the cryostat. ~10 sections were placed on a glass slide, and a total of around 150 sections were prepared for each sample per mouse. Tissue sections on glass slides were then transferred onto metal plates placed on dry ice. The tissue sections were exposed or not to 1 J/cm2 of 254 nm UV light in a XL 1500 UV Spectrolinker (Spectronics Corporation) and subjected to eRIC to determine the RNA-bound proteome. eRIC eluates obtained from the respective organs of two mice were combined per independent experiment. The analyses were conducted in duplicate for each organ studied. For the no crosslink controls, organ sections from four mice were pooled to generate one unique no crosslink eRIC sample per organ studied.

2023-03-02 | PXD032113 | Pride

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics

Project description:Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONEÃ‚Â® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows Ã¢â‚¬Ëœon-the-flyÃ¢â‚¬â„¢ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 Ã‚Âµm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.

2024-03-22 | PXD047762 | Pride

The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer

Project description:One key barrier for improving efficacy of cancer immunotherapy remains patient stratification. While patients with CD3+CD8+ T cell inflamed Ã¢Â€Â˜hotÃ¢Â€Â™ tumors typically show better response to immune checkpoint inhibitors, it is still unknown if the repertoire of HLA bound peptides (HLAp) presented in Ã¢Â€Â˜hotÃ¢Â€Â™ and Ã¢Â€Â˜coldÃ¢Â€Â™ tumors is substantially different. We surveyed 61 tumor regions and adjacent non-malignant lung tissues from eight lung cancer patients and performed deep antigen discovery combining immunopeptidomics, genomics, bulk and spatial transcriptomics and explored the heterogenic expression and presentation of tumor (neo)antigens. We associated diverse immune cell populations with the immunopeptidome in CD3+CD8+ T cell excluded, infiltrated, hot and cold tumors and found evidence for lack of immune-editing and higher presentation efficiency of tumor antigens in cold and CD3+CD8+ T cell excluded tumors. This could have implications for the choice of combination therapies tailored to the patientÃ¢Â€Â™s mutanome and microenvironment.

| EGAS00001006298 | EGA

Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression

Project description:Childhood brain tumor ependymoma remains incurable in approximately 50 percent of cases. No oncogenic mechanism has been firmly established for the commonest ependymoma variant posterior fossa subgroup A (PFA), impeding clinical advances. Uncovering how heterogeneous cell types within the tumor microenvironment interact is crucial to a complete understanding of PFA disease progression. The underlying cellular components of the PFA tumor microenvironment have been revealed by single cell transcriptomics, identifying divergent epithelial differentiation and EMT lineages. Here we utilize spatial transcriptomics (Visium) of 14 PFA samples to chart neoplastic and immune cell architecture and identify novel biological processes.

2022-10-13 | GSE195661 | GEO

Periodontal pathogens do not exacerbate macroscopic arthritis but alter the synovial proteome

Project description:Rheumatoid arthritis (RA) and periodontitis (PD) are chronic inflammatory diseases that appear to occur in tandem. Autoantibodies against citrullinated peptide antigens linked pathogeneses with PD preceding RA. However, the mutual impact PD exerts on RA and vice versa has not yet been defined. To address this issue, we set up an animal model and analyzed how the prime inducers of citrullination - Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans ÃƒÂ¢Ã¢â€šÂ¬Ã¢â‚¬Å“ differ in their pathogenic potential. Our experimental setup included collagen induced arthritis (CIA) in the mouse, oral inoculation with P. gingivalis or A. actinomycetemcomitans to induce alveolar bone loss and the combination of both diseases in inverted orders of events. Label-free quantitative proteome analysis revealed that P. gingivalis and A. actinomycetemcomitans led to differential expression patterns in the synovial membranes that were reminiscent of cellular and humoral immune responses, respectively. The P. gingivalis and A. actinomycetemcomitans specific signatures in the synovial proteomes suggest a role for oral pathogens in shaping disease subtypes and setting the stage for subsequent therapy response.

2020-12-04 | PXD020397 | 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

Spatial transcriptomics analysis of soft tissue sarcomas.

Project description:The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used spatial transcriptomics to analyze the spatial distribution of malignant, immune, and other stromal cells present within soft tissue sarcomas.

2023-12-12 | GSE212526 | GEO

Mapping immune development across tissues in the human fetus - 10X spatial transcriptomics

Project description:To study the spatial localisations of the cell populations in an early haematopoietic tissue and lymphoid organs critical for T and B cell development, we profiled fetal liver, thymus and spleen from 3 donors at 18 PCW with sequencing-based spatial transcriptomics (10x Genomics Visium).

2022-05-12 | E-MTAB-11341 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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