Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-plex spatial RNA profiling reveals cell type-specific biomarker expression during melanoma development

ABSTRACT: High-plex spatial RNA profiling reveals cell type-specific biomarker expression during melanoma development

PROVIDER: PRJNA705876 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13824100_1.fastq.gz	Fastqsanger.gz
	SRR13824100_2.fastq.gz	Fastqsanger.gz
	SRR13824200_1.fastq.gz	Fastqsanger.gz
	SRR13824200_2.fastq.gz	Fastqsanger.gz
	SRR13824300_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 2526

Similar Datasets

High-plex spatial RNA profiling reveals cell type-specific biomarker expression during melanoma development

Project description:Early diagnosis of melanoma is critical for improved survival. However, biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 200µm-diameter regions of interest enriched in melanocytes, neighboring keratinocytes or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8’s binding partner S100A9, suggesting that injury to the epidermis may be an early and easily detectable indicator of melanoma development Together, our results establish a framework for high-plex, spatial and cell type-specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor-microenvironment interactions in tumor evolution. In this dataset, we capture the GeoMx DSP RNA profiling data associated with this study. The files here represent patients with melanocytic tumors (n = 16) which were profiled with the NanoString GeoMx pilot panel (n=4 patients, n=108 gene targets) or CTA developmental panel v1.0 (n=12 patients, n=1,412 gene targets). These panels were read out using Illumina sequencing according to manufacturer protocols. For access to high resolution (single channel, composite, or ROI) images please contact mkriner@nanostring.com.

2021-03-03 | GSE168013 | GEO

High-Plex Spatial RNA Profiling Reveals Cell Type‒Specific Biomarker Expression during Melanoma Development.

Project description:Early diagnosis of melanoma is critical for improved survival. However, the biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure the expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 regions of interest (each 200 μm in diameter) enriched in melanocytes, neighboring keratinocytes, or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8's binding partner S100A9, suggesting that injury to the epidermis may be an early and readily detectable indicator of melanoma development. Together, our results establish a framework for high-plex, spatial, and cell type‒specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor microenvironment interactions in tumor evolution.

| S-EPMC9714472 | biostudies-literature

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

Project description:We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 189 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 273 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research.

2023-01-04 | GSE213264 | GEO

The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment

Project description:Head and neck squamous cell carcinoma (HNSCC) is the seventh most common cancer globally. Despite advancements in treatment modalities, patient prognoses remain unimproved. Insight into the tumour microenvironment (TME) using spatially resolved approaches, and its association with clinical endpoints, may provide useful prognostic tools and refine current treatment outcomes. We profiled 84 mucosal HNSCC tissue samples using next-generation ultra-high plex spatial protein and transcriptome mapping (580-proteins, 18,000 mRNA targets). We found patient survival outcomes (both disease-free and overall survival) were associated with anatomical subsite and tumour stage. We identified proteomic and transcriptomic functional T cell markers within discrete TME regions that were associated with survival. GSEA revealed elevated glycolysis and hypoxia pathways in patients with worse outcomes. Key proteomic findings (including CD34 and CD44) were independently validated using single-cell protein profiling. This study provides a systematic workflow for high-plex protein and transcriptomic profiling in mucosal HNSCC.

2025-06-01 | GSE288406 | GEO

The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment (GeoMx WTA)

2025-06-01 | GSE290057 | GEO

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

Project description:High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

| PRJNA880290 | ENA

The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment

Project description:The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment

| PRJNA1217386 | ENA

Adipophilin as a metabolic biomarker for Uveal Melanoma

Project description:Adipophilin as a metabolic biomarker for Uveal Melanoma

| PRJNA935315 | ENA

High-Plex Predictive Marker Discovery for Melanoma Immunotherapy-Treated Patients Using Digital Spatial Profiling.

Project description:PurposeProtein expression in formalin-fixed, paraffin-embedded tissue is routinely measured by IHC or quantitative fluorescence (QIF) on a handful of markers on a single section. Digital spatial profiling (DSP) allows spatially informed simultaneous assessment of multiple biomarkers. Here we demonstrate the DSP technology using a 44-plex antibody cocktail to find protein expression that could potentially be used to predict response to immune therapy in melanoma.Experimental Design: The NanoString GeoMx DSP technology is compared with automated QIF (AQUA) for immune marker compartment-specific measurement and prognostic value in non-small cell lung cancer (NSCLC). Then we use this tool to search for novel predictive markers in a cohort of 60 patients with immunotherapy-treated melanoma on a tissue microarray using a 44-plex immune marker panel measured in three compartments (macrophage, leukocyte, and melanocyte) generating 132 quantitative variables.ResultsThe spatially informed variable assessment by DSP validates by both regression and variable prognostication compared with QIF for stromal CD3, CD4, CD8, CD20, and PD-L1 in NSCLC. From the 132 variables, 11 and 15 immune markers were associated with prolonged progression-free survival (PFS) and overall survival (OS). Notably, we find PD-L1 expression in CD68-positive cells (macrophages) and not in tumor cells was a predictive marker for PFS, OS, and response.ConclusionsDSP technology shows high concordance with QIF and validates based on both regression and outcome assessment. Using the high-plex capacity, we found a series of expression patterns associated with outcome, including that the expression of PD-L1 in macrophages is associated with response.

| S-EPMC6744974 | biostudies-literature

Drug combination sci-Plex Data

Project description:Drug combination sci-Plex Data

| PRJNA851906 | ENA