Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter RNA]

ABSTRACT: This study employed the NanoString nCounter platform to perform targeted, quantitative molecular profiling of longitudinally collected FFPE tumor samples to elucidate molecular mechanisms underlying resistance to anti–PD-1 therapy. nCounter® Vantage 3D™ Single Nucleotide Variant assay was integrated using a solid tumor panel to screen 104 driver variants across 25 genes frequently mutated in solid tumors. We quantified the expression of 770 cancer-related mRNA transcripts to identify persistently activated oncogenic pathway signatures in non-responders, which were further complemented by quantitative profiling of 27 total and phosphoproteins using antibody–oligonucleotide conjugates for functional validation of pathway activity. To characterize the tumor microenvironment spatially, GeoMx Digital Spatial Profiler analysis was utilized to assess the distribution of 38 proteins across distinct histological regions, revealing an immunosuppressive spatial architecture associated with treatment resistance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE317937 | GEO | 2026/01/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [SNV]

Project description:This study employed the NanoString nCounter platform to perform targeted, quantitative molecular profiling of longitudinally collected FFPE tumor samples to elucidate molecular mechanisms underlying resistance to anti–PD-1 therapy. nCounter® Vantage 3D™ Single Nucleotide Variant assay was integrated using a solid tumor panel to screen 104 driver variants across 25 genes frequently mutated in solid tumors. We quantified the expression of 770 cancer-related mRNA transcripts to identify persistently activated oncogenic pathway signatures in non-responders, which were further complemented by quantitative profiling of 27 total and phosphoproteins using antibody–oligonucleotide conjugates for functional validation of pathway activity. To characterize the tumor microenvironment spatially, GeoMx Digital Spatial Profiler analysis was utilized to assess the distribution of 38 proteins across distinct histological regions, revealing an immunosuppressive spatial architecture associated with treatment resistance.

2026-01-31 | GSE317918 | GEO

A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [DSP protein]

2026-01-31 | GSE318248 | GEO

A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma [nCounter protein]

2026-01-31 | GSE317936 | GEO

Genomic and immune profiling of prognostic risk groups in IgM gammopathy reveals novel biomarkers beyond MYD88 L265P

Project description:Bone marrow samples were obtained from each patient and underwent CD19+ enrichment by immunomagnetic beads to obtain a purity of at least 90% to perform targeted next generation sequencing covering 54 lymphoma driver genes. The remaining depleted samples underwent RNA isolation and further quantitative measurement of gene expression by the NanoString nCounter platform using the PanCancer Immune Profiling assay that involved 770 genes.

2025-06-16 | GSE284434 | GEO

Gene-expression analysis after intratumoral treatment with CMV-derived peptides

Project description:Analysis of whole tumor mRNA with nanostring PanCancer Immune profiling platforrm In the study presented, we analyzed the expression of 770 genes from the total tumor RNA extracted from 24 solid murine tumors

2022-07-06 | GSE205574 | GEO

Comprehensive immunophenotyping of gastric adenocarcinoma identifies an inflamed class of tumors amenable to immunotherapies

Project description:RNA from 56 gastric adenocarcinoma was analyzed on the nCounter system using the PanCancer IO 360, a curated panel including 770 genes across key immuno-oncology pathways and processes

2025-03-23 | GSE263115 | GEO

RNA-Seq in undifferentiated and differentiated retinoblastoma

Project description:Contributor to high-risk subgroup were successfully identified with the help of NanoString nCounter platform for digital gene expression analysis with the appurtenant PanCancerProfiling panel, consisting of 770 genes as well as 30 reference genes

2025-11-01 | GSE241692 | GEO

NanoString PanCancer Immune Profiling of 4′‐bromo‐resveratrol treated BrafV600E/PtenNULL melanoma mice

Project description:We performed differential gene expression analysis using high throughput multiplex analysis via NanoString nCounter PanCancer Immune Profiling panel, which analyzes 770 genes related to cancer-immune pathways (cancer progression, chemokines and cytokines and their receptors, and innate and adaptive immune response). nSolver software was used to analyze the data and a heat map was generated to show differential expression of 770 genes. Further, using a fold cut-off of ≥2 and p-value <0.05, we observed that 4'-BR significantly modulated expression of multiple cancer immune genes.

2021-11-29 | GSE168564 | GEO

The impact of remote solid tumors on bone marrow ecosystem at single-cell resolution

Project description:The bone marrow (BM) environment (BME) is inhabited by hematopoietic stem and progenitor cells (HSPCs) and niche cells, which are sources of bone homeostasis, hematopoiesis and immune response. The BM senses many pathological insults, including solid cancers. However, a comprehensive understanding of BM ecosystem response to solid cancer is lacking. Herein, by single-cell RNA sequencing, we characterized the BM landscape in tumor-bearing models prior to metastasis. We found that remote tumors induce dramatic systemic BM niche remodeling that drives HSPC reprogramming and dysfunctional hematopoiesis, which is distinct from innate immune responses.

2023-05-03 | GSE188648 | GEO

A Longitudinal, Multi-omic Atlas Reveals the Emergence of a Spatially Organized Immunosuppressive Ecosystem in Resistant Melanoma

Project description:The goal of this study is to explore the mechanisms of resistance in melanoma under various immunotherapy treatments, particularly focusing on anti-PD-1 therapy, through the analysis of RPPA data. The study includes 38 tumor samples from two melanoma patients, with samples collected at pre-treatment, on-treatment, and post-treatment time points. These two patients were classified as non-responders (NRs). The RPPA data covers more than 300 antibodies targeting key signaling pathways, including hormone receptor signaling, HER family signaling, cell cycle/proliferation pathways, immune checkpoint regulation, DNA repair deficiency, AKT/mTOR/PI3K pathways, apoptosis/autophagy, IGF1R signaling, and RTK pathways. These data will serve as a valuable resource for validating resistance markers and understanding the signaling mechanisms driving tumor progression despite immune checkpoint blockade therapies.

2026-01-31 | GSE317912 | 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