Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic and spatial transcriptomics identify fibroblast-associated microenvironment in early mycosis fungoides progression

ABSTRACT: Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma. To characterize the tumor microenvironment at single-cell spatial resolution, we applied NanoString CosMx Spatial Molecular Imaging (SMI) with a 1000-plex panel to formalin-fixed paraffin-embedded (FFPE) skin biopsies from MF patients. This dataset includes patch-stage and plaque-stage MF lesions from 16 patients, comprising 65,717 cells profiled across multiple fields of view per patient.

ORGANISM(S): Homo sapiens

PROVIDER: GSE337336 | GEO | 2026/07/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mycosis fungoides

Project description:Mycosis fungoides (MF) is the most common and best studied of cutaneous T-cell lymphoma (CTCL). Three clinical cutaneous stages have been described (patch, plaque and tumor) as the disease progress developing also the disease lymph node, peripheral blood or systemic involvement in late stages. Clinical and pathologic diagnosis of early MF stages (patch and plaque) is difficult as its morphologic similarity to inflammatory dermatoses and low proportion of tumoral cells.

2018-06-21 | GSE109421 | GEO

Mycosis fungoides

Project description:Mycosis fungoides

| PRJNA430861 | ENA

Genetic characterization of tumor-stage mycosis fungoides

Project description:Mycosis fungoides patients who develop tumors or extracutaneous involvement usually have a poor prognosis with no curative therapy available so far. In the present EORTC multicenter study, the genomic profile of 41 skin biopsies from tumor-stage mycosis fungoides was analyzed using a high-resolution oligo-array comparative genomic hybridization platform. Seventy-six percent of cases showed genomic aberrations. The most common imbalances were gains of 7q33.3q35 followed by 17q21.1, 8q24.21, 9q34qter and 10p14 and losses of 9p21.3 followed by 9q31.2, 17p13.1, 13q14.11, 6q21.3, 10p11.22, 16q23.2 and 16q24.3. Three specific chromosomal regions, 9p21.3, 8q24.21 and 10q26qter were defined as prognostic markers exhibiting a significant correlation with overall survival (P= .042, P= .017 and P= .022, respectively). Moreover, we have established two MFt genomic subgroups distinguishing a stable group (0-5 DNA aberrations) and an unstable group (> 5 DNA aberrations), showing that the genomic unstable group had a shorter overall survival (P=.05). We therefore conclude that specific chromosomal abnormalities, such as gains of 8q24.21 (MYC) and losses of 9p21.3 (CDKN2A, CDKN2B and MTAP), and 10q26qter (MGMT and EBF3) may play an important role in prognosis. In addition, we describe the MFt genomic instability profile. Forty-one MFt were studied by arrayCGH using the Human Genome CGH 44K microarrays (G4410B and G4426B, Agilent Technologies, Palo Alto, CA, USA). In each microarray experiment, DNA obtained from a 20x10 um sections snap frozen samples from tumoral MF lesions was compared with commercial pools of healthy female DNA (Promega, Madison, WI, USA).

2010-05-06 | E-GEOD-18098 | biostudies-arrayexpress

Proteomic discovery and verification for the screening of biomarkers in different stages of mycosis fungoides: a pilot study

Project description:Mycosis fungoides (MF) is the most common T-cell lymphoma in cutaneous malignant lymphoma, which may involve multiple organs in the advanced stage with a poor prognosis. Till now, early identification of the disease is still urgent and also there is no optimal therapy for advanced MF. In the present study, quantitative proteomic analyses (Label Free Quantitation, LFQ) and a parallel reaction monitoring (PRM) assay were applied in tissue samples of different stages of MF and the control group, so as to conduct preliminary molecular analysis of the significantly expressed proteins which may involve in the pathogenesis of the disease. The results revealed that genes and proteins implicated in DNA replication initiation, nucleosome assembly, cell adhesion activity, together with the cellular component and molecules that connecting extracellular region part may be involved in the pathogenesis and metastasis of MF. Some special proteins expressed obviously differently from the early to advanced stage of MF, indicating that they may be the key molecules for the progression of the disease. We believe that proteomics is a powerful tool to identify potential biomarkers for diagnosis and these molecules may be promising therapeutic targets for MF. For that, further studies are still needed.

2021-11-23 | PXD027714 | Pride

RNAseq of the skin of patients with Mycosis fungoides

Project description:We performed transcriptome analysis and multimodal data integration of the transcriptome and the microbiome of the skin of Mycosis fungoides Patients.

2023-12-01 | GSE221148 | GEO

NanoString CosMx SMI (human) on ten human MASLD samples

Project description:CosMx SMI is a high-plex in situ analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI is an integrated system with mature cyclic fluorescent in situ hybridization (FISH) chemistry, high-resolution imaging readout, interactive data analysis and visualization software. Herein we used the CosMx SMI with the CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) supplemented with 14 custom genes of interest to probe different disease stages of MASLD/MASH, previously known as NAFLD.

2025-12-18 | GSE312698 | GEO

Spatial and functional dissection of cancer-associated fibroblasts-mediated immune modulation in H. pylori-associated gastric cancer

Project description:We performed high-plex spatial molecular imaging (NanoString CosMx SMI) on 200,182 cells collected from 71 gastric cancer samples.

2025-12-04 | GSE308624 | GEO

Genetic characterization of tumor-stage mycosis fungoides

2009-09-15 | GSE18098 | GEO

Project description:Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma (CTCL), is a malignancy of mature, skin-homing T cells. SÃ©zary syndrome (Sz) is often considered to represent a leukemic phase of MF. In this study the pattern of numerical chromosomal alterations in MF tumor samples was defined using array-based CGH; simultaneously gene expression was analyzed using microarrays. Highly recurrent chromosomal alterations in MF include copy number gain of 7q36, 7q21-7q22 and loss of 5q13 and 9p21. This pattern characteristic of MF differs markedly from chromosomal alterations observed in Sz. Integration of data from array-based CGH and gene expression analysis yielded several candidate genes with potential relevance in the pathogenesis of MF. We confirmed that the FASTK and SKAP1 genes, residing in loci with recurrent gain, demonstrated increased expression. The RB1 and DLEU1 tumor suppressor genes showed diminished expression associated with loss. In addition, it was found that presence of chromosomal alterations on 9p21, 8q24 and 1q21-1q22 was associated with poor prognosis in patients with MF. This study provides novel insight into genetic alterations underlying MF. Furthermore, our analysis uncovered genomic differences between MF and Sz, which suggest that the molecular pathogenesis and therefore therapeutic requirements of these CTCLs may be distinct. To identify candidate oncogenes and tumor suppressor genes residing in chromosomal regions with recurrent copy number alteration in MF. To this end chromosomal alteration and gene expression patterns of 22 MF tumor samples were integrated to determine which genes located in minimal common regions (MCRs) with CNA demonstrated dysregulated expression associated with chromosomal alteration Keywords: aCGH and gene expression integration 22 tumors for aCGH and gene expression

2008-09-29 | E-GEOD-12902 | biostudies-arrayexpress

CD8+ T lymphocytes in hypopigmented mycosis fungoides: malignant cells or reactive clone?

Project description:We used targeted single cell RNA sequencing using a gene set composed of the BD Rhapsody Human Immune Response Panel, TCR panel, and a custom panel of 61 malignancy-associated genes and T/B cell receptor sequencing to characterize single cell populations in hypopigmented mycosis fungoides (HMF). Using a reference mapping model built on publically deposited classic mycosis fungoides single cell RNA sequencing datasets, we identified a predicted malignant cell population independent from the clonal T cell population in HMF.

2023-10-17 | GSE212146 | 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