Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Alternative NF-kB pathway hierarchy defines a DNA-binding network in Hodgkin Lymphoma

ABSTRACT: NF-kB transcription factors regulate different sets of genes in distinct germinal center derived B-cell lymphomas. ChIP-Seq and expression array data merged showed that Rel-B hierarchical network defined HL and cRel hierarchical network characterized DLBCL.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110348 | GEO | 2018/02/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of Hodgkin Lymphoma cell line following REL-B depletion

Project description:The expression array data will be merged with Rel-B ChIP-Seq data in HL cell lines. This will show REL-B direct and indirect controlled downstream target genes

2012-01-20 | GSE35224 | GEO

Gene expression profiling of Hodgkin Lymphoma cell line following REL-B depletion

Project description:The expression array data will be merged with Rel-B ChIP-Seq data in HL cell lines. This will show REL-B direct and indirect controlled downstream target genes HL cells were infected with a retrovirus that delivers a specific shRNA sequence to knock down the expression of REL-B

2012-01-20 | E-GEOD-35224 | biostudies-arrayexpress

Hodgkin lymphoma-educated macrophages

Project description:Comparative proteome analysis of HL and DLBCL educated human macrophages by SWATH-MS.

2020-01-29 | PXD016128 | Pride

Expression data from 40 lymphomas (Hodgkin, B cell, T cell)

Project description:We produced and analyzed the transcriptomic profiles of 40 lymphoma patients. We used microarrays to compare the global gene expression profile between the different subtypes. These samples were analyzed with a tool predictive of immune escape mechanisms previously developped, IEGS33. Depending on lymphoma subtype, different immune escape signatures can be observed. Therapeutic based on PD-1/PD-L1 blockade shows promising results in Hodgkin lymphoma (HL) and in some diffuse large B-cell lymphoma (DLBCL) patients but biomarkers predicting therapeutic response are still lacking. To gain understanding on the overall immune-escape (IE) mechanism, we recently developed a tool to score the transcriptional IE hallmarks in lymphoma samples and identified four stages of cancer immune-editing in DLBCL that correlated with overall survival. Through this method, we described here the IE profiles in HL and DLBCL from a meta-analysis of large series of microarrays. We observed that HL clustered together at the late equilibrium-early escape stage of cancer immune-editing with significant enrichment of genes involved in IE and T-cell activation as compared to DLBCL. Deconvolution of transcriptomes and immunohistochimistry showed that HL had higher CD3+ and CD4+ T-cells than all DLBCL and shared high abundance of CD8+ T-cells with DLBCL ABC and low infiltrates of CD68+CD163+ macrophages with DLBCL GC. HL and DLBCL shared the same cellular distribution of PD-1 and TIM3 staining but HL exhibited a higher expression of PD-L1 in tumor cells as well as LAG3 overexpression in ME as compared to DLBCL. Finally, our bioinformatic tools based on IEGS33 and T cell activation scores as global approach of immune escape mechanisms help to investigate in details the ME of HL. This method may be useful tool to identify HL as well as DLBCL patients who better benefit from immunotherapy strategies.

2018-12-26 | GSE120124 | GEO

Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma

Project description:We integrate high-resolution copy number data with transcriptional profiles and identify the immunoregulatory genes, PD-L1 and PD-L2, as key targets at the 9p24.1 amplification peak in HL and MLBCL cell lines. DNA copy number alterations were defined in DLBCL and HL cell lines, normalized to healthy donors, by GISTIC analysis of Affymetrix SNP 6.0 single nucleotide polymorphism microarray data. Using this analysis, we identified 9p24 amplification to be over-represented in HL cell lines compared to DLBCL cell lines.

2010-10-06 | E-GEOD-22208 | biostudies-arrayexpress

RNA-seq of CD8 single positive thymocytes from WT and Rela fx/fx CD4Cre Nfkb1KO RelKO mice.

Project description:Gene expression by CD8 thymocytes was compared between cells from WT mice, and cell from mice with gremlin deletions of cRel and Nfkb1, and a T cell specific deletion of Rel using CD4 Cre.

2019-08-23 | E-MTAB-7470 | biostudies-arrayexpress

Alternative NF-kB pathway hierarchy defines a DNA-binding network in Hodgkin Lymphoma

Project description:Alternative NF-kB pathway hierarchy defines a DNA-binding network in Hodgkin Lymphoma

| PRJNA433511 | ENA

Transcription profiling by array of cRel-/-p50-/- (DKO) and wild type (WT) peritoneal macrophages stimulated with endotoxin for 2, 6 or 18 hours.

Project description:NF-kB plays a crucial role in immunity to infection. This transcription factor consists in different combinatory homo- and hetero-dimers of the five members of the Rel family. cRel/p50-containing dimers have been involved in the development and function of the immune cells. However, the transcriptional roles of these two subunits still remain poorly explored in innate immune cells. By a multiple approach integrating ex vivo genomic analysis and an in vivo experimental study, we have investigated the consequences of the combined absence of cRel and p50 subunits of NF-kB in the innate response to infection. We have performed gene profiling of cRel-/-p50-/- (DKO) and wild type (WT) peritoneal macrophages stimulated with endotoxin for 2, 6 or 18 hours.

2012-11-21 | E-MEXP-3446 | biostudies-arrayexpress

Gene expression analysis to identify target genes of miR-150 in Hodgkin lymphoma cell lines

Project description:In Burkitt lymphoma (BL), a network consisting of MYC, MYC-repressed miR-150, known miR-150 target MYB and two novel targets of miR-150, ZDHHC11 and ZDHHC11B, has been established. This network plays an important role on the growth of BL cells. Here, we confirmed that MYB, ZDHHC11 and ZDHHC11B are targeted by miR-150 in Hodgkin lymphoma (HL) cell lines too.

2021-11-06 | GSE188310 | GEO

Long non-coding RNA expression profiling in normal B-cell subsets and Hodgkin lymphoma reveals Hodgkin and Reed-Sternberg cell specific long non-coding RNAs

Project description:Hodgkin lymphoma (HL) is a malignancy of germinal center (GC) B-cell origin. To explore the role of long non-coding RNAs (lncRNAs) in HL, we studied lncRNA expression patterns in normal B-cell subsets, HL cell lines and tissues. Naive and memory B-cells showed a highly similar lncRNA expression pattern, distinct from GC-B cells. Significant differential expression between HL and normal GC-B cells was observed for 475 lncRNA loci. For two validated lncRNAs an enhanced expression was observed in HL, diffuse large B cell lymphoma and lymphoblastoid cell lines. For a third lncRNA, increased expression levels were observed in HL and part of Burkitt lymphoma cell lines. RNA-FISH on primary HL tissues revealed a tumor cell-specific expression pattern for all three lncRNAs. A potential cis-regulatory role was observed for 107 differentially expressed lncRNA-mRNA pairs localizing within a 60kb region. In line with a cis-acting role, we showed a preferential nuclear localization for two selected candidates. Thus, we showed dynamic lncRNA expression changes during the transit of normal B-cells through the GC reaction and widely deregulated lncRNA expression patterns in HL. Three lncRNAs showed a tumor cell-specific expression pattern in HL tissues and might therefore be of value as a biomarker.

2016-05-26 | GSE81086 | GEO

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