Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mentored Patient Oriented Research in Lymphoma

ABSTRACT: Mentored Patient Oriented Research in Lymphoma

PROVIDER: PRJNA730943 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Mentored Patient Oriented Research in Lymphoma

Project description:Mentored Patient Oriented Research in Lymphoma

| PRJNA730944 | ENA

Pediatric Leukemia and Lymphoma patient stool microbiome

Project description:Pediatric Leukemia and Lymphoma patient stool microbiome

| PRJEB53954 | ENA

Human lymphoma cell membrane proteomics by Pitchfork strategy

Project description:We combined glycopeptide enrichment by SPEG (Tian et al., 2007) with a hydrophobic segment-oriented hpTC method (Vít et al 2016) and a standard “detergent and trypsin” approach into a tree-pronged “Pitchfork” strategy for the analysis of membrane proteome in human lymphoma cells.

2019-03-29 | PXD012647 | Pride

circRNA-sequencing of a lymph node in a primary effusion lymphoma patient

Project description:Total RNA was extracted from a lymph node of a primary effusion lymphoma patient and treated with Rnase R to degrade linear, but not circular, RNA followed by deep-sequencing (PE150).

2021-06-30 | GSE165525 | GEO

Patient-derived lymphoma spheroids integrating immune tumor microenvironment as preclinical follicular lymphoma models for personalized medicine

Project description:Background Follicular lymphoma (FL), the most common indolent non-Hodgkin’s Lymphoma, is a heterogeneous disease and a paradigm of the contribution of immune tumor microenvironment to disease onset, progression, and therapy resistance. Patient-derived models are scarce and fail to reproduce immune phenotypes and therapeutic responses. Methods To capture disease heterogeneity and microenvironment cues, we developed a patient-derived lymphoma spheroid (FL-PDLS) model culturing FL cells from lymph nodes (LN) with an optimized cytokine cocktail that mimics LN stimuli and maintains tumor cell viability. Results FL-PDLS, mainly composed of tumor B cells (60% on average) and autologous T cells (13% CD4 and 3% CD8 on average, respectively), rapidly organizes into patient-specific three-dimensional (3D) structures of three different morphotypes according to 3D imaging analysis. RNAseq analysis indicates that FL-PDLS reproduces FL hallmarks with the overexpression of cell cycle, BCR, or mTOR signaling related gene sets. FL-PDLS also recapitulates the exhausted immune phenotype typical of FL-LN, including expression of BTLA, TIGIT, PD-1, TIM-3, CD39 and CD73 on CD3+ T cells. These features render FL-PDLS an amenable system for immunotherapy testing. With this aim, we demonstrate that the combination of obinutuzumab (anti-CD20) and nivolumab (anti-PD1) reduces tumor load in a significant proportion of FL-PDLS. Interestingly, B cell depletion inversely correlates with the percentage of CD8+ cells positive for PD-1 and TIM-3. Conclusions In summary, FL-PDLS is a robust patient-derived 3D system that can be used as a tool to mimic FL pathology and to test novel immunotherapeutic approaches in a context of personalized medicine.

2024-02-28 | GSE256457 | GEO

Building patient-oriented research capacity by co-designing a research handbook for patient partners.

Project description: Not available

| S-EPMC9258416 | biostudies-literature

Molecular classification of tumour cells in a patient with intravascular large B-cell lymphoma

Project description:Intravascular large B-cell lymphoma (IVLBCL) is a rare type of extranodal LBCL. It is characterized by the proliferation of tumour cells exclusively intraluminally in small blood vessels of different organs. We used microarray-based analysis of gene expression of tumour cells isolated from a patient with primary manifestation of the lymphoma in the skin and compared it with various other diffuse LBCLs (DLBCLs) as well as a previously published DLBCL classifier.

2017-11-15 | GSE106876 | GEO

meiose non oriented RNA-Seq data

Project description:meiose non oriented RNA-Seq data

| PRJEB5029 | ENA

DNA methylation profile of a hepatosplenic gamma/delta T-cell lymphoma patient associated with response to interferon-α therapy

Project description:We report changes in the DNA methylome in a patient with γδ hepatosplenic T-cell lymphoma (HSTCL) who responded to treatment with interferon-α2c. We studied the methylome by 450k methylation array in 5 blood samples taken within a time period of 20 months. During this time period, the WBC counts dropped from 22,300 to 7,200/μl blood, yet the proportion of γδ T cell lymphoma blasts remained around 90%. We observed time-dependent changes in overall DNA methylation and performed an in-depth bioinformatic analysis of the modulated CpG sites associated with disease progression. We identified a CpG site differentially regulating methylation, possibly related to the interferon response during the course of treatment in this particular case. Therefore, the present case report will help to understand the substantial changes in DNA methylation of lymphoma resulting in a survival benefit of this γδ HSTCL patient.

2020-10-05 | GSE105078 | GEO

Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

Project description:By analysis of ChIP-exo of FOXA1 in LNCaP, we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis. We have performed ChIP-seq of eight chromatin remodeler factors.

2016-08-01 | E-GEOD-72690 | biostudies-arrayexpress

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