Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell transcriptomic analysis of diffuse large B cells in cerebrospinal fluid of central nervous system lymphoma

ABSTRACT: Diffuse large B-cell lymphoma (DLBCL) is the predominant type in central nervous system lymphoma (CNSL) including primary CNSL and secondary CNSL. Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs) have offered great promise for the diagnostics and therapeutics of CNSL leptomeningeal involvement. To explore the distinct phenotypic states of CSF-DLBCs, we analyzed the transcriptomes of CSF-DLBCs from seven CNSL-DLBCL patients using single-cell RNA sequencing technology. We defined CSF-DLBCs based on abundant expression of B-cell markers, as well as the enrichment of cell proliferation and energy metabolism pathway. CSF-DLBCs within individual patient have monoclonality with similar variable region of light chains (VL) expression. It is interesting to find some CSF-DLBCs have double classes of VL (lambda and kappa) transcripts. We identified substantial heterogeneity in CSF-DLBCs, and found significantly greater among-patient heterogeneity compared to among-cell heterogeneity within patient. The transcriptional heterogeneity across CSF-DLBCs are manifested in cell cycle state and cancer-testis antigens expression. Our results will provide insight into the mechanism research and new diagnostic direction of CNSL-DLBCL leptomeningeal involvement.

ORGANISM(S): Homo sapiens

PROVIDER: GSE175510 | GEO | 2021/08/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genomic alterations of 332 malignant lymphoma using BAC array CGH analysis

Project description:Clonal heterogeneity in lymphoid malignancies has been recently reported in adult T-Cell lymphoma/leukemia, peripheral T-cell lymphoma, not otherwise specified, and mantle cell lymphoma (MCL). Our analysis was extended to other types of lymphoma including marginal zone lymphoma, follicular lymphoma, and diffuse large B-cell lymphoma (DLBCL). We examined the results of array comparative genomic hybridization analysis for 332 cases to determine if clonal heterogeneity existed in each case. Results showed that frequencies of clonal heterogeneity varied from 25% to 69% among different types of lymphoma. Multivariate analysis indicated that MCL and DLBCL with clonal heterogeneity showed a significantly poorer prognosis. Interestingly, 9p21.3 (CDKN2A/ 2B) loss and 17p13 (TP53, ATP1B2, SAT2, SHBG) loss were common regions among various types of lymphoma with clonal heterogeneity, suggesting at least in part that loss of these genes may play a role in clonal heterogeneity. We analyzed previously untreated 332 cases of lymphoma (comprising 29 cases of mantle cell lymphoma, 117 cases of diffuse large B-cell lymphoma (DLBCL), 79 cases of Follicular lymphoma, 24 cases of Burkitt lymphoma, 31 cases of mucosa-associated lymphoid tissue (MALT) lymphoma, and 51 peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS)).

2014-04-01 | E-GEOD-54303 | biostudies-arrayexpress

Genetic Heterogeneity of DLBCL

Project description:Diffuse large B-cell lymphoma (DLBCL) is the most common form of lymphoma in adults. The disease exhibits a striking heterogeneity in gene expression profiles and clinical outcomes, but its genetic causes remain to be fully defined. Through whole genome and exome sequencing, we characterized the genetic diversity of DLBCL. In all, we sequenced 73 DLBCL primary tumors (34 with matched normal DNA). Separately, we sequenced the exomes of 21 DLBCL cell lines. We identified 322 DLBCL cancer genes that were recurrently mutated in primary DLBCLs. We identified recurrent mutations implicating a number of known and not previously identified genes and pathways in DLBCL including those related to chromatin modification (ARID1A and MEF2B), NF-κB (CARD11 and TNFAIP3), PI3 kinase (PIK3CD, PIK3R1, and MTOR), B-cell lineage (IRF8, POU2F2, and GNA13), and WNT signaling (WIF1). We also experimentally validated a mutation in PIK3CD, a gene not previously implicated in lymphomas. The patterns of mutation demonstrated a classic long tail distribution with substantial variation of mutated genes from patient to patient and also between published studies. Thus, our study reveals the tremendous genetic heterogeneity that underlies lymphomas and highlights the need for personalized medicine approaches to treating these patients. 21 DLBCL cell lines and 70 DLBCL patient samples.

2013-01-23 | E-GEOD-43606 | biostudies-arrayexpress

Epigenomic Evolution of Diffuse Large B-cell Relapse

Project description:Here we characterize an association between disease progression and DNA methylation in Diffuse Large B cell Lymphoma (DLBCL). By profiling genome-wide DNA methylation at single base-pair resolution in thirteen DLBCL diagnosis-relapse sample pairs, we show DLBCL patients exhibit heterogeneous evolution of tumor methylomes during relapse. We identify differentially methylated regulatory elements and determine a relapse–associated methylation signature converging on key pathways such as transforming growth factor beta (TGF-beta) receptor activity. We also observe decreased intra-tumor methylation heterogeneity from diagnosis to relapsed tumor samples. Relapse-free patients display lower intra-tumor methylation heterogeneity at diagnosis compared to relapsed patients in an independent validation cohort. Furthermore, intra-tumor methylation heterogeneity is predictive of time to relapse. Therefore, we propose that epigenomic heterogeneity may support or drive the relapse phenotype and can be used to predict DLBCL relapse. Using ERRBS, we profiled genome-wide DNA methylation patterns of non-relapse DLBCL tumor samples at diagnosis, relaspe DLBCL patient samples at diagnosis and relaspe.

2015-04-14 | E-GEOD-66329 | biostudies-arrayexpress

Expression data from diagnostic samples of diffuse large B-cell lymphomas (DLBCL), follicular lymphoma (FL) and primary and relapsed transformed FL [SNP]

Project description:Comparison of gene expression profiles from diagnostic samples of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) to a patient case withsamples of primary and relapsed transformed FL.

2017-03-08 | GSE86621 | GEO

Expression data from diagnostic samples of diffuse large B-cell lymphomas (DLBCL), follicular lymphoma (FL) and primary and relapsed transformed FL [RNA]

2017-03-08 | GSE86613 | GEO

Genomic alterations of 332 malignant lymphoma using BAC array CGH analysis

2014-04-01 | GSE54303 | GEO

Genetic Heterogeneity of DLBCL

2013-01-23 | GSE43606 | GEO

cDNA microarray assay of lymph node biopsies diagnosed as lymphoma or as reactive tissue

Project description:Gene expression profiling of biopsied human lymph node (LN) tissue comparing each patient sample against mobilised peripheral blood stem cells (PBSC), the reference channel Evaluate whether gene expression microarray can diagnose lymph node biopsies as reactive or as one of three main types of lymphoma: classical Hodgkin’s lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL).

2012-11-28 | GSE23647 | GEO

Single cell profiling of CD4+ T cells from follicular lymphoma, diffuse large B cell lymphoma and tonsilar samples

Project description:Tumor-infiltrating regulatory T cells contribute to an immunosuppressive tumor microenvironment. We applied single-cell RNA sequencing (scRNA-seq) , TCR sequencing combined with cellular indexing of transcriptomes and epitopes (CITE-seq) on CD4 T cells to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), compared with non-malignant tonsillar tissue.

2023-09-12 | GSE242756 | GEO

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

2024-11-01 | E-MTAB-14560 | 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