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Microarray expression of B-cell Non-Hodgkins Lymphoma cases

ABSTRACT: Transcriptional profiling of major types of B-cell NHL clinical samples. While comparing all the types together, their expression was compared against reactive lymph nodes, except SMZL whose expression was compared against normal splenic cells. Keywords: disease state analysis Clinical samples; 8 reactive lymph nodes, 5 splenic controls Vs 187 cases (38 MCL, 38 CLL, 9 BL, 27 SMZL, 36 DLBCL, 33 FL , 6 nMZL)

ORGANISM(S): Homo sapiens

SUBMITTER: Miguel Piris

PROVIDER: E-GEOD-9327 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Lentiviral (HIV)-based RNA interference screen in human B-cell receptor regulatory networks reveals MCL1-induced oncogenic pathways.

Ruiz-Vela Antonio A Aggarwal Mohit M de la Cueva Paloma P Treda Cezary C Herreros Beatriz B Martín-Pérez Daniel D Dominguez Orlando O Piris Miguel A MA

Blood 20071121 3

Aberrant inhibition of B-cell receptor (BCR)-induced programmed cell death pathways is frequently associated with the development of human auto-reactive B-cell lymphomas. Here, we integrated loss-of-function, genomic, and bioinformatics approaches for the identification of oncogenic mechanisms linked to the inhibition of BCR-induced clonal deletion pathways in human B-cell lymphomas. Lentiviral (HIV)-based RNA interference screen identified MCL1 as a key survival molecule linked to BCR signaling ...[more]

PMID: 18032706

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Microarray expression of B-cell Non-Hodgkins Lymphoma cases

Project description:Transcriptional profiling of major types of B-cell NHL clinical samples. While comparing all the types together, their expression was compared against reactive lymph nodes, except SMZL whose expression was compared against normal splenic cells. Keywords: disease state analysis

2008-07-01 | GSE9327 | GEO

Molecular characterization of the chromosome 7 in SMZL

Project description:Splenic marginal zone lymphomas (SMZL) are an uncommon type of B-cell non-Hodgkin’s lymphoma (NHL-B) in which no specific chromosomal translocations have been described. In contrast, the most frequent cytogenetic abnormality is the loss of the long arm of chromosome 7 (7q). Previous reports have located this loss in the 7q32 region. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 73 patients with SMZL. To gain insight into the mapping at 7q a tiling array was also used. Our results confirmed the presence of a new region of loss on chromosome 7 in these NHL. In order to better characterize the genomic imbalances in SMZL, molecular studies were carried out in 69 patients with SMZL.

2011-10-10 | E-GEOD-31203 | biostudies-arrayexpress

Gene expression profiling of human peripheral T cell lymphoma cases vs. reactive lymph nodes

Project description:Peripheral T cell lymphoma (PTCL) is a very aggressive disease which currently lacks efficient targeted therapy. New therapeutic strategies are needed to improve the very poor outcome of these patients. However, little is known about the molecular pathogenesis of this disease. In this study, we performed a gene expression profiling analysis of a series of 38 PTCL cases in order to find deregulated pathways or genes that could become therapeutic agents for PTCL patients. 38 PTCL cases and 6 reactive lymph nodes were hybridized with the Universal Human Reference RNA (Stratagene, La Jolla, CA), which served as the reference sample.

2012-07-31 | E-GEOD-36172 | biostudies-arrayexpress

A single cell RNA-Seq study of splenic marginal zone lymphomas (SMZL)

Project description:Purpose: Single cell RNA-Seq was used to characterize in depth splenic samples obtained from splenic marginal zone lymphomas Methods: 3 frozen samples of spleen from SMZL patients were selected and thawed for performing a 10X genomics single cell RNA-Sequencing 3' assay. Results: Tumor cells formed mainly patient specific-B cell clusters, while T-cells from the 3 patients clustered together. Conclusion: Single RNA-Seq unveils the cellular composition of splenic tumors from SMZL patients.

2021-10-31 | GSE175785 | GEO

Tissue proteomics of splenic marginal zone lymphoma

Project description:Splenic marginal zone lymphoma (SMZL) is a rare chronic B lymphoproliferative disease, whose molecular pathogenesis is still not well established. For the first time a proteomic approach was undertaken to analyse the protein profiles of SMZL tissue. Western blot, immunohistochemical analysis and functional data mining were also performed in order to validate results, classify proteins, and explore their potential relationships. We demonstrated that SMZL is characterized by modulation of proteins related to energetic metabolism and apoptosis pathways. We also reported specific proteins (such as biliverdin reductase A, manganese superoxide dismutase, beta-2 microglobulin, growth factor receptor-bound protein 2, acidic leucine-rich nuclear phosphoprotein 32 family member A, and SET nuclear oncogene) directly involved in NF-kBand BCR pathways, as well as in chromatin remodelling and cytoskeleton. Our findings shed new light on SMZL pathogenesis and provide a basis for the future development of novel biomarkers.

2015-04-23 | PXD001124 | Pride

Genomic profiling of splenic marginal zone lymphoma (SMZL)

Project description:Array-based comparative genomic hybridization comparing splenic marginal zone lymphoma (SMZL) specimens with control DNA

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An integrated genomic and expression analysis of 7q deletion in SMZL (Oligo aCGH)

Project description:Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL. Keywords: Genome variation profiling by genome tiling array For aCGH. 21 fresh frozen splenic samples from patients with SMZL were hybridized against a reference control of pooled PBMC genomic DNA from 10 normal subjects. High-resolution oligonucleotide analysis of copy number variations in splenic marginal zone lymphoma (SMZL) in regions of recurrent alteration. Regions included on the array: 7q (2k resolution) and regions of interest on chromosomes 3q, 6q and 9q at 12k resolution.

2012-08-30 | E-GEOD-35425 | biostudies-arrayexpress

Gene expression profiling of Splenic Marginal Zone Lymphoma

Project description:Splenic marginal zone lymphoma (SMZL) is a rare, indolent non-Hodgkin’s lymphoma that affects 0.13 per 100,000 persons annually. Overall survival of SMZL is estimated to reach 8 to 11 years in most cases, but up to 30% of SMZL cases develop aggressive presentations resulting in greatly diminished time of survival. SMZL presents with a very heterogeneous molecular profile, making diagnosis problematic and accurate prognosis even less likely. The study herein has utilized this data to assist in identifying a potential diagnostic gene expression signature with highly specific predictive utility for further evaluation among control and SMZL patient samples. Delineation of a unique SMZL signature that could provide diagnostic utility for a malignancy that has historically been difficult to identify. These results should be further investigated and validated in subsequent molecular investigations of SMZL so it may be potentially incorporated into standard oncology practice for improving the understanding and outlook for SMZL patients.

2020-05-28 | GSE146814 | GEO

Tiling-set aCGH data for oral dysplasias and oral squamous cell carcinomas

Project description:Analysis of DNA from 89 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization Genomic DNA isolated from 89 formalin-fixed paraffin-embedded oral dysplasias and tumors, then profiled by whole genome tiling-path array CGH to identify DNA copy alterations for each case.

2009-07-01 | E-GEOD-11275 | biostudies-arrayexpress

Molecular characterization of the chromosome 7 in SMZL

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