A single cell RNA-Seq study of splenic marginal zone lymphomas (SMZL)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE175785 | GEO | 2021/10/31
REPOSITORIES: GEO
Similar Datasets
Project description:Array-based comparative genomic hybridization comparing splenic marginal zone lymphoma (SMZL) specimens with control DNA
2014-01-01 | GSE34768 | GEO
Project description:A single cell RNA-Seq study of splenic marginal zone lymphomas (SMZL)
| PRJNA733659 | ENA
Project description:Array-based comparative genomic hybridization comparing splenic marginal zone lymphoma (SMZL) specimens with control DNA A custom high-definition oligonucleotide microarray (4x44K, Agilent) was designed for aCGH from the online application tool eArray (version 5.3) and HD-CGH probe library (sequence source UCSC hg18 / NCBI Build 36). This custom microarray combines the capability to scan human genome-wide with an average resolution of approximately 100 Kb and to focus on regions of interest for highest resolution tiling (11 Kb-resolution for either chromosomes 3q and 7q). The array contains about 8,500 and 9,000 oligonucleotides spanning 97 Mb and 105 Mb of the 7q and the 3q chromosomes respectively. Twenty-seven SMZL specimens (9 males, 18 females) were analyzed using a dye-swap methodology to confirm the copy number variations. Two samples (one male, one female, namely M-CTRL and F-CTRL) collected from healthy volunteers blood from national Etablissement FranM-CM-'ais du Sang were used as DNA reference for aCGH experiments.
2014-01-01 | E-GEOD-34768 | biostudies-arrayexpress
Project description:Unique and shared cytogenetic abnormalities have been documented for marginal zone lymphomas (MZLs) arising at different sites. Recently, homozygous deletions of the chromosomal band 6q23, involving the tumor necrosis factor alpha-induced protein 3 (TNFAIP3, A20) gene, a negative regulator of NF-kappa B, were described in ocular adnexal MZL, suggesting a role for A20 as a tumor suppressor in this disease entity. Here, we investigated inactivation of A20 by DNA mutations or deletions in a panel of extranodal (EMZL), nodal (NMZL) and splenic (SMZL) MZLs. Inactivating mutations encoding truncated A20 proteins were identified in 6/32 (18.8%) MZLs, including 3/11 (27.3%) EMZLs, 2/9 (22.2%) NMZLs, and 1/12 (8.3%) SMZLs. Two additional unmutated non-splenic MZLs also showed mono- or biallelic A20 deletions by FISH and/or array-CGH. Thus, A20 loss by both somatic mutations and/or deletions represents a common genetic aberration across all MZL subtypes, which may contribute to lymphomagenesis by inducing constitutive NF-kappa B activation. Keywords: Genome variation profiling by SNP array 27 MZL samples. No technical replications.
2009-04-01 | E-GEOD-13989 | biostudies-arrayexpress
Project description:Unique and shared cytogenetic abnormalities have been documented for marginal zone lymphomas (MZLs) arising at different sites. Recently, homozygous deletions of the chromosomal band 6q23, involving the tumor necrosis factor alpha-induced protein 3 (TNFAIP3, A20) gene, a negative regulator of NF-kappa B, were described in ocular adnexal MZL, suggesting a role for A20 as a tumor suppressor in this disease entity. Here, we investigated inactivation of A20 by DNA mutations or deletions in a panel of extranodal (EMZL), nodal (NMZL) and splenic (SMZL) MZLs. Inactivating mutations encoding truncated A20 proteins were identified in 6/32 (18.8%) MZLs, including 3/11 (27.3%) EMZLs, 2/9 (22.2%) NMZLs, and 1/12 (8.3%) SMZLs. Two additional unmutated non-splenic MZLs also showed mono- or biallelic A20 deletions by FISH and/or array-CGH. Thus, A20 loss by both somatic mutations and/or deletions represents a common genetic aberration across all MZL subtypes, which may contribute to lymphomagenesis by inducing constitutive NF-kappa B activation. Keywords: Genome variation profiling by SNP array
2009-04-01 | GSE13989 | GEO
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
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
Project description:The transformation mechanism into a high-grade malignancy of SMZL has not been well studied. To define and compare the differentially expressed genes between primary SMZL cells at the different clinical periods, we analyzed the gene expression profiles using the CodeLink Human Whole Genome Bioarray.
2017-10-31 | GSE94318 | GEO
Project description:Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis. 9 samples. 6 patient samples with 7q32 deletion and 3 patient samples without 7q32 deletion. Splenic Marginal Zone Lymphoma patient samples with 7q32 deletion vs. Splenic Marginal Zone Lymphoma patient samples without 7q32 deletion
2012-07-31 | E-GEOD-35082 | biostudies-arrayexpress
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