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MicroRNA-expression profile in a series of Nodal marginal zone lymphoma patients [miRNA expression]

ABSTRACT: Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZLs. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B cell subtypes were included. The results were validated by qRT-PCR in an independent paraffin-embedded series including 61 NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NFkB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL. microRNA-expression profiling was conducted in a series of 40 B-cell non-Hodgkin lymphoma patients (NMZL, and FL). Six lymph nodes with reactive lymphoid hyperplasia (RLN) were used as controls

ORGANISM(S): Homo sapiens

SUBMITTER: Alberto Arribas

PROVIDER: E-GEOD-32232 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Molecular characterization of Nodal marginal zone lymphoma [Gene Expression]

Project description:Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by qRT-PCR in an independent series including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NF-kB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-221, miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by qRT-PCR in an independent series including 61 paraffin-embedded NMZLs

2011-09-20 | E-GEOD-32231 | biostudies-arrayexpress

microRNA-expression profile in a series of Nodal marginal zone lymphoma patients [miRNA expression]

2011-09-21 | GSE32232 | GEO

Molecular characterization of Nodal marginal zone lymphoma [Gene Expression]

2011-09-21 | GSE32231 | GEO

Molecular characterization of Nodal marginal zone lymphoma [CGH]

2011-09-29 | GSE32436 | GEO

Molecular characterization of Nodal marginal zone lymphoma [CGH]

Project description:Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by qRT-PCR in an independent series including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NF-kB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-221, miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL. Copy number alteration (CNA) was assayed with the DNA from 14 NMZL of frozen-tissue cases, extracted using the standard phenol-chloroform protocol. For CNA, the DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1 x 44K (Agilent Technologies) following the manufacturer’s instructions. Human female and male pooled gDNA (Promega) was used to normalize the CGH results. Results were considered valuable in 12 cases. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.

2011-09-28 | E-GEOD-32436 | biostudies-arrayexpress

Gene-expression profile in a series of non-Hodgkin lymphoma (NHL) patients

Project description:PIM serine/threonine kinases are overexpressed, translocated or amplified in multiple B-cell lymphoma types. We have explored the frequency and relevance of PIM expression in different B-cell lymphoma types, and investigated whether PIM inhibition could be a rational therapeutic approach. Increased expression of PIM2 was detected in subsets of mantle cell lymphoma (MCL), diffuse large B-cell lymphoma (DLBLC), follicular lymphoma (FL), marginal zone lymphoma-MALT type (MZL-MALT), chronic lymphocytic leukemia (CLL) and nodal marginal zone lymphoma (NMZL) cases. Increased PIM2 protein expression was associated with an aggressive clinical course in ABC-DLBCL patients. Pharmacological and genetic inhibition of PIM2 revealed p4E-BP1(Thr37/46) and p4E-BP1(Ser65) as molecular biomarkers characteristic of PIM2 activity, and indicated the involvement of PIM2 kinase in regulating mTORC1. The simultaneous genetic inhibition of all three PIM kinases induced changes in apoptosis and cell cycle. In conclusion, we show that PIM2 kinase inhibition is a rational approach in DLBCL treatment, identify appropriate biomarkers for pharmacodynamic studies, and provide a new marker for patient stratification. Gene-expression profiling was conducted in a series of 114 B-cell non-Hodgkin lymphoma patients (DLBCL, FL, MALT, MCL, CLL and NMZL). Seven freshly frozen lymph nodes and six freshly frozen reactive tonsils were used as controls.

2011-10-16 | E-GEOD-32018 | biostudies-arrayexpress

Characterizing the genetic background of nodal marginal zone lymphoma

Project description:Nodal marginal zone lymphoma (NMZL) is a rare small B cell lymphoma lacking disease-defining phenotype and precise diagnostic markers. To better understand the mutational landscape of NMZL, particularly in comparison to other small nodal B cell lymphomas, we performed whole exome sequencing, targeted high throughput sequencing and array comparative genomic hybridization on a retrospective series. Our study identified for the first time recurrent, diagnostically useful and potentially therapeutically relevant BRAF mutations in NMZL. Sets of somatic mutations that could help to discriminate NMZL from other closely related small B cell lymphomas were uncovered and tested on unclassifiable small B cell lymphoma cases, in which clinical, morphological and phenotypical features were equivocal. Application of targeted gene panel sequencing gave at many occasions valuable clues for more specific classification.

2018-03-12 | GSE109487 | GEO

Molecular characterization of Nodal marginal zone lymphoma

Project description:This SuperSeries is composed of the following subset Series: GSE32231: Molecular characterization of Nodal marginal zone lymphoma [Gene Expression] GSE32232: microRNA-expression profile in a series of Nodal marginal zone lymphoma patients [miRNA expression] Refer to individual Series

2011-09-20 | E-GEOD-32233 | biostudies-arrayexpress

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 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)

2010-05-26 | E-GEOD-9327 | biostudies-arrayexpress

Gene expression profiles from human splenic Marginal Zone and Naive (Follicular) B cells

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