Genomics

Dataset Information

4

Molecular characterization of Nodal marginal zone lymphoma [CGH]


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 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.

ORGANISM(S): Homo sapiens  

SUBMITTER: Alberto Arribas   M A Piris  Y Campos-Martín  J A Arribas  N Martinez  P Algara  J Alves-Ferreira  M Sánchez-Beato  M Mollejo  S Montes-Moreno  C Gómez-Abad  M S Rodriguez-Pinilla 

PROVIDER: E-GEOD-32436 | ArrayExpress | 2011-09-28

SECONDARY ACCESSION(S): GSE32436PRJNA154543

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-32436.README.txt Txt
E-GEOD-32436.eSet.r Other
E-GEOD-32436.idf.txt Idf
E-GEOD-32436.processed.1.zip Processed
E-GEOD-32436.raw.1.zip Raw
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