Dataset Information

Gene knock down studies revealed CCDC50 as candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia

ABSTRACT: The two B-cell non-Hodgkin lymphoma (NHL) entities chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) show recurrent chromosomal gains of 3q25 q29, 12q13 q14 and 18q21-q22. The pathomechanisms affected by these aberrations are not understood. The aim of this study was to identify genes, located within these gained regions, which control cell death and cell survival of MCL and CLL cancer cells. Blood samples from 24 CLL and 6 MCL patients as well as 6 cell lines representing both malignancies were analyzed by gene expression profiling. By comparison of genomic DNA and gene expression, 72 candidate genes were identified. We performed a limited RNAi screen with these candidates in order to identify genes affecting cell survival. CCDC50, SERPINI2 and SMARCC2 mediated a reduction of cell viability in primary CLL cells as well as in cell lines. Gene knock down and a NFkB reporter gene assay revealed that CCDC50 is required for survival in MCL and CLL cells and controls NFkB signaling. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE16413 | GEO | 2010/06/03

SECONDARY ACCESSION(S): PRJNA116351

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Lymphomas are classified according to the World Health Organization (WHO) classification which defines subtypes on the basis of clinical, morphological, immunophenotypic, molecular and cytogenetic criteria. Using this model, 8 of 9 of the validation samples were classified successfully. This pilot study demonstrates that such a microarray tool may be a promising diagnostic approach for small B-cell non-Hodgkin’s lymphoma. Keywords: Small B-Cell non-Hodgkin’s Lymphoma, Low Density DNA Microarray, Diagnosis Fresh-frozen tumor biopsies performed before treatment and clinical data were obtained retrospectively from 68 patients in five different institutions after lab investigations involving cytology, immunohistochemistry, cytogenetics (conventional cytogenetics and fluorescent in situ hybridization [FISH]), and/or molecular analysis. The samples were then classified unanimously by a panel of five pathologists as one of the 4 subtypes: 17 B-CLL, 14 MZL, 23 FL and 14 MCL. The immunohistochemical criteria used for identifying the 4 subtypes of SBCL were: CD20+/-, CD5+, CD23+ for B-CLL; CD20+, CD5+, CD23-, Cyclin D1+ for MCL; CD20+, CD10+, Bcl2+ for FL; CD20+, CD5-, CD10- for S-MZL. 28 samples were rejected for technical issues with RNA. The remaining 40 samples include the 4 different subtypes with this following distribution: Follicular Lymphoma/FL (n=15), Mantle Cell Lymphoma/MCL (n=7), B-Chronic Lymphocytic Leukemia/B-CLL (n=6) and Splenic Marginal Zone Lymphoma/S-MZL (n=12). The expression profile of 107 genes was evaluated in these 40 samples defined as a training set. Replicates were performed for samples of sufficient quantity, and a total of 79 gene expression profiles, comprised of 12 samples in triplicate, 15 samples in duplicate and 13 samples evaluated singly, were then analyzed. A second group of 13 patients was defined as test set and used to validate the gene signatures highlighted from the training set analysis. These patients were selected by a pathologist independent from the first analysis and include 4 FL, 3 B-CLL, 5 MCL and 1 S-MZL. Four samples were rejected for technical issues with RNA. The remaining 9 samples include the 4 different subtypes: 2 FL, 3 B-CLL, 3 MCL and 1 S-MZL. A total of 13 gene expression profiles were analyzed (4 samples evaluated in duplicate and 5 samples investigated singly).

Dataset Information

Gene knock down studies revealed CCDC50 as candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets