Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

IGR_U985_CLL_EGR2_GE_STUDY_OB

ABSTRACT: Chronic lymphocytic leukemia (CLL), the most frequent adult leukemia in western countries, is a clonal accumulation of mature B-lymphocytes and its natural history is yet unclear. By using sequencing and cellular biology approaches on a cohort of CLL patient samples, we show here that acquired CLL mutations are observed in hematopoietic multipotent progenitor fractions in the majority of patients. These early CLL mutations include recurrent inactivating mutations in NFKBIE (10.7%) and missense mutations in BRAF (3.6%) and EGR2 (8.3%). Functional analyses demonstrated that BRAF-G469R affects lymphoid differentiation and transforms the T-cell lineage in vivo. In addition, the EGR2 recurrent mutations were associated with transcriptional activation of EGR2 target genes in patients and cell cycle abnormality in cellular model. Our findings indicate that CLL may develop from an initial infra-clinic, pre-leukemic phase affecting immature hematopoietic cells. The present study concerns gene expression of mouse EML cell line transfected by EGR2 wt gene and 2 mutated forms (E356K and H384N) and controls with the empty vector. Gene expression was performed in single color on Agilent 8x60K Mouse Genome array (design 028005).

ORGANISM(S): Mus musculus

SUBMITTER: Philippe DESSEN

PROVIDER: E-MTAB-1764 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Acquired initiating mutations in early hematopoietic cells of CLL patients.

Damm Frederik F Mylonas Elena E Cosson Adrien A Yoshida Kenichi K Della Valle Véronique V Mouly Enguerran E Diop M'boyba M Scourzic Laurianne L Shiraishi Yuichi Y Chiba Kenichi K Tanaka Hiroko H Miyano Satoru S Kikushige Yoshikane Y Davi Frederick F Lambert Jérôme J Gautheret Daniel D Merle-Béral Hélène H Sutton Laurent L Dessen Philippe P Solary Eric E Akashi Koichi K Vainchenker William W Mercher Thomas T Droin Nathalie N Ogawa Seishi S Nguyen-Khac Florence F Bernard Olivier A OA

Cancer discovery 20140611 9

<h4>Unlabelled</h4>Appropriate cancer care requires a thorough understanding of the natural history of the disease, including the cell of origin, the pattern of clonal evolution, and the functional consequences of the mutations. Using deep sequencing of flow-sorted cell populations from patients with chronic lymphocytic leukemia (CLL), we established the presence of acquired mutations in multipotent hematopoietic progenitors. Mutations affected known lymphoid oncogenes, including BRAF, NOTCH1, a ...[more]

PMID: 24920063

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Project description:Genomic rearrangements leading to intragenic gene fusion are mainly found in some types of haematopoietic malignancies and sarcomas. Recently they have been described also in carcinomas such as the papillary thyroid histotype (60%-70%) and the Hürthle thyroid tumours (58%). The presence of junction oncogene constitutes an area of exciting research for emerging therapy as targeting the RET-PTC1 fusion oncogene by using small interfering RNA (siRNA) strategies since it is present only in the tumour cells and not in the surrounding normal cells. Therefore, we developed a siRNA against RET-PTC1 junction and assess its efficiency on the human papillary thyroid carcinoma cell line TPC-1 which spontaneously harbours the RET-PTC1 oncogene. The targeted genes are assessed by microarray analysis by comparing the regulated genes by the siRNA_RET-PTC1 vs a siRNA_RET developed on the RET part of the mRNA minus the siRNA_control that contain four mutation within the RET-PTC1 sequence. To test the targeted genes in the TPC-1 cell line that spontaneously harbours RET-PTC1 junction of two siRNAs developed: Within the RET-PTC1 junction, and in the mRNA RET part. A non-specific siRNA harbouring 4 mutations within the RET-PTC1 sequence was used as negative control (siRNA_control). By real-time PCR (Q-RT-PCR) we demonstrated that both siRNAs (siRNA_RET-PTC1 and siRNA_RET) significantly reduce RET mRNA levels of about 85 % in TPC-1 cells. The negative control did not show an effect of RET mRNA levels. Three independent transfections were performed on TPC-1 cells using 5 µl of Lipofectamine 2000 transfection reagent (Invitrogen, Cergy-Pontoise, France) and 50nM of i) siRNA_RET-PTC1 or ii) siRNA_RET or iii) siRNA_control that harbour 4 mutations within its sequence. Total RNAs of untreated cells and transfected cells were purified using the RNA cleanup and concentration kit (QIAGEN, Hilden, Germany) and gathered in 4 pools : 1) TPC-1 harbouring RET-PTC1 ; 2) TPC-1 silenced for RET-PTC1 with siRNA RET-PTC1 ; 3) TPC-1 silenced for siRNA RET ; 4) TPC-1 treated with the siRNA control.

Dataset Information

IGR_U985_CLL_EGR2_GE_STUDY_OB

Publications

Acquired initiating mutations in early hematopoietic cells of CLL patients.

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