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E-GEOD-61873 - Development of gene expression signatures with lncRNAs for T-cell subsets (CD34+ and CD4+CD8+)

Status
Released on 27 October 2014, last updated on 1 November 2014
Organism
Homo sapiens
Samples (13)
Array (1)
Protocols (6)
Description
Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting an essential driver role for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling. For this purpose, we measured the transcriptional response of all protein coding genes and long non-coding RNAs upon pharmacological Notch inhibition in the human T-cell acute lymphoblastic leukemia cell line CUTLL1 using RNA-sequencing. Similar Notch dependent profiles were established for normal human CD34+ thymic T-cell progenitors exposed to Notch signaling activity in vivo. In addition, we generated long non-coding RNA expression profiles (array data) from GSI treated T-ALL cell lines, ex vivo isolated Notch active CD34+ and Notch inactive CD4+CD8+ thymocytes and from a primary cohort of 15 T-cell acute lymphoblastic leukemia patients with known NOTCH1 mutation status. Integration of these expression datasets with publically available Notch1 ChIP-sequencing data resulted in the identification of long non-coding RNAs directly regulated by Notch activity in normal and malignant T-cell context. Given the central role of Notch in T-cell acute lymphoblastic leukemia oncogenesis, these data pave the way towards development of novel therapeutic strategies that target hyperactive Notch1 signaling in human T-cell acute lymphoblastic leukemia. Gene expression was measured in sorted T-cell subsets of 4 healthy donors.
Experiment type
transcription profiling by array 
Contacts
Annelynn Wallaert <annelynn.wallaert@ugent.be>, Frank Speleman, Inge Van de Walle, Jo Vandesompele, Kaat Durinck, Pieter Mestdagh, Pieter-Jan Volders, Tom Taghon, Wouter Van Loocke
Citation
The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. Durinck K, Wallaert A, Van de Walle I, Van Loocke W, Volders PJ, Vanhauwaert S, Geerdens E, Benoit Y, Van Roy N, Poppe B, Soulier J, Cools J, Mestdagh P, Vandesompele J, Rondou P, Van Vlierberghe P, Taghon T, Speleman F. , PMID:25344525
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-61873.idf.txt
Sample and data relationshipE-GEOD-61873.sdrf.txt
Raw data (1)E-GEOD-61873.raw.1.zip
Processed data (1)E-GEOD-61873.processed.1.zip
Array designA-GEOD-19197.adf.txt
Links