E-MEXP-313 - Transcription profiling of human T-ALL patients at diagnosis and relapse

Status
Submitted on 4 November 2004, released on 15 April 2005, last updated on 11 September 2012
Organism
Homo sapiens
Samples (104)
Array (1)
Protocols (7)
Description
A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). 104 samples; Affymetrix U133A micro-arrays.

Ninety two patients with T-ALL were diagnosed and treated at Saint-Louis hospital, Paris. Seven patients were studied at diagnosis and relapse (total 99 T-ALL samples). There were 56 children (median age 9 years old; range 1 to 16), and 36 adults (median age 27; range 17 to 66). Informed consent was obtained from the patients and/or relatives. T-ALL diagnosis was based on morphological and immunophenotypical criteria using flow cytometry and an extended monoclonal antibody panel.

Using a combination of molecular cytogenetic and large-scale expression analysis in human T-ALL, we identified and characterized a new recurrent chromosomal translocation, targeting the major homeobox gene cluster HOXA and the TCRB locus. Specific quantitative PCR analysis showed that the expression of the whole HOXA gene cluster was dramatically dysregulated in the HOXA-rearranged cases, and also in MLL and CALM-AF10-related T-ALL cases, strongly suggesting that HOXA genes are oncogenic in these leukemias. Inclusion of HOXA-translocated cases in a general molecular portrait of 92 T-ALL based on large-scale expression analysis shows that this rearrangement defines a new homogeneous subgroup, which shares common biological networks with the TLX1 and TLX3-related cases. Since T-ALLs derive from T-cell progenitors, expression profiles of the distinct T-ALL subgroups were analyzed with respect to those of normal human thymic sub-populations. Inappropriate utilization or perturbation of specific molecular networks involved in thymic differentiation was detected. Moreover, we found a significant association between T-ALL oncogenic subgroups and ectopic expression of a limited set of genes, including several developmental genes, namely HOXA, TLX1, TLX3, NKX3-1, SIX6 and TFAP2C. These data strongly support the view that the abnormal expression of developmental genes, including the prototypical homeobox genes HOXA, is critical in T-ALL oncogenesis.

Project Leader:
FranC'ois Sigaux
Institut Universitaire d'Hematologie
Hopital Saint Louis, Paris, France

Data submission:
Fabien Petel
Experiment types
transcription profiling by array, disease state, is expressed
Contacts
Fabien X Petel <PetelF@ligue-cancer.net>, Andre Baruchel, Armelle Regnault, Emmanuelle Clappier, Francois Sigaux, Herve Dombret, Jean Soulier, Jean-Michel Cayuela, Maria-Luisa Toribio, Marina Garcia-Pedro
Citation
HOXA genes are included in genetic and biological networks defining human acute T-cell leukemia (T-ALL). Jean Soulier, Emmanuelle Clappier, Jean-Michel Cayuela, Armelle Regnault, Marina García-Peydró, Hervé Dombret, André Baruchel,Maria-Luisa Toribio, and François Sigaux. Blood  (2005)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MEXP-313.idf.txt
Sample and data relationshipE-MEXP-313.sdrf.txt
Raw data (3)E-MEXP-313.raw.1.zip, E-MEXP-313.raw.2.zip, E-MEXP-313.raw.3.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-MEXP-313.eSet.r
Links