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E-GEOD-18497 - Diagnosis-relapse in ALL

Status
Released on 23 March 2010, last updated on 1 May 2014
Organism
Homo sapiens
Samples (82)
Array (1)
Protocols (6)
Description
Almost a quarter of pediatric patients with Acute Lymphoblastic Leukemia (ALL) suffer from relapses. The biological mechanisms underlying therapy response and development of relapses have remained unclear. In an attempt to better understand this phenomenon, we have analyzed 41 matched diagnosis relapse pairs of ALL patients using genome–wide expression arrays (82 arrays) on purified leukemic cells. In roughly half of the patients very few differences between diagnosis and relapse samples were found (“stable group”), suggesting that mostly extra-leukemic factors (e.g., drug distribution, drug metabolism, compliance) contributed to the relapse. Therefore, we focused our further analysis on 20 samples with clear differences in gene expression (“skewed group”), reasoning that these would allow us to better study the biological mechanisms underlying relapsed ALL. After finding the differences between diagnosis and relapse pairs in this group, we identified four major gene clusters corresponding to several pathways associated with changes in cell cycle, DNA replication, recombination and repair, as well as B cell developmental genes. We also identified cancer genes commonly associated with colon carcinomas and ubiquitination to be upregulated in relapsed ALL. Thus, about half of relapses are due to selection or emergence of a clone with deregulated expression of a genes involved in pathways that regulate B cell signaling, development, cell cycle, cellular division and replication. The study contains 41 pairs of samples taken from patients at diagnosis and relapse (a total of 82 arrays).
Experiment type
transcription profiling by array 
Contacts
Dick de Ridder <d.deridder@tudelft.nl>, Dick deRidder, Elizabeth R vanWering, Els C vanderLinden, Frank J Staal, Jacques J vanDongen, Tom Schonewille, Tomasz Szczepanski, Vincent H vanderVelden
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-18497.idf.txt
Sample and data relationshipE-GEOD-18497.sdrf.txt
Raw data (3)E-GEOD-18497.raw.1.zip, E-GEOD-18497.raw.2.zip, E-GEOD-18497.raw.3.zip
Processed data (1)E-GEOD-18497.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-18497.eSet.r
Links