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| Status |
Public on Jul 01, 2013 |
| Title |
Genome wide gene expression array analysis in T-ALL |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
In short: The objective with the gene expression array (Illumina HT-12 v.4) analysis of 17 T-ALL samples was to correlate gene expression levels with DNA promoter methylation status.
Manuscript Abstract:
Background: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided.
Design and Methods: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n=43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n= 32).
Results: Based on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p=0.02 and p=0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes.
Conclusions: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.
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| Overall design |
RNA was extracted with TRIZOL according to manufacturer instructions. Total RNA was amplified bu the Illumina TotalPrep RNA Amplification kit.
Gene expression array analysis was performed on the 17/43 pediatric T-ALL samples from which RNA was availible. 2 control samples of stimulted T-cells were included and one replicate.
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| Contributor(s) |
Borssen M, Palmqvist L, Karrman K, Abrahamsson J, Behrendtz M, Heldrup J, Forestier E, Roos G, Degerman S |
| Citation(s) |
23762353 |
| Submission date |
Oct 16, 2012 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Sofie Degerman |
| E-mail(s) |
sofie.degerman@umu.se
|
| Organization name |
Umeå University
|
| Department |
Medical Biosciensces
|
| Lab |
Pathology
|
| Street address |
NUS, Blg 6M, 2nd floor
|
| City |
Umeå |
| State/province |
Sweden |
| ZIP/Postal code |
90185 |
| Country |
Sweden |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE42080 |
Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioProject |
PRJNA179087 |
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