C69
Genome-wide epigenetic analysis of childhood acute lymphoblastic leukaemia
Thomas Dunwell1, Luke Hesson1, Tibor Rauch2, Daniel Catchpoole3, Eamonn Maher1, John Minna4, Gerd Pfeifer2, Farida Latif1
1University of Birmingham, UK, 2City of Hope, Duarte, USA, 3The Children's Hospital at Westmead, Australia, 4University of Texas, USA
Method
We undertook a high throughput genome-wide screen for identification of novel
genes methylated in childhood acute lymphoblastic leukaemia (ALL). We used the
MIRA assay (Methylated-CpG Island Recovery Assay) in combination with
genome-wide CpG island arrays.
Results
We identified 26 genes with frequent cancer specific methylation in childhood
ALL (range of frequencies 25-85%). We demonstrated that the majority of the
methylated genes showed loss or absence of gene expression in leukaemia cell
lines and that expression could be reintroduced after treatment with a
demethylating agent.
We could divide the genes amongst 4 categories:
(1) those only methylated in leukaemia cell lines (n=7)
(2) those frequently methylated both in leukaemia and in blood or bone marrow DNA from healthy controls (n=4)
(3) genes showing cancer specific methylation (n=26)
(4) and genes showing significantly different methylation frequencies in specific cell type of childhood leukaemia (B-ALL or T-ALL; n=7)
Furthermore, of the 26 leukaemia specific genes, 15 were novel genes that had not been previously shown to be methylated in any cancer, whilst for the rest this is the first report of their frequent methylation in childhood ALL. The cancer specific genes fell into several important functional pathways including genes involved in cell cycle regulation, apoptosis, cell growth etc. We also tested the above genes for methylation across a range of epithelial cancers (lung, breast, kidney, colorectal, brain). Several of the genes demonstrated frequent methylation across these common epithelial cancers.
Conclusion
In conclusion, we have identified a large number of frequently epigenetically
inactivated genes in childhood ALL and demonstrated that some of these are also
methylated across common epithelial cancers. Hence making them ideal candidates
as potential diagnostic markers across a panel of common childhood and adult
cancers.
