Poster Presentation 30th Lorne Cancer Conference 2018

The epigenetic landscape of paediatric acute myeloid leukaemia   (#223)

Braydon Meyer 1 2 , Leah Morenos 1 , Louise Ludlow 1 , Daniel Catchpoole 3 , Andrew Moore 4 , Andrew Elefanty 1 2 , Paul Ekert 1 2 5 , Richard Saffery 1 2
  1. Murdoch Children's Research Institute, Parkville, VIC, Australia
  2. Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
  3. The Children's Hospital at Westmead, Westmead, NSW, Australia
  4. Royal Children's Hospital, Brisbane, QLD, Australia
  5. Children's Cancer Centre, Royal Children's Hospital, Parkville, Victoria, Australia

Acute myeloid leukaemia (AML) is a cancer of the blood and bone marrow. In the paediatric setting, close to 40% of all children with AML will not survive, primarily due to the high rate of relapse. It is becoming increasingly clear that specific methylation signatures of patients with malignancies offer a new approach to refining diagnosis of childhood cancers, with potential to more accurately predict long term outcome. We hypothesise that characterising the epigenetic signature of AML at diagnosis will help predict relapse. The aims of this study are to explore the utility of DNA methylation to accurately predict outcome in children with AML, while simultaneously discovering cellular pathways subject to epigenetic dysregulation in association with disease progression.

Using the Human Methylation 450k BeadChip Array (HM450k), we have interrogated over 450,000 methylation sites in 115 samples from children diagnosed with AML. DNA was extracted from bone marrow acquired from tissue banks Australia-wide. Publicly available data from healthy bone marrow was also included for comparative purposes. Data was normalised using Illumina normalisation methods with the ‘minfi’ package. Differential methylation analysis was undertaken using the package ‘RUVm’.

We have defined methylation signatures at diagnosis associated with AML relative to matched, healthy control samples and also with outcome (5 year event free survival vs. relapsed samples). Similar signatures can be utilised to differentiate between cytogenetic subtypes and disease progression within AML. Several genes identified in these analyses have previously been implicated in AML pathogenesis or progression. Aberrant DNA methylation has been identified in MEIS1 and MN1 as well as in global methylation repetitive elements LINE1 and ALU.

With the use of DNA methylation we are beginning to understand how some pathways are disrupted and regulated. Utilising this information, we intend on further refining these signatures so that they can be used to determine the outcome of a child and better inform treatment regimens and care.