Investigating differential methylation of molecular markers in Pediatric astrocytoma.
Johns, Dona Ann1, Samarasinghe, Rasika,2,
1, 2 Faculty of Health, School of Medicine, Deakin University, Waurn Ponds, Australia
Background
Untreatable gliomas, constitute one of the major causes of cancer related deaths in children. High grade gliomas, such as anaplastic astrocytoma, progress rapidly and responds poorly to treatment with a higher chance of relapse leading to very low survival rates. Epigenetic changes affecting major molecular markers such as BRAF and HDAC have been shown to facilitate tumor progression. Few other studies have identified differential methylation of major developmental genes such as NR2E1 and EN2, suggesting possible involvement in promoting metastatic progression and invasion of pediatric high grade and low grade astrocytomas (Sexton‐Oates, Dodgshun et al. 2018). Considering these studies our project investigates the differential methylation of molecular markers in pediatric astrocytoma samples at diagnosis and relapse to identify molecular pathways undergoing epigenetic alterations, which may have roles in cancer relapse and metastasis.
Methods
Freely available methylation datasets were downloaded from NCBI along with datasets obtained from collaborators upon strict MTAs. The datasets were filtered based on age, diagnostic/relapse samples and the location of origin which were then analysed using R based methylome analyser ‘RnBeads’. Principal component analysis was used to determine the major sources of variation within the data set and the significant differences in variables such as patient sex, age, or tumour location between cohorts (all P > 0.05, Fisher's exact test) were determined to identify the differentially methylated regions.
Results
A total of 575 studies were shortlisted for the analysis which were narrowed down to 370 studies based on the availability of methylation array data. The list was further narrowed down to 100 studies based on the selection criteria. After elimination of duplicate datasets, 43 studies with Illumina 450k beadchip array data, were chosen for final analysis. The raw data set was combined and normalised using RnBeads and sex chromosome probes were removed which generated approximately 50,000 common probes for methylation analysis.
Conclusion
Extensive literature search yielded 370 studies which had methylation array data which were narrowed down 43 studies when subjected to carefully determined selection parameters. Most studies were eliminated due to lack of pediatric samples (0 – 15 years of age). Probes for sex chromosomes were removed prior to RnBeads analysis. Further study must be done to arrive at definitive conclusions. The importance of epigenetic alterations in favouring tumorigenesis and metastasis in pediatric astrocytoma may have effects on such alterations. Such a study will help researchers to identify differentially expressed gene sequences which can be used as potential targets for drugs and to devise better strategies for prognosis and classification of pediatric tumor (Capper, Jones et al. 2018).
References
Capper, D., et al. (2018). "DNA methylation-based classification of central nervous system tumours." Nature 555(7697): 469-474.
Sexton‐Oates, A., et al. (2018). "Methylation profiling of paediatric pilocytic astrocytoma reveals variants specifically associated with tumour location and predictive of recurrence." Molecular oncology 12(8): 1219-1232.