EPEN-21. Developing a sensitive method for detection of minimal residual disease in ependymoma using metabolomic analysis of cerebrospinal fluid

Ependymoma (EPN) is the second most common malignant paediatric brain tumour with poor survival and significant neuro-cognitive impairment from current treatments (surgery and radiotherapy). Relapse occurs in 50% of patients within 2 years, despite no evidence of tumour on MRI. This suggests that they have minimal residual disease (MRD) at the end of treatment. Developing an accurate MRD detection method could help select patients who would benefit from further continuation chemotherapy, thereby improving survival. There is also an unmet need for an accurate test to diagnose relapse early when the disease could be more treatable. METHODS: Pilot untargeted liquid chromatography-mass spectrometry (LC-MS) analysis was carried out in cerebrospinal fluid (CSF) samples from patients with ependymoma. CSF from patients in remission from leukemia were used as controls. RESULTS: Pilot data from analysis of CSF using LC-MS demonstrates that this is a feasible approach to characterise CSF metabolomic profile. Also, EPN CSF profile is significantly different from control CSF, with significant elevation of few key metabolites (Vitamin D derivatives and betaine) in EPN CSF compared to control CSF. Immunohistochemical analysis of EPN tumour tissue microarrays confirms the expression of betaine / one-carbon pathway enzymes such as methionine synthase and betaine—homocysteine S-methyltransferase. Further validation of CSF profile with tumour metabolomic profile and serial CSF sample profiling is currently underway. Subgroup-specific differences and targeted analysis to develop a panel of biomarkers is also being explored. CONCLUSION: Early results suggest that CSF-based metabolite profiling using LC-MS is feasible and could help detect minimal residual disease in ependymoma. Further validation is required to analyse subgroup-specific differences and correlate quantitative changes in metabolites with changing disease burden

Characterisation of Aberrant Metabolic Pathways in Hepatoblastoma Using Liquid Chromatography and Tandem Mass Spectrometry (LC-MS/MS)

Hepatoblastoma (HB) is a rare childhood tumour with an evolving molecular landscape. We present the first comprehensive metabolomic analysis using untargeted and targeted liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS) of paired tumour and non-tumour surgical samples in HB patients (n = 8 pairs). This study demonstrates that the metabolomic landscape of HB is distinct from that of non-tumour (NT) liver tissue, with 35 differentially abundant metabolites mapping onto pathways such as fatty acid transport, glycolysis, the tricarboxylic acid (TCA) cycle, branched-chain amino acid degradation and glutathione synthesis. Targeted metabolomics demonstrated reduced short-chain acylcarnitines and a relative accumulation of branched-chain amino acids. Medium- and long-chain acylcarnitines in HB were similar to those in NT. The metabolomic changes reported are consistent with previously reported transcriptomic data from tumour and non-tumour samples (49 out of 54 targets) as well as metabolomic data obtained using other techniques. Gene set enrichment analysis (GSEA) from RNAseq data (n = 32 paired HB and NT samples) demonstrated a downregulation of the carnitine metabolome and immunohistochemistry showed a reduction in CPT1a (n = 15 pairs), which transports fatty acids into the mitochondria, suggesting a lack of utilisation of long-chain fatty acids in HB. Thus, our findings suggest a reduced metabolic flux in HB which is corroborated at the gene expression and protein levels. Further work could yield novel insights and new therapeutic targets