MB-84. IDENTIFICATION OF MEDULLOBLASTOMA MOLECULAR SUBGROUPS USING METABOLITE PROFILES Sarah Kohe1,2, Simrandip K. Gill1,2, Debbie Hicks3, Ed C. Schwalbe3, Stephen Crosier3, Lisa Storer4, Anbarasu Lourdusamy4, Christopher D. Bennett1,2, Martin Wilson1,2, Simon Bailey3, Daniel Williamson3, Richard G. Grundy4, Steven C. Clifford3, and Andrew C. Peet1,2; Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Childrens Hospital, Birmingham, UK; Northern Institute for Cancer Research, Newcastle University, Newcastle, UK; Childrens Brain Tumour Research Centre, Queens Medical Centre, University of Nottingham, Nottingham, UK Identification of the four consensus molecular subgroups of medulloblastoma is becoming increasingly important for determining risk-based treatment strategies. Metabolite profiles can distinguish between brain tumour types, therefore we investigated whether profiling can discriminate the molecular subgroups within medulloblastoma. Metabolite concentrations were determined using high resolution magnetic resonance spectroscopy (MRS) on biopsied tissue from 29 medulloblastomas. Molecular subgroup was determined by Illumina 450K DNA methylation array and consensus clustering. Mean metabolite concentrations showed taurine, characteristic of PNETs, was prominent in all subgroups. Lipid was significantly elevated in high-risk Group 3 tumours (n 1⁄4 5, p , 0.0002) consistent with it being a marker of poor prognosis. The ratio of glutamate to glutamine was significantly higher in SHH (n 1⁄4 6), and lower in Group 4 (n 1⁄4 15), p , 0.03. Decreased creatine was detected in SHH tumours, p , 0.002. Only low risk WNT tumours (n 1⁄4 3) contained GABA suggesting it may be a subgroup specific marker, supported by links between GABA and WNT signalling in the developing cerebellum. Glycine, typically associated with poor prognosis, was also significantly lower in WNT tumours (p , 0.003). Multivariate PLS discriminant analysis found metabolite profiles could discriminate subgroup with a classification accuracy of 85% in this pilot set. Lipid, glutamate, glutamine, taurine, hypotaurine, GABA, myoinositol, glycine and creatine were most discriminatory. Matched 1.5T in-vivo MRS concentrations (n 1⁄4 19) found significant correlations with ex-vivo values for taurine, glutamate, glutamine, glycine, creatine, and myoinositol (Pearson’s r range:0.61-0.67, p , 0.05). Identified profiles will inform non-invasive MRS methods for pre-operative subgroup identification, with potential to guide extent of surgical resection and enhanced disease monitoring. Neuro-Oncology 18:iii97–iii122, 2016. doi:10.1093/neuonc/now076.80 #The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Abstract Determinants of survivorship outcomes are emerging from limited studies of medulloblastoma (MB) survivors. We undertook an integrated analysis of biological (tumour group, host genetics) and clinico-demographic features in patients treated on the SIOP-UKCCSG-PNET3 and HIT-SIOP-PNET4 clinical trials with available quality of survival (QoS) data (n=218), to determine key correlates of survivorship, and their clinical potential. Treatment/demographic factors and molecular subgroup (MBWNT, MBSHH, MBGrp3, MBGrp4) were assessed against health status, behavioural functioning, and health-related quality of life (HrQoL). In DNA from HIT-SIOP-PNET4 (n=74), 39 candidate SNPs with known modifying effects on neurocognitive outcomes (e.g., involved in oxidative stress/inflammation) were genotyped and assessed against Wechsler Intelligence Scale (WISC) scores. As expected, MBSHH was associated with improved HrQoL, but subgroup did not associate further with QoS outcomes. SIOP-UKCCSG-PNET3 patients receiving chemotherapy before craniospinal irradiation (CSI) had significantly lower health status (p=0.021) and behavioural functioning (p<0.016) compared to patients treated with CSI alone, and those treated on both arms (maintenance chemotherapy and hyperfractionated (36Gy) or standard (23.4Gy) CSI) of HIT-SIOP-PNET4. SIOP-UKCCSG-PNET3 patients receiving CSI-only had better HrQoL scores than those who received pre-CSI chemotherapy and both HIT-SIOP-PNET4 arms (p=0.004). Females reported worse HrQoL/behavioural functioning across both trials (p<0.04). In HIT-SIOP-PNET4, longer intervals from diagnosis to CSI predicted worse HrQoL/health status (p<0.05). Neither molecular group nor clinico-demographic features tested were associated with neurocognition. In contrast, 6 SNPs significantly associated with ≥1 WISC domain; 4/6 showed multiple associations and were independently prognostic; further associations were apparent at the gene/pathway level. This large, integrated and multi-disciplinary analysis of two independent trials cohorts has revealed multiple factors predictive of medulloblastoma survivorship including treatment (chemotherapy, time to CSI), tumour (molecular group) and host genetic factors. Assessment in further prospective series are required to determine their potential as a basis for modifications to disease management.
Journal aims for the development of technologies for providing insights into the molecular, genetic and cellular basis of diseases, with growing opportunities for improving individualized patient care. It also focuses on genome technologies, including high-throughput genotyping, sequencing and the study of gene expression
Most children with medulloblastoma fall within the standard-risk clinical disease group defined by absence of high-risk features (metastatic disease, large-cell/anaplastic histology, and MYC amplification), which includes 50-60% of patients and has a 5-year event-free survival of 75-85%. Within standard-risk medulloblastoma, patients in the WNT subgroup are established as having a favourable prognosis; however, outcome prediction for the remaining majority of patients is imprecise. We sought to identify novel prognostic biomarkers to enable improved risk-adapted therapies.The HIT-SIOP PNET 4 trial recruited 338 patients aged 4-21 years with medulloblastoma between Jan 1, 2001, and Dec 31, 2006, in 120 treatment institutions in seven European countries to investigate hyperfractionated radiotherapy versus standard radiotherapy. In this retrospective analysis, we assessed the remaining tumour samples from patients in the HIT-SIOP PNET 4 trial (n=136). We assessed the clinical behaviour of the molecularly defined WNT and SHH subgroups, and identified novel independent prognostic markers and models for standard-risk patients with non-WNT/non-SHH disease. Because of the scarcity and low quality of available genomic material, we used a mass spectrometry-minimal methylation classifier assay (MS-MIMIC) to assess methylation subgroup and a molecular inversion probe array to detect genome-wide copy number aberrations. Prognostic biomarkers and models identified were validated in an independent, demographically matched cohort (n=70) of medulloblastoma patients with non-WNT/non-SHH standard-risk disease treated with conventional therapies (maximal surgical resection followed by adjuvant craniospinal irradiation [all patients] and chemotherapy [65 of 70 patients], at UK Children's Cancer and Leukaemia Group and European Society for Paediatric Oncology (SIOPE) associated treatment centres between 1990 and 2014. These samples were analysed by Illumina 450k DNA methylation microarray. HIT-SIOP PNET 4 is registered with ClinicalTrials.gov, number NCT01351870.We analysed methylation subgroup, genome-wide copy number aberrations, and mutational features in 136 assessable tumour samples from the HIT-SIOP PNET 4 cohort, representing 40% of the 338 patients in the trial cohort. This cohort of 136 samples consisted of 28 (21%) classified as WNT, 17 (13%) as SHH, and 91 (67%) as non-WNT/non-SHH (we considered Group3 and Group4 medulloblastoma together in our analysis because of their similar molecular and clinical features). Favourable outcomes for WNT tumours were confirmed in patients younger than 16 years, and all relapse events in SHH (four [24%] of 17) occurred in patients with TP53 mutation (TP53mut) or chromosome 17p loss. A novel whole chromosomal aberration signature associated with increased ploidy and multiple non-random whole chromosomal aberrations was identified in 38 (42%) of the 91 samples from patients with non-WNT/non-SHH medulloblastoma in the HIT-SIOP PNET 4 cohort. Biomarkers associated with this whole chromosomal aberration signature (at least two of chromosome 7 gain, chromosome 8 loss, and chromosome 11 loss) predicted favourable prognosis. Patients with non-WNT/non-SHH medulloblastoma could be reclassified by these markers as having favourable-risk or high-risk disease. In patients in the HIT-SIOP PNET4 cohort with non-WNT/non-SHH medulloblastoma, with a median follow-up of 6·7 years (IQR 5·8-8·2), 5-year event-free survival was 100% in the favourable-risk group and 68% (95% CI 57·5-82·7; p=0·00014) in the high-risk group. In the validation cohort, with a median follow-up of 5·6 years (IQR 3·1-8·1), 5-year event-free survival was 94·7% (95% CI 85·2-100) in the favourable-risk group and 58·6% (95% CI 45·1-76·1) in the high-risk group (hazard ratio 9·41, 95% CI 1·25-70·57; p=0·029). Our comprehensive molecular investigation identified subgroup-specific risk models which allowed 69 (51%) of 134 accessible patients from the standard-risk medulloblastoma HIT-SIOP PNET 4 cohort to be assigned to a favourable-risk group.We define a whole chromosomal signature that allows the assignment of non-WNT/non-SHH medulloblastoma patients normally classified as standard-risk into favourable-risk and high-risk categories. In addition to patients younger than 16 years with WNT tumours, patients with non-WNT/non-SHH tumours with our defined whole chromosomal aberration signature and patients with SHH-TP53wild-type tumours should be considered for therapy de-escalation in future biomarker-driven, risk-adapted clinical trials. The remaining subgroups of patients with high-risk medulloblastoma might benefit from more intensive therapies.Cancer Research UK, Swedish Childhood Cancer Foundation, French Ministry of Health/French National Cancer Institute, and the German Children's Cancer Foundation.
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