Prognostic effect of whole chromosomal aberration signatures in standard-risk, non-WNT/non-SHH medulloblastoma: a retrospective, molecular analysis of the HIT-SIOP PNET 4 trial

Abstract

Background: 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.

Methods: 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.

Findings: 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 (TP53^mut) 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.

Interpretation: 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-TP53^wild-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.

Funding: Cancer Research UK, Swedish Childhood Cancer Foundation, French Ministry of Health/French National Cancer Institute, and the German Children's Cancer Foundation.

Figure 1

Clinical and disease-associated molecular features of the HIT-SIOP PNET 4 cohort All 147 patient samples available from the HIT-SIOP PNET 4 cohort with subgroup information are shown, including 11 samples without data on chromosomal aberrations. Black indicates positivity for an assessed feature (for sex, black indicates male and white indicates female). Grey indicates missing data. Red indicates chromosomal losses and blue indicates chromosomal gains. NA=not assessed. Residual scores from χ² tests of association are shown (darker shades of grey indicate stronger enrichment) alongside p values from Fisher's exact tests.

Figure 2

Event-free survival in the HIT-SIOP PNET 4 cohort by clinical and disease-associated molecular features Patients (n=136) were grouped as (A) treated with standard radiotherapy vs hyperfractionated radiotherapy, (B) those who had a gross total resection vs subtotal resection, (C) classified as per the four consensus medulloblastoma molecular subgroups, and (D) those with or without whole chromosomal aberrations. Event-free survival for patients with non-WNT/non-SHH disease (n=91) grouped as (E) patients with MYCN amplified vs non-amplified tumours, (F) patients with medulloblastomas presenting an i17q or not, and (G) patients with medulloblastomas with or without whole chromosomal aberration. HR=hazard ratio.

Figure 2

Event-free survival in the HIT-SIOP PNET 4 cohort by clinical and disease-associated molecular features Patients (n=136) were grouped as (A) treated with standard radiotherapy vs hyperfractionated radiotherapy, (B) those who had a gross total resection vs subtotal resection, (C) classified as per the four consensus medulloblastoma molecular subgroups, and (D) those with or without whole chromosomal aberrations. Event-free survival for patients with non-WNT/non-SHH disease (n=91) grouped as (E) patients with MYCN amplified vs non-amplified tumours, (F) patients with medulloblastomas presenting an i17q or not, and (G) patients with medulloblastomas with or without whole chromosomal aberration. HR=hazard ratio.

Figure 3

Identification of two cytogenetically distinct subgroups within non-WNT/non-SHH standard-risk medulloblastoma All 91 patient samples with non-WNT/non-SHH standard-risk medulloblastoma available from HIT-SIOP PNET 4 cohort are shown. (A) The frequency of p, q, and whole chromosome gains and losses for all autosomal chromosomes. (B) Unsupervised hierarchical clustering of chromosomal features. Grey indicates missing data. Residuals from χ² indicate where whole chromosomal aberration cytogenetic group enrichment has occurred (darker shades of grey indicate stronger relationships), alongside p values from Fisher's exact tests. Total numbers of whole chromosomal losses (red), gains (blue), and changes (black) are shown. Increasing colour intensity indicates a larger number of changes. Chromosomal changes with incidence >15% are shown. We defined whole chromosomal aberration cytogenetic groups by hierarchical clustering. Green represents Group4 medulloblastoma and yellow represents Group3 medulloblastoma. (C) Correlation plot for recurrent (>15% incidence) cytogenetic changes. Circle area is proportional to the strength of correlation, with positive correlations shown in red and negative correlations shown in blue.

Figure 4

Whole chromosomal aberration-derived risk stratification schemes for non-WNT/non-SHH medulloblastomas All 91 available samples from patients in the HIT-SIOP PNET 4 cohort with non-WNT/non-SHH standard-risk medulloblastoma are shown. Event-free survival per (A) whole chromosomal aberration cytogenetic subgroup and (B) recurrent whole chromosomal losses (0 vs 1 or more changes). (C) Proposed optimally performing risk stratification model, with the two identified risk groups. (D) Incidence and distribution of prognostically relevant chromosomal changes. For molecular subgroup, green indicates Group4 and yellow indicates Group3. For risk group, blue indicates high-risk and red indicates low-risk. Black and white indicate presence or absence of a feature, respectively. (E) Event-free survival by the scheme shown in part C. HR=hazard ratio. *HR estimates for favourable-risk vs high-risk were not possible due to the group with no events. p value reported from log-rank test.

Figure 5

Validation of the whole chromosomal aberration-derived subgroups and risk stratification schemes All samples from the independent cohort of non-WNT/non-SHH-medulloblastoma (n=70) are shown in A and B. (A) Unsupervised clustering of chromosomal features by relevant chromosomal aberration cytogenetic subgroups. Residuals from χ² tests indicate where whole chromosomal cytogenetic group enrichment has occurred. Darker shades of grey indicate stronger relationships. p values are from Fisher's exact tests. Total numbers of whole chromosomal losses (red), gains (blue), and changes (black) are shown. Increasing colour intensity indicates a higher number of changes. (B) Relationship of whole chromosomal aberration-defined risk groups to novel Group3 and Group4 disease subtypes. The standard-risk medulloblastoma validation cohort is indicated by filled and open circles according to risk, with relationship to the Schwalbe and colleagues and Northcott and colleagues cohorts shown by t-distributed stochastic neighbour embedding plots. (C) Event-free survival by whole chromosomal aberration-defined risk scheme. (D) Pooled analysis of event-free survival in the molecularly characterised HIT-SIOP PNET 4 cohort and validation cohort, stratified by derived whole chromosomal aberration-defined risk scheme. (E) Patterns of prognostically important cytogenetic changes in the combined cohort. The validation cohort is labelled black. Risk stratification is labelled red (favourable-risk) and blue (high-risk). HR=hazard ratio. TSNE=t-distributed stochastic neighbour embedding.