PATH-06. Molecular subgrouping of medulloblastoma via low-depth whole genome bisulfite sequencing

INTRODUCTION: International consensus recognises four molecular subgroups of medulloblastoma, each with distinct molecular features and clinical outcomes. Assigning molecular subgroup is typically achieved via the Illumina DNA methylation microarray. Given the rapidly-expanding WGS capacity in healthcare institutions, there is an unmet need to develop platform-independent, sequence-based subgrouping assays. Whole genome bisulfite sequencing (WGBS) enables the assessment of genome-wide methylation status at single-base resolution. To date, its routine application for subgroup assignment has been limited, due to high economic cost and sample input requirements. Currently, no optimised pipeline exists that is tailored to handle samples sequenced at low-pass (i.e., <10x depth). METHODOLOGY: Two datasets were utilised; 36 newly sequenced low-depth (10x) and 42 publicly available high-depth (30x) WGBS medulloblastoma samples (n=34), alongside cerebellar control samples (n=8), all with matched DNA methylation microarray data. We applied imputation to low-pass WGBS data, assessed inter-platform correlation and identified molecular subgroups by directly integrating WGBS sample data with pre-existing array-trained models. We developed machine learning WGBS-based classifiers and compared performance against microarray. We optimised reference-free aneuploidy detection with low-pass WGBS and assessed concordance with microarray-derived aneuploidy calls. RESULTS: We optimised a pipeline for processing, QC, and analysis of low-pass WGBS data, suitable for routine molecular subgrouping and reference-free aneuploidy assessment that achieves 96% sensitivity compared to microarray approaches. A pilot study of the suitability of FFPE was promising, and we demonstrate that WGBS data can be integrated into existing array-trained models with high assignment probabilities. Also, WGBS-derived classifier performance measures exceeded microarray-derived classifiers. CONCLUSION: We describe a platform-independent WGBS assay for molecular subgrouping of medulloblastoma. It performs equivalently to array-based methods at increasingly comparable cost ($400 vs $580) and provides a proof-of-concept for routine clinical adoption using standard WGS technology. Finally, the full methylome enabled elucidation of additional biological heterogeneity that has hitherto been inaccessible.

MEDB-14. Clinical outcome of pediatric medulloblastoma patients with Li-Fraumeni syndrome

PURPOSE: The prognosis for SHH-medulloblastoma (MB) patients with Li-Fraumeni syndrome (LFS) is poor. Due to lack of comprehensive data for these patients, it is challenging to establish effective therapeutic recommendations. We here describe the largest retrospective cohort of pediatric LFS SHH-MB patients to date and their clinical outcomes. PATIENTS AND METHODS: N=31 patients with LFS SHH-MB were included in this retrospective multicenter study. TP53 variant type, clinical parameters including treatment modalities, event-free survival (EFS) and overall survival (OS), as well as recurrence patterns and incidence of secondary neoplasms, were evaluated. RESULTS: All LFS-MBs were classified as SHH subgroup, in 30/31 cases based on DNA methylation analysis. The majority of constitutional TP53 variants (72%) represented missense variants, and all except two truncating variants were located within the DNA-binding domain. 54% were large cell anaplastic, 69% gross totally resected and 81% had M0 status. The 2-(y)ear and 5-(y)ear EFS were 26% and 8,8%, respectively, and 2y- and 5y-OS 40% and 12%. Patients who received post-operative radiotherapy (RT) followed by chemotherapy (CT) showed significantly better outcomes (2y-EFS:43%) compared to patients who received CT before RT (30%) (p<0.05). The 2y-EFS and 2y-OS were similar when treated with protocols including high-dose chemotherapy (EFS:22%, OS:44%) compared to patients treated with maintenance-type chemotherapy (EFS:31%, OS:45%). Recurrence occurred in 73.3% of cases independent of resection or M-status, typically within the radiation field (75% of RT-treated patients). Secondary malignancies developed in 12.5% and were cause of death in all affected patients. CONCLUSIONS: Patients with LFS-MBs have a dismal prognosis. This retrospective study suggests that upfront RT may increase EFS, while intensive therapeutic approaches including high-dose chemotherapy did not translate into increased survival of this patient group. To improve outcomes of LFS-MB patients, prospective collection of clinical data and development of treatment guidelines are required.

OMIC-06. MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA VIA LOW-DEPTH WHOLE GENOME BISULFITE SEQUENCING

Introduction

International consensus recognises four molecular subgroups of medulloblastoma, each with distinct molecular features and clinical outcomes. The current gold-standard for subgroup assignment is DNA methylation microarray. There is an unmet need to develop platform-independent subgrouping assays which are both non-proprietary and compatible with rapidly-expanding WGS capacity in healthcare. Whole Genome Bisulfite Sequencing (WGBS) enables the assessment of genome-wide methylation status at single-base resolution. Previously, WGBS adoption has been limited by cost and sample quality/quantity requirements. Its application for routine detection of medulloblastoma subgroups has not previously been reported.

Methodology

Two datasets were utilised; 36 newly-sequenced low-depth (10x coverage) and 34 publicly-available high-depth (30x) WGBS medulloblastomas, all with matched DNA methylation microarray data. We compared platform concordance and identified molecular subgroups. Machine-learning WGBS-based subgroup classifiers were optimised and compared between platforms. Aneuploidy and mutation detection using WGBS was optimised and compared to microarray-derived estimates where possible. Finally, comprehensive subgroup-specific DNA methylation signatures were identified.

Results

We optimised a pipeline for processing, quality control and analysis of low-depth WGBS data, suitable for routine molecular subgrouping and aneuploidy assessment. We demonstrated the suitability of fresh-frozen and FFPE DNA for WGBS, and, using downsampling, showed that subgroup calling is robust at coverages as low as 2x. We identified differentially methylated regions that, due to poor representation, could not be detected using methylation microarrays. Molecular subgroups of medulloblastoma assigned using WGBS were concordant with array-based definitions, and WGBS-derived classifier performance measures exceeded microarray-derived classifiers.

Conclusion

We describe a platform-independent assay for molecular subgrouping of medulloblastoma using WGBS. It performs equivalently to current array-based methods at comparable cost ($405 vs $596) and provides a proof-of-concept for its routine clinical adoption using standard WGS technology. Finally, the full methylome enabled elucidation of additional biological heterogeneity that has hitherto been inaccessible.

EMBR-25. GENOME-WIDE GENETIC AND EPIGENETIC ASSESSMENT OF GROUP 4 MEDULLOBLASTOMA FOR IMPROVED, BIOMARKER DRIVEN, PROGNOSTICATION AND RISK-STRATIFICATION

Introduction

Medulloblastoma (MB) is the most common malignant brain tumour in children. The most frequent molecular subgroup, Group 4 (MBGrp4) accounts for ~35/40% of cases, however it has the least understood underlying biology. Clinical outcomes are heterogeneous in MBGrp4 and are not accounted for by established clinico-pathological risk factors. There is now a requirement for a comprehensive study of MBGrp4, considering established clinico-pathological features and novel molecular biomarkers to enhance risk-stratification and identify novel therapeutic targets.

Methods

A clinically-annotated, retrospective MBGrp4 discovery cohort (n = 420) was generated from UK CCLG institutions, collaborating European centres and SIOP-UKCCSG-PNET3 and HIT-SIOP-PNET4 clinical trials. Contemporary, multi-omics profiling was performed. Focal and arm level copy number aberrations (CNAs) were determined from molecular inversion probe (MIP) or DNA methylation array which additionally provided next generation non-WNT/non-SHH (Grp3/Grp4) subtype classifications. Targeted next-generation DNA sequencing was performed to overlay the mutational landscape. Survival modelling was carried out with patients &gt;3 years old who received craniospinal irradiation.

Results

MBGrp4 subtypes were assigned to 88% of tumours with available data. Subtype VIII was strongly associated with i17q (p&lt;0.0001). The favourable-risk cytogenetic signature (2 or 3 of; chromosome 7 gain, chromosome 8 loss and/or chromosome 11 loss) associated with both subtypes VI and VII (p&lt;0.0001). MYCN amplifications were strongly associated with subtype V (p&lt;0.0001) in addition to 16q loss (p&lt;0.0001). The high-risk CNA group was enriched for mutations in genes involved in chromatin remodelling (p&lt;0.0001). Risk factors were identified from multivariate survival modelling. Subtype and CNA groups contributed to improved risk-stratification models that outperformed current clinical schemes.

Conclusion

Comprehensive genetic and epigenetic profiling in this large retrospective cohort has improved our understanding of the molecular and clinical heterogeneity within MBGrp4. Incorporation of molecular biomarkers improved risk-stratification for MBGrp4.

MBRS-69. METABOLITE PROFILING OF SHH MEDULLOBLASTOMA IDENTIFIES A SUBSET OF CHILDHOOD TUMOURS ENRICHED FOR HIGH-RISK MOLECULAR BIOMARKERS AND CLINICAL FEATURES

SHH medulloblastoma patients have a variable prognosis. Infants (&lt;3–5 years at diagnosis) are associated with a good prognosis, while disease-course in childhood is associated with specific prognostic biomarkers (MYCN amplification, TP53 mutation, LCA histology; all high-risk). There is an unmet need to identify prognostic subgroups of SHH tumours rapidly in the clinical setting, to aid in real-time risk stratification and disease management. Metabolite profiling is a powerful technique for characterising tumours. High resolution magic angle spinning NMR spectroscopy (HR-MAS) can be performed on frozen tissue samples and provides high quality metabolite information. We therefore assessed whether metabolite profiles could identify subsets of SHH tumours with prognostic potential. Metabolite concentrations of 22 SHH tumours were acquired by HR-MAS and analysed using unsupervised hierarchical clustering. Methylation profiling assigned the infant and childhood SHH subtypes, and clinical and molecular features were compared between clusters. Two clusters were observed. A significantly higher concentration of lipids was observed in Cluster 1 (t-test, p=0.012). Cluster 1 consisted entirely of childhood-SHH whilst Cluster 2 included both childhood-SHH and infant-SHH subtypes. Cluster 1 was enriched for high-risk markers - LCA histology (3/7 v. 0/5), MYCN amplification (2/7 v. 0/5), TP53 mutations (3/7 v. 1/5) and metastatic disease - whilst having a lower proportion of TERT mutations (0/7 v. 2/5) than Cluster 2. These pilot results suggest that (i) it is possible to identify childhood-SHH patients linked to high-risk clinical and molecular biomarkers using metabolite profiles and (ii) these may be detected non-invasively in vivo using magnetic-resonance spectroscopy.

Abstract 1275: Identification of cancer-specific synthetic lethal genes as novel therapeutic targets

Introduction

Genomic level data has significantly increased the depth of our understanding of genetic and epigenetic changes in cancer. However, using this complex data to improve patient management is challenging. Synthetic lethal (SL) genes (which are only required for growth/survival of cancer cells and not normal cells), represent ideal targets for the development of more targeted, less toxic and more effective cancer treatments. Here we report a novel bioinformatics approach that exploits the complexity of DNA methylation/expression changes to identify cancer subtype specific SL genes.

Materials and Method

Publicly available genome wide DNA methylation and expression data was obtained for ALL (n=517), medulloblastoma (n=763) and neuroblastoma (n=213). For neuroblastoma, which lacks established subgroups, novel subgroups were defined based on differential methylation (using the t-SNE/dbSCAN method) SL gene candidates were derived from genomic methylation/expression data using our in-house developed bioinformatic pipeline.

Functional validation of identified candidate SL genes was performed using siRNA-mediated knockdown, coupled with analysis of cell proliferation (MTT assay) and apoptosis (annexin-V staining/caspase activity).

Results

22 candidate SL genes were identified across six ALL genetic subgroups, ranging from nine in the TCF3-PBX1 to one in the iAMP21 subgroup. The identified genes lack any apparent genetic/epigenetic alterations, and thus most of the candidates have not previously been implicated in cancer. siRNA-mediated partial knockdown of ETV6/RUNX1 and TCF3-PBX1-specific candidate SL genes TUSC3 and FAT1 respectively resulted in a 40-60% reduction in cell proliferation (p &lt;0.01) and induction of apoptosis (p &lt;0.01), which was specific to the subtype in which the genes were predicted to be synthetically lethal. In medulloblastoma, seven candidate SL genes each were identified in the well-defined WNT and SHH subgroups, while identification of SL genes was limited in group 3 (0) and group 4 (1) tumours, which lack known group-defining molecular defects. However, using the recently defined further subtyping of Group3/Group4 tumours, nine additional candidates were identified across three of the novel subtypes. siRNA mediated knockdown of 5 candidate genes tested to date in the SHH subtype led to significant inhibition of cell growth (p&lt;0.001) and induction of apoptosis (p&lt;0.001). In neuroblastoma, we identified five novel methylation-dependent subgroups, which correlate with known molecular and clinical data. Six candidate SL genes were identified in methylation cluster 3, which consists almost exclusively of high-risk MYCN amplified cases.

Conclusion

We have demonstrated that SL genes, specific for defined molecular subtypes of cancer, can be identified utilising a novel approach combining methylation/expression data in multiple cancer types.

Citation Format: Lalchung Nunga, Ed Schwalbe, Fadhel Lafta, Deborah Tweddle, John Maris, Timothy Barrow, Gordon Strathdee. Identification of cancer-specific synthetic lethal genes as novel therapeutic targets [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1275.

Predicting oligonucleotide therapeutic efficacy at the population level

BACKGROUND

DNA-directed RNA interfering (RNAi) mediators that follow the classic Watson-Crick base pairing to bind to their molecular targets and exert their silencing capacities have been identified to be relatively insensitive to single nucleotide polymorphisms (SNPs). The experimental evaluation of a few putative genomic SNPs in a quasi-species population is the only approach scientists have been employing so far for the experimental validation of the efficacy of oligonucleotide drugs on a given population. These studies are inherently constrained by the number of SNPs that can be experimentally supported in the context of an identified molecular target.

MATERIALS AND METHODS

To address this sampling limitation, we have developed a method to report the relative sensitivity of all known and unknown polymorphisms to a prospective therapeutic drug. The power of ultra-deep next generation sequencing (NGS) allows us to test drug effect in vitro on all possible SNPs of a molecular target, in a patient-free manner. We are presenting the technical details to our approach that is empowering unbiased pharmacodynamic studies at the population level for sequence-specific oligonucleotide drugs and genome editing tools.

Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs

Low allelic and clonal variability among endogenous RNAi targets has focused mismatch tolerance studies to RNAi-active guide strands. However, the inherent genomic instability of RNA viruses such as hepatitis C virus (HCV) gives rise to quasi-species mutants within discrete clones: this facilitates mismatch tolerance studies from a target perspective. We recently quantified the slicing imprecision of Argonaute 2 using small interfering RNA (siRNA) analogs of the DNA-directed RNAi drug TT-034 and next-generation sequencing of 5' RNA ligase-mediated rapid amplification of cDNA ends (RACE-SEQ). Here, we present an open-source, customizable, and computationally light RACE-SEQ bioinformatic pipeline, describing adaptations that semiquantitatively report the impact of RNAi hybridization site mismatches from the target perspective. The analysis shows that Argonaute 2 has a substitution-specific, 3- to 5-log activity window between fully complementary targets and targets with mismatches across positions 10-11. It further focuses the endonucleotic Slicer imprecision around positions 13-17, demonstrating its dependence on guide strand central region complementarity, and potentiation by even a single mismatch. We further propose pharmacogenomics value in testing endogenous targets using recombinant replicon systems and RACE-SEQ to report the pharmacodynamics of sequence-specific oligonucleotide therapeutics against all possible polymorphisms in a population, in a minimally biased, patient-free manner.

The use of anthracyclines in the treatment of endemic Burkitt lymphoma

Burkitt lymphoma is the most common malignancy in children in Malawi, the world's poorest country, where there is a long history of treating this disease using a 28-day cyclophosphamide-based protocol. Stage III/IV disease has had poor outcomes. In an attempt to improve the outcome for higher stage disease, anthracyclines were added to the existing protocol. The disease-free (DFS) and overall survival (OS) of 58 children with cytologically confirmed Burkitt lymphoma admitted during 2012-2014 and treated using this protocol were calculated. Six (10%) children had stage I disease, ten (17%) stage II and 42 stage III or IV (73%). Overall 12-month DFS (OS) was 68·5% (72·9%); for stage I disease 100% (100%), stage II 56·2% (60%), stage III/IV 66·3% (72·2%). The DFS was significantly improved from the previous protocol (P = 8 × 10^-4 ). The addition of doxorubicin to stage III and IV disease resulted in a markedly improved DFS. Anthracyclines are deliverable in resource-poor settings and possibly improve the survival of children with Burkitt lymphoma.

Abstract 3823: Identification of critical DNA methylation events in medulloblastoma using functional epigenomics

Most studies of cancer DNA methylation have focused on defining aberrant gene promoter and, in particular, CpG island-associated events and their contribution to tumour development. A number of genes have been found to be epigenetically silenced by promoter hypermethylation in medulloblastoma (MB), however, the genome-wide role of DNA methylation in this disease has not been widely investigated. Using a functional epigenomics analysis of methylation-dependent gene expression alterations, combined with a genome-wide analysis of DNA methylation, we sought to undertake a comprehensive characterisation of methylation events that are associated with expression alterations and that may play a role in MB development.

We treated a panel of 10 MB cell lines with the DNA methylation inhibitor 5-aza-2′-deoxycytidine (5azaCdR) and assessed methylation-dependent changes in gene expression using the Illumina HT12v4.0 array. In total, 283 genes showed methylation-dependent expression in 2 or more cell lines. Using the Illumina 450K Methylation array, a relationship between methylation-dependent expression and methylation at specific CpG residues was found for 63 genes (encompassing 184 CpG sites), suggesting a direct role for their methylation in transcription regulation and tumour development.

Thirty-seven of the 63 genes identified (59%) had events occurring at multiple CpG residues, while the remaining 26 showed a relationship between expression and methylation at a single CpG residue only. Detailed characterisation of the distribution of the 184 CpG sites identified found them harboured mainly within gene promoter regions and associated with CpG islands and shores. However, for 33 genes (52% of total), events were also found at one or more sites located within the gene body. Ten of these genes contained one or more gene body events that were isolated sites, not in an island or shore, and for 3 of these, an isolated non-CpG island/shore gene body event was the only event found.

We have identified a series of methylation events that show a strong relationship to gene expression and may contribute to MB tumourigenesis. In addition to extensive CpG island/gene promoter events, isolated CpG gene body events may play a significant role in regulating gene transcription in tumour development. Further work will now be undertaken to validate the methylation events identified and to establish their role in primary tumours, as well as their functional significance in tumour development.

Citation Format: Dolores M. Hamilton, Matthew Partington, Ed Schwalbe, Janet Lindsey, Daniel Williamson, Simon Bailey, Steven Clifford. Identification of critical DNA methylation events in medulloblastoma using functional epigenomics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3823. doi:10.1158/1538-7445.AM2013-3823

Simvastatin attenuates the activity of matrix metalloprotease-9 in aneurysmal aortic tissue

To investigate whether statins reduce the concentration of MMP-9 in the aortic wall, we randomised patients undergoing elective open repair of an abdominal aortic aneurysm (AAA) to a pre-operative course of either simvastatin or placebo. MMPs in aortic biopsies were measured using gelatin zymography. Although recruitment closed early because of increasing statin use among eligible patients, with only 21 patients we demonstrated a 40% reduction in MMP-9 levels in the AAA wall in patients randomised to simvastatin. This provides a possible molecular mechanism to explain the reportedly beneficial effects of statins to slow AAA growth.

Chemotherapy for mobilisation of Ph-negative progenitor cells from patients with CML: impact of different mobilisation regimens

Mobilised peripheral blood stem cells are widely used for autografting in patients with chronic myeloid leukaemia (CML) and it is generally thought that a high proportion of Ph-negative progenitor cells in the graft is desirable. We report here the results of 91 stem cell mobilisations performed with various chemotherapy regimens followed by G-CSF. We show that mobilisation of Ph-negative cells is possible after diagnosis as well as in advanced stages of the disease. The yield of Ph-negative cells is highly dependent on the chemotherapy regimen: while the combination of idarubicin and cytarabin for 3-5 days (IC3-5) mobilised Ph-negative cells in most patients, high-dose cyclophosphamide was ineffective. Mobilisation of Ph-negative progenitor cells after IC3 was at least as effective as after IC5; however, less apheresis sessions were required, and toxicity was much reduced after IC3. Compared to historical controls, IC was equally effective as the widely used ICE/miniICE (idarubicin, cytarabin, etoposide) protocol. No correlation was found between graft quality and the cytogenetic response to subsequent treatment with interferon-alpha. We conclude that IC3 is an effective and well-tolerated regimen for mobilising Ph-negative cells that compares well with more aggressive approaches such as IC5 and ICE/miniICE.