Advanced molecular pathology for rare tumours: A national feasibility study and model for centralised medulloblastoma diagnostics

Aims: Application of advanced molecular pathology in rare tumours is hindered by low sample numbers, access to specialised expertise/technologies and tissue/assay QC and rapid reporting requirements. We assessed the feasibility of co-ordinated real-time centralised pathology review (CPR), encompassing molecular diagnostics and contemporary genomics (RNA-seq/DNA methylation-array). Methods: This nationwide trial in medulloblastoma (<80 UK diagnoses/year) introduced a national reference centre (NRC) and assessed its performance and reporting to World Health Organisation standards. Paired frozen/formalin-fixed, paraffin-embedded tumour material were co-submitted from 135 patients (16 referral centres). Results: Complete CPR diagnostics were successful for 88% (120/135). Inadequate sampling was the most common cause of failure; biomaterials were typically suitable for methylation-array (129/135, 94%), but frozen tissues commonly fell below RNA-seq QC requirements (53/135, 39%). Late reporting was most often due to delayed submission. CPR assigned or altered histological variant (vs local diagnosis) for 40/135 tumours (30%). Benchmarking/QC of specific biomarker assays impacted test results; fluorescent in-situ hybridisation most accurately identified high-risk MYC/MYCN amplification (20/135, 15%), while combined methods (CTNNB1/chr6 status, methylation-array subgrouping) best defined favourable-risk WNT tumours (14/135; 10%). Engagement of a specialist pathologist panel was essential for consensus assessment of histological variants and immunohistochemistry. Overall, CPR altered clinical risk-status for 29% of patients. Conclusion: National real-time CPR is feasible, delivering robust diagnostics to WHO criteria and assignment of clinical risk-status, significantly altering clinical management. Recommendations and experience from our study are applicable to advanced molecular diagnostics systems, both local and centralised, across rare tumour types, enabling their application in biomarker-driven routine diagnostics and clinical/research studies

Advanced molecular pathology for rare tumours: a national feasibility study and model for centralised medulloblastoma diagnostics

Aims Application of advanced molecular pathology in rare tumours is hindered by low sample numbers, access to specialised expertise/technologies and tissue/assay QC and rapid reporting requirements. We assessed the feasibility of co-ordinated real-time centralised pathology review (CPR), encompassing molecular diagnostics and contemporary genomics (RNA-seq/DNA methylation-array). Methods This nationwide trial in medulloblastoma (<80 UK diagnoses/year) introduced a national reference centre (NRC) and assessed its performance and reporting to World Health Organisation standards. Paired frozen/formalin-fixed, paraffin-embedded tumour material were co-submitted from 135 patients (16 referral centres). Results Complete CPR diagnostics were successful for 88% (120/135). Inadequate sampling was the most common cause of failure; biomaterials were typically suitable for methylation-array (129/135, 94%), but frozen tissues commonly fell below RNA-seq QC requirements (53/135, 39%). Late reporting was most often due to delayed submission. CPR assigned or altered histological variant (vs local diagnosis) for 40/135 tumours (30%). Benchmarking/QC of specific biomarker assays impacted test results; fluorescent in-situ hybridisation most accurately identified high-risk MYC/MYCN amplification (20/135, 15%), while combined methods (CTNNB1/chr6 status, methylation-array subgrouping) best defined favourable-risk WNT tumours (14/135; 10%). Engagement of a specialist pathologist panel was essential for consensus assessment of histological variants and immunohistochemistry. Overall, CPR altered clinical risk-status for 29% of patients. Conclusion National real-time CPR is feasible, delivering robust diagnostics to WHO criteria and assignment of clinical risk-status, significantly altering clinical management. Recommendations and experience from our study are applicable to advanced molecular diagnostics systems, both local and centralised, across rare tumour types, enabling their application in biomarker-driven routine diagnostics and clinical/research studies

The molecular basis for central nervous system primitive neuroectodermal tumour development

PhD ThesisCentral nervous system primitive neuroectodermal tumours (CNS-PNETs) are highly aggressive tumours with similar histopathological features to other intracranial PNETs (medulloblastomas). These two tumours have accordingly been treated using unified approaches, but CNS-PNETs have a dismal prognosis. Few studies have investigated the genetic features of CNS-PNETs. The molecular basis of CNS-PNET was therefore investigated in a cohort containing CNS-PNETs from children (n=33) and adults (n=5), to aid improvements in disease classification and treatment. The common medulloblastoma molecular defects were investigated in CNS-PNETs, and showed RASSF1A promoter hypermethylation is a frequent event (18/22, 82%), and MYC family gene amplification occurs in a subgroup (MYCN: 3/25 (12%), MYCC: 0/25 (0%)). In contrast and in distinction to medulloblastoma, chromosome 17p loss is not a common feature (2/23, 9%), whilst p53 pathway signalling appears to play a major role (20/22, 91%), and associated with TP53 mutations (4/22, 18%). Aberrant Wnt signalling was identified in 2 cases (2/22, 9%) and coupled with CTNNB1 mutation in a single case. IDH1 mutations (2/25, 8%) however, appear to occur in adult but not childhood CNS-PNETs or medulloblastoma. Subsequent genome-wide investigations of the CNS-PNET DNA methylome aimed at a wider characterisation of the molecular features of CNS-PNETs and its relationships to other childhood tumours identified CNS-PNETs as a heterogenous disease group without defined sub-clusters, which were predominantly distinct from medulloblastomas, but exhibited overlap with high-grade gliomas. A panel of 76 tumour-specific methylation events were identified as disease markers. The combination of either RASSF1A hypermethylation or HLA-DPB1 hypomethylation discerned normal brain from CNS-PNET in 94% of cases (64/68). In addition, hypermethylation of TAL1, MAP3K1 and IGFBP1 is associated with non-infant disease. In conclusion, this study has shown CNS-PNETs are a heterogenous group of tumours that are molecularly distinct from medulloblastomas, and has implicated developmental pathways and genetic events in their tumorigenesis. The associations between molecular events identified and clinical features warrant further investigation to aid classification and treatment advancements.North of England Children’s Cancer Research Fund (NECCR), Clic Sargent and the Samantha Dickinson Brain Tumour Trust (SDBTT

Experimental models of pediatric brain tumors. Establishment, immunophenotyping and clinical implications.

Brain tumors are the most common solid tumors in children. Current treatment protocols fail in 25% of patients and are associated with significant long-term adverse effects in survivors. Experimental models of these tumors are scarce and will be crucial for the development of more efficient treatment strategies, including molecular targeting and immunotherapy. In this thesis, I describe the establishment and characterization of novel in vitro and in vivo models of pediatric brain tumors. I initially define a standardized protocol for establishment of patient-derived cell cultures, based on the concept of serum-free monolayer culturing. In addition, I describe the generation of an orthotopic xenograft model of a high-risk Group 3 medulloblastoma (MB-LU-181) by cerebellar inoculation of low-passage tumor cells. The newly established experimental models were phenotyped alongside patient samples, with emphasis on inflammatory mediators that could serve as future targets for therapeutic intervention. Tumor markers, cytokine signatures and components of the COX-2/mPGES-1/PGE2 pathway were generally preserved following propagation of tumor cells in vitro and in vivo, demonstrating the biological faithfulness of the models. CD24 was identified as a clinically and experimentally useful immunomarker for medulloblastoma cells, but additional detailed studies are needed to determine the prerequisites for targeted treatment. PTGS2 (COX-2) and VEGFA were overexpressed in Group 3 medulloblastoma compared to other medulloblastoma subgroups; COX-2 was further evaluated as a therapeutic target in an immunocompetent high-grade glioma model, where simultaneous administration of COX-2 inhibitors and GM-CSF based immunotherapy cured >60% of tumor-bearing mice. I finally performed a systemic immune characterization of children with brain tumors. Multiplex analysis of preoperative plasma samples identified patient groups with distinct cytokine profiles, which could have important implications for the development and clinical implementation of immunotherapies. In brief, this thesis presents novel experimental models that recapitulate the phenotype of pediatric brain tumors and will serve as tools for future studies of tumor biology and preclinical drug evaluation. The results also implicate a role for immune intervention and monitoring in the treatment of children with brain tumors