Purpose of Review
Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system ...(CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors.
Recent Findings
We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier.
Summary
Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such ...discoveries, the Children’s Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.
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•OpenPBTA collaborative analyses establish resource for 1,074 pediatric brain tumors•NGS-based WHO-aligned integrated diagnoses generated for 644 of 1,074 tumors•RNA-Seq analysis infers medulloblastoma subtypes, TP53 status, and telomerase activity•OpenPBTA will accelerate therapeutic translation of genomic insights
The OpenPBTA is a global, collaborative open-science initiative that brought together researchers and clinicians to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Shapiro et al. create over 40 open-source, scalable modules to perform cancer genomics analyses and provide a richly annotated somatic dataset across 58 brain tumor histologies. The OpenPBTA framework can be used as a model for large-scale data integration to inform basic research, therapeutic target identification, and clinical translation.
Abstract Unlike many high-grade tumors, low-grade glioma (LGG) has faced challenges in advancing scientific and clinical breakthroughs, affected by the limited capacity to develop representative ...preclinical tumor models. Major barriers to establishing traditional LGG cell culture systems have been cellular senescence and the need to introduce additional genetic modifications to obtain cultured growth. Such LGG models, while extremely valuable, require extensive periods for development and result in clonally selected lines which may not present the complexity of LGG tumor biology. To mitigate such challenges in LGG model development and address the need for three-dimensional tissue cultures, we have successfully generated organoids from fresh tissue specimens obtained from surgical resection. We have demonstrated success of this method on various pediatric brain tumor histologies and have expanded these approaches successfully to LGG. Through such efforts, we have developed 14 LGG tumors’ organoid models as well as other low-grade tumor’s models such as craniopharyngioma, schwannoma, meningioma, optic glioma, and oligodendroglioma. The tissue was processed immediately post-extraction and cultured in media solution on rotating platform. Organoid growth was observed within 1-3 weeks of initiation and tested for growth for up to 3 months. Phenotypic analysis revealed organoid cell composition representing clinical histology. The immune component was preserved in organoids for up to 40 days. MAPK pathway activity, a hallmark marker for KIAA-BRAF fusion positive pilocytic astrocytoma was preserved for up to 4 weeks. Our successful deployment of three-dimensional patient-tissue derived organoids provides for an efficient, simple workflow for the generation of unique and transformative preclinical models for the LGG field. Supported by the Children’s Brain Tumor network’s open science model, 3D organoids will provide investigations with broader resources for LGG tumor biology preclinical testing and support translational studies on behalf of the development of novel clinical trials.
Abstract BACKGROUND Over the past two decades, the understanding of miRNA biology has drastically increased as miRNAs have been found to pervade most aspects of molecular biology–from cellular growth ...to apoptosis. Nevertheless, there has been little understanding of the role of miRNAs in pediatric brain tumors. In this study, we sought to correlate miRNA expression with pediatric brain tumor histologies. METHODS Weighted gene co-expression network analysis (WGCNA) was performed to determine co-expressed miRNA networks that correlated with distinct brain tumor histologies. Our study cohort consisted of miRNA-sequencing of 262 pediatric brain tumor histologies consisting of Atypical Teratoid/Rhabdoid tumors, Craniopharyngioma, Ependymomas, Ganglioglioma, Low-grade astrocytic tumors, High-grade astrocytic tumors, and Medulloblastoma. We utilized associated multi-omics data from the Open Pediatric Brain Tumor Atlas to validate the results. RESULTS WGCNA analysis revealed a distinct miRNA network consisting of 32 miRNAs with miR-17-5p as the hub miRNA that was markedly upregulated in the aggressive brain tumor group (p<0.001). Interestingly, the majority of the miRNA network consisted of the miR-17/92 family of miRNAs, which are known for their oncogenic role in various cancers. To determine the transcriptional regulatory mechanism of miR-17/92 miRNAs, we first looked at sample-matched RNA-sequencing data. The gene encoding for the miR-17/92 miRNAs, MIR17HG, was significantly overexpressed (p<0.001). Further upstream, we observed that E2F1/2/3, known transcriptional regulators of MIR17HG, gene and protein expressions were significantly overexpressed (p<0.01). Sample-matched phospho-proteomics data indicated the E2F regulator, RB1, being hyperphosphorylated–additionally supporting the E2F activity in these samples. CONCLUSION These findings reveal a network of oncogenic miRNAs consisting of the miR-17/92 family that are distinctly overexpressed in aggressive pediatric brain tumors. Moreover, we suggest that the E2F-RB1 axis is the upstream regulator of the miR-17/92 family of miRNAs.
Abstract BACKGROUND High-grade gliomas (HGG) comprise ~10% of pediatric brain tumors; 40% of pediatric HGG use the alternative lengthening of telomeres (ALT) mechanism to maintain replicative ...immortality. ALT cancers share a unique biology providing potential therapeutic targets. Extrachromosomal telomere DNA repeats, termed C-circles, can be detected by a unique PCR assay, providing a sensitive and specific biomarker for ALT cancers. C-circles have been detected in ALT tumors and serum of ALT patients. We have adapted the C-circle assay (CCA) to provide a sensitive and specific assay with cfDNA in patient plasma. Here we determined if cfDNA in plasma can be used to detect patients with ALT-positive HGG. METHODS Frozen plasma samples were collected in Streck tubes at time of surgery prior to resection from patients with HGG. DNA was extracted and quantified. Isothermal rolling C-circle amplification and real-time telomere PCR was performed followed by analysis. The C-circle positive neuroblastoma cell line, CHLA-90, and C-circle negative neuroblastoma cell line, CHLA-20, served as the positive and negative controls respectively. CCA values in plasma of 2 and above indicate positivity for C-circles. RESULTS Plasma samples were analyzed by CCA from three pediatric patients whose brain tumors were previously biopsied and identified as ATRX mutation positive. ATRX mutation indicates ALT however, not all ALT cancers have ATRX mutations. All plasma samples were above the 2.0 cutoff at 3.37, 3.13, and 4.59 and thus classified as C-circle positive. CONCLUSIONS This preliminary cohort shows that the CCA has potential for identifying ALT pediatric brain tumors using cfDNA from plasma. As novel therapies effective against ALT HGG are developed, the plasma CCA may allow accelerated initiation of neoadjuvant therapy to shrink tumor prior to surgical resection and lessen or prevent the need for tumor biopsy. Expansion of the initial test cohort is underway. Supported by NCI UO1 CA63988.
Abstract BACKGROUND Current management of pediatric brain tumor patients relies on imaging as the only non-invasive tool available for monitoring therapeutic response and tumor progression. Results ...are often inconclusive and unable to capture biologically relevant changes that presage progression on imaging. Circulating miRNA provides an attractive non-invasive biomarker because miRNA has an essential role in regulating gene expression, stability in bio-fluids, selective over-expression in tumors, and is actively released from tumors into the extracellular environment. We aimed to establish the diagnostic and monitoring value of miRNA biomarkers for pediatric brain tumors in cerebrospinal fluid (CSF). METHODS We performed HTG EdgeSeq miRNA panel profiling (2100 targets) of CSF (n=33) samples across pediatric brain tumors from 5 histologies (low grade glioma, ependymoma, germ cell tumor, medulloblastoma, high-grade glioma). We utilized unsupervised consensus clustering, differential expression analysis, and machine learning approaches to investigate miRNA biomarkers. Results were validated using qPCR and ddPCR methods. RESULTS CSF miRNA signatures revealed a correlation with leptomeningeal disease and higher disease burden (p<0.05). Differentially expressed miRNA revealed histology-specific signatures for low grade glioma, medulloblastoma, and germinoma (p<0.05). miR216 expression was significantly elevated in medulloblastoma patients with active disease, indicating a potential novel biomarker for tumor monitoring. The miR216b-5p expression in CSF was confirmed using qPCR and ddPCR. The analysis of independent tumor tissue-based dataset confirmed miR216b-5p and its coding gene MIR217HG expression upregulated in medulloblastoma. MiR-216b-5p expression was also confirmed in patient-derived medulloblastoma cell lines and detected in cell free-media composition indicating extracellular release of miR216b-5p. CONCLUSIONS These results support the use of circulating miRNA in CSF as a potential biomarker for diagnosis and clinical monitoring of medulloblastoma. Further utilization of this approach provides a unique platform to inform liquid biopsy-based management in the clinical setting.
Abstract BACKGROUND Craniopharyngiomas are rare, low histologic grade neoplasms of the suprasellar region. Despite their benign histology, these tumors can be challenging to manage due to the ...morbidities associated with surgery or radiation and their tendency to recur after treatment. In this study, we set out to identify transcriptional factors that may influence or predict recurrence. METHODS We analyzed RNA-sequencing data of 77 craniopharyngioma tissue samples from the Open Pediatric Brain Tumor Atlas cohort and corresponding clinical data. Kaplan-Meier survival analysis was performed using R. Differential expression analysis and gene set enrichment analysis (GSEA) of hallmark pathways was performed. RESULTS The transcription factor NKX3.1 was found to be markedly upregulated in craniopharyngioma relative to other brain tumor histologies (p<0.05). NKX3.1 is a well-studied tumor suppressor in prostate cancer and its reduction or loss of expression is seen with disease progression. Patients with higher NKX3.1 expression had better event-free survival (p=0.0049) and had an average of 530 days longer event-free survival (p=0.036). There was no statistically significant difference in age, sex, tumor location, and extent of tumor resection between high and low NKX3.1 expression groups. There was no significant difference in overall survival (p=0.23). GSEA revealed that patients with high NKX3.1 expression had decreased activation of the Epithelial-Mesenchymal Transition pathway (NES=-1.84, adj. p<0.001) and reduced activation of inflammatory pathways, including the complement, inflammatory response, and IL6-JAK-STAT3 pathways (NES<-1.6, adj. p<0.001). CONCLUSION These findings reveal NKX3.1 as a potential prognostic marker for craniopharyngioma recurrence. Low NKX3.1 expression also correlated with inflammatory pathway activation, a factor that has been previously associated with more aggressive behavior and worse prognosis. Future work is planned to validate NKX3.1 protein expression in patient specimens.
Abstract BACKGROUND Pediatric brain and spinal cord tumors are the leading cause of cancer-related mortality in children. An incomplete understanding of brain tumor biology and associated limited ...access to high-quality biological samples for research are the main factors driving the lack of clinical therapeutic development for pediatric brain tumors that recur or progress. Post-mortem tissue donation provides an unprecedented resource for addressing some of these limitations. METHODS The Gift from a Child (GFAC) program by the Swifty Foundation has a unique mission to increase post-mortem pediatric brain tissue donations through advocacy as well as the education of clinicians and families. Through GFAC’s strategic collaboration with the Children’s Brain Tumor Network (CBTN), CBTN has leveraged postmortem tissue to expand the Pediatric Brain Tumor Atlas (PBTA), a cross-histology multi-omics atlas resource. As part of the effort CBTN has sequenced and released data for over 350 post-mortem pediatric brain tumor specimens including multiple brain region sampling cases with specimen and sequencing quality metrics. RESULTS Here we present an assessment of postmortem samples and available multi-omic data on postmortem samples within the PBTA dataset. Data have been harmonized and released with no publication embargo. To access data, researchers can utilize existing open source data resources and platforms including PedCbioPortal and OpenPedCan to: (1) Identify tumor spatial and temporal specific alterations (2) Establish tumor evolution trajectory leading to therapeutic resistance and tumor progression; (3) Understand tumor heterogeneity longitudinally across multiple ‘omics layers; and (4) Identify and request specimens and derived tumor models. CONCLUSIONS Together, we present the largest deeply characterized cohort of postmortem pediatric brain tumor samples as powerful expansion of the PBTA cohort of >3,000 pediatric brain tumors. CBTN’s open-science model supported by the GFAC mission highlights the value and utility of autopsy-based specimen collection on behalf of improving outcomes for children with brain tumors.
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