Abstract
Pediatric low-grade gliomas (PLGGs) are the most common brain tumors in children, with varying degrees of brain invasion. Recent whole-genome sequencing has identified a rare gene fusion ...involving RAF1, a RAF isoform. Unlike other RAF fusions, RAF1 fusions are resistant to existing RAF inhibitors. Therefore, aside from surgical resection with adjuvant chemotherapy and radiation therapy, there are few targeted therapeutic alternatives for RAF1-fusion-driven PLGGs. Despite the prevalence and challenges this disease presented, our understanding of PLGGs was limited by a lack of genetic models. We ultimately picked Drosophila melanogaster as our model organism due to the conservation of major signaling pathways between flies and humans. Furthermore, this connection between humans and flies, coupled with other technical advantages associated with this model organism, like short generation cycle and its powerful genetic toolbox, makes Drosophila melanogaster an ideal organism to study the genesis and progression of PLGGs. With the help of the GAL4/UAS system, we established four fusion-driven PLGG fly genetic models and found that glial overexpression of QKI-RAF1, a fusion gene in pilocytic astrocytomas, induces an invasion-like phenotype with aberrant glial migration. This migration defect was suppressed by glial overexpression of repulsive guidance signaling receptors Robo2 or PlexA/B, indicating the dysregulation of repulsive guidance signaling pathways. Immunostaining coupled with quantitative analysis revealed that Robo2 expression is downregulated in migrating tumor cells in flies, which is recapitulated in mouse astrocytes overexpressing QKI-RAF1 and PLGG patients with RAF fusions. We further broaden our findings by profiling the tumor transcriptomes, revealing potential downstream effectors, including the G protein-coupled receptor GPR180/CG9304, and inhibition of which suppresses tumor invasion in flies. Taken together, we present the PLGG fly model system, leading to the discovery of Robo2, Plexins, and GPR180/CG9304 as potential therapeutic targets.
Abstract
Brain tumors are the leading cause of cancer-related death in children. An important hurdle to scientific and clinical progress in the field has been the limited availability of preclinical ...tumor models. In recent years, the Children’s Brain Tumor Network (CBTN) has accelerated the development of patient-derived cell lines and xenografts, offering these resources to the community through open-source access. While these models are extremely valuable, their development process can be lengthy and result in clonally selected lines which presents a challenge for studying complex tumor biology. To address the need for three-dimensional tissue culture, our group in conjunction with CBTN, generates organoids from fresh tissue specimens obtained directly from surgical resection. This effort resulted in numerous organoid models generated for high-grade glioma (HGG), medulloblastoma, ependymoma, atypical teratoid-rhabdoid tumor, and low-grade glioma tumors. The tissue was processed within an hour post-extraction and cultured in growth factor-free media. Organoid formation and growth were observed as early as in 2 weeks post initiation and continued for up to three months. Banked organoids established growth upon return to culture and resembled similar cell composition to those in the original culture. This provides an excellent preclinical testing model for precision medicine-driven trials. To represent this, we utilized CAR-T testing approach and treated GD2-positive HGG organoids with GD2 CAR-T cells and control CD19 CAR-T cells. 72h exposure to GD2 CAR-T induced morphological changes and significant increase in dead cells within organoids, which was not observed in CD19 CAR-T treated counterparts (p<0.05). Here we provide a simple and efficient workflow for the generation and testing of three-dimensional tumor organoid models generated from fresh surgical tissue. The platform can accelerate not only tumor biology explorations but also empower a diverse array of precision medicine-driven testing for pediatric brain tumors.
Abstract BACKGROUND Pediatric low-grade gliomas (pLGGs) have variable prognosis and treatment responses. Complete resection cannot be achieved for all tumors, especially for highly infiltrative or ...deep-seated tumors, necessitating additional therapy, from chemotherapy to targeted inhibitors. We integrated imaging-derived phenotypes with genotypic traits from transcriptional analysis, offering an in-depth characterization of pLGG immune microenvironment, progression risk, and likelihood of multiple treatments. METHODS Analyzing 549 treatment-naïve pLGGs with multiparametric MRI and RNA sequencing, we identified distinct immunological groups using XCell scores based on immune cell infiltration. We developed a radiomic signature using conventional MRI and machine learning techniques (support vector machines with a linear kernel and nested cross-validation) to distinguish the ‘immune-hot’ group, and incorporated diffusion MRI to improve signature accuracy. Additionally, a clinicoradiomic model predicting tumor progression risk and treatment response was trained, integrating clinical and radiomic data. Transcriptomic analysis was conducted to identify pathways correlated with clinicoradiomic risk, predictive of pLGG progression. RESULTS Three immunological groups were revealed, the ‘immune-hot’ group characterized by poor prognosis due to a high concentration of pro-tumorigenic M2-polarized macrophages, despite a higher preponderance of T-lymphocytes. The radiomic signature effectively distinguished the ‘immune-hot’ group with balanced accuracies of 76.8%/86.0% in discovery/replication sets, improved by diffusion MRI to 81.5%/84.4%. The clinicoradiomic model showed concordance indices of 0.71 (discovery) and 0.77 (replication), predicting patient progression risk. Significant differences (p=0.0010) were found in clinicoradiomic risk scores between patients undergoing one versus multiple treatments post-diagnosis, linking higher scores to a likelihood of multiple treatments. Transcriptomic pathways associated with higher clinicoradiomic risk highlighted the importance of fatty acid oxidation, a tumor-promoting mechanism that drives adaptive resistance to cytolytic immune cell effectors. CONCLUSIONS This first large-scale radiogenomic analysis in pLGGs aids in prognostication, assessing progression risk, predicting treatment response to standard-of-care therapies, and stratification of patients to identify potential candidates for novel therapies targeting aberrantly regulated pathways.
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.
Abstract Between May 2021 and December 2023, approximately 33% of patients were being treated inpatient at the time of consent for post-mortem tissue donation through Gift From A Child. In the past, ...a major obstacle preventing families from donating post-mortem tissue was the inability to leave the hospital. Care teams and patient families are often concerned that in order to donate, the patient would have to pass away at the hospital. This creates a situation where the desire to donate comes at the cost of patient care and comfort. Through GFAC, children can pass at home, hospital, or hospice and still donate tissue successfully. The ability to donate post-mortem tissue is independent of patient location, ensuring that the focus of the family and care team remains on the child’s care rather than donation logistics. Additionally, patients can successfully donate tissue independent of status at the time of inquiry (declining, stable, urgent). The ability to quickly access a resource at a low burden to the family has been crucial in allowing tissue donation to happen. This also improves patient equity by eliminating access to hospital resources as a reason for a patient family to be required to live near a hospital. This is oftentimes a tremendous financial difficulty for patient families. Through establishing standard operating procedures and appointing tissue navigators, GFAC has streamlined what was previously an extremely complicated process mired in logistical obstacles. Patient families now have access to an efficient process for tissue donation. Previously, families would need to navigate complicated logistics unsupported, now they (or someone on their behalf) only need to contact GFAC or a Research Center of Excellence via phone or email and consent for donation. This ensures that post-mortem tissue can be donated easily, efficiently, and from wherever the patient family chooses.
Abstract The Gift From A Child post-mortem brain tumor tissue donation program was developed with patient families, care teams, and researchers to ensure patients can choose to donate brain tumor ...tissue regardless of logistics and circumstances. In the past 5 years, the program has developed a network of 7 Research Centers of Excellence (RCOE) that work with over 75 referring institutions, non-profit foundations, patient communities, and consortiums. Since the institution of this program, there has been an increase in the total number of donations. External donations also continue to grow as awareness builds, independent of new RCOEs joining the network. Program success is demonstrated by the increasing percentage of external donations and the number of new referral institutions each year. There has also been an overall increase in both total and percentage of donations from external referral sources, with an increasing majority of donations being external. From 2019 to 2023, the total number of external donations has jumped from 45 to 89 per year, reflecting an increase from 42% to 65% of the total donations. The referrals for external donations come from the treating neuro-oncology and general care teams, self-referrals from patient families directly, and from the patient family community on behalf of current patients. Resources are accessible via a 1-800 number, the GFAC website, and calls directly to RCOE or the GFAC team. Overcoming institutional and other logistical barriers ensures that all patients have access to GFAC. Patients who would otherwise be unable to donate are now represented in research that informs future treatments, leading to pre-clinical research that better represents the actual patient population. All data from donations via GFAC is shared with CBTN to ensure open access. This has led to an increase in successful projects and cell lines developed from the donated tissue.
Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult ...cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.
Abstract
MRI is the current gold standard imaging technique for diagnostic evaluation and monitoring of pediatric CNS tumors, however MRI measures are unable to fully relate to tumor biology and ...molecular stratification. Circulating in blood and cerebrospinal fluid (CSF), miRNAs are an abundant and stable nucleic acid which can be utilized as a tumor biomarker. Relating miRNA biomarkers and radiological tumor measurements may provide improved diagnostic and monitoring tools for pediatric brain tumors. Using a cohort of 54 pediatric brain tumors including low grade glioma, ependymoma, germ cell tumor, medulloblastoma, atypical teratoid rhabdoid tumor and high-grade glioma we attempted to combine MRI findings and circulating miRNA data. The miRNA expression was profiled in 33 CSF and 52 plasma samples using the HTG EdgeSeq platform. Clinically acquired, multi-parametric MRI scans at time-points close in proximity to liquid biopsy collection were collected retrospectively and used to generate volumetric tumor segmentations. We identified unique miRNA targets significantly correlated with MRI features, clinical findings, and patient outcomes. In both CSF and plasma, miRNA expression was identified to correlate with diagnosis and clinical features including tumor grade and survival status (p < 0.05). In CSF, miRNA expression was correlated with MRI measurements including cystic core volume, non-enhancing tumor volume, leptomeningeal disease, tumor size and location (p < 0.05). Combination of miRNA targets and radiomic tumor measurements improved diagnostic predictions between low- and high-grade tumors. In plasma, miRNA expression was correlated with MRI measurements including cystic core volume, location, and leptomeningeal disease (p < 0.05). These results demonstrate utility of miRNAs as a pediatric brain tumor biomarker which combined with imaging features can improve minimally to non-invasive diagnostics and management of pediatric brain tumors.
Pediatric solid and central nervous system tumors are the leading cause of cancer-related death among children. Identifying new targeted therapies necessitates the use of pediatric cancer models that ...faithfully recapitulate the patient’s disease. However, the generation and characterization of pediatric cancer models has significantly lagged behind adult cancers, underscoring the urgent need to develop pediatric-focused cell line resources. Herein, we establish a single-site collection of 261 cell lines, including 224 pediatric cell lines representing 18 distinct extracranial and brain childhood tumor types. We subjected 182 cell lines to multi-omics analyses (DNA sequencing, RNA sequencing, DNA methylation), and in parallel performed pharmacological and genetic CRISPR-Cas9 loss-of-function screens to identify pediatric-specific treatment opportunities and biomarkers. Our work provides insight into specific pathway vulnerabilities in molecularly defined pediatric tumor classes and uncovers biomarker-linked therapeutic opportunities of clinical relevance. Cell line data and resources are provided in an open access portal.
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•Single-site atlas of 261 cell lines, focused on pediatric brain cancer and sarcomas•Multi-omics analysis of cell lines (DNA, RNA, methylation, drug, gene essentiality)•Machine learning approaches find biomarker-linked therapeutic vulnerabilities
Sun et al. establish a pediatric cancer cell line atlas of 261 cell lines, representing 18 distinct childhood tumor types. A total of 182 cell lines were subjected to multi-omics analyses (DNA sequencing, RNA sequencing, DNA methylation), pharmacological and genetic CRISPR-Cas9 loss-of-function screens to identify pediatric-specific treatment opportunities and biomarkers of response.
Abstract
Implementation of access to donate post mortem tissue among pediatric brain tumor patients remains a challengeDSM1 . Previous attempts to develop a post-mortem network have been jeopardized ...by barriers such as a lack of education, logistical coordination of donation, and difficulties effectively communicating the benefit of post-mortem donations to families. CC2 Utilizing feedback from patients’ families, clinicians, and researchers, standard operating procedures (SOP) were developed and utilized by six “tissue navigators” (TN) working across institutions. Tissue navigators are critical in implementation of access to donate as they serve as a liaison between patients’ families and clinical team to ensure post-mortem tissue is procured correctly and respectfully. From 2018 through 2021, there has been an increase in donations, which has led to establishment of tumor cell cultures translating rapidly to clinical development, and a growing network of centers participating in GFAC procedures. Donations have been facilitated at over 75 institutions. GFAC has coordinated 146 donations in this 3-year launch timeframe, with nearly half from families outside GFAC’s primary institutional network. Barriers to implementation were addressed with the design of GFAC’s SOPs, which lead to the successful implementation of access to donation. GFAC is developing CME training for clinicians and researchers to address communication of post-mortem donation, continuing awareness campaigns with collaborators in the field, advocating for families to receive feedback on the donation, and expanding on the SOPs as more is learned from clinicians and families.
