PLGA Fund Basic and Translational Research Projects
Pediatric brain tumor treatments do not simply appear, but rather start out as ideas in labs. Basic and translational research serve as the foundational work that makes the transition from ‘light-bulb moment’ to lifesaving cure possible.
Basic research serves as a starting point and involves researchers asking fundamental scientific questions and gaining an understanding of how basic biology works. Translational research applies these findings to develop solutions.
The Pediatric Brain Tumor Foundation’s commitment to supporting novel concepts brought forward by clinicians and scientists around the world is at the very core of our philosophy that finding the next targeted therapy will only happen when new ideas, new strategies, new hypotheses have opportunity for testing. Taking risks in the lab with the assurance of financial support regardless of the outcome is invaluable to jump-starting bold new ideas that would not be eligible for government funding.
Click one of the research projects below to learn more about the basic and translational research the PLGA Fund has made possible.
- The David Andrysiak Tissue Harvesting Clinical Research Assistant at the Dana Farber Cancer Institute
- Human iPSC PLGA Models for Drug Discovery
- Optimizing Outcomes in PLGG Survivorship Study
- Novel universal classification of childhood low grade gliomas using clinical, pathological and molecular methods
- DNA Analysis of Paediatric Low-Grade Astrocytomas Identifies Tumour-Specific Signature in Pilocytic Astrocytomas
- Using Human Neural Stem Cells to Create Genetically Accurate Models of PLGG, Developing PLGG Models Using Patient-Derived Tumor Tissue, Dual mTOR/NOTCH inhibition as a Therapeutic Strategy for PLGG
- Long Term Clinical Implications of PLGG Molecular Subgroups
- Genomic Analysis of Matched Primary and Progressive Recurrent PLGAs
- Clinical Trial Determinants of Response and Resistance in PLGG - Everolimus
- DFCI Clinical Research Assistant – Tissue Harvesting
- Evaluation of MYBL1 fusion oncogene in pediatric diffuse astrocytoma
- Neural Stem Cells and Low Grade Glioma
- Childhood Brain Tumor Tissue Consortium (CBTTC) targets PLGA
- Development of Permanent Juvenile Pilocytic Astrocytoma Cell Lines for Preclinical Trails
- Controlling Pilocytic Astrocytoma Growth: Effects of location, age and Telomerase
- Identification of Key Genetic and Growth Control Pathway Changes in JPA
- Molecular Pathology and Genetics of Low Grade Glioma, Focus on Diffuse Astrocytoma (WHO Grade II)
- Chromatin Immune Precipitation Sequencing
- RNAi Screening Core
- Mouse Modeling Core for Invivo Drug Testing
- Genetic Characterization Grade II LGA
- Analysis of BRAF in WHO Grade II Fibrillary Pediatric Astrocytomas
- Peptide Vaccine Based Immunotherapy for Pediatric Low-Grade Glioma
- Identification of the Molecular Signature of Progressive JPA
- Targeting the Hedgehog Pathway in Pediatric Low-Grade Glioma
- Establishment of PLGA Research Program at Dana Farber Cancer Institute
- Identification of Key Genetic and Growth Control Pathway Changes in Fibrillary Astrocytoma that Represents Potential Molecular
- Controlling Pilocytic Astrocytoma Growth: Effects of location, age and Telomerase
- Development of Permanent Juvenile Pilocytic Astrocytoma Cell Lines for Preclinical Trails
- Molecular Prognostic Markers for Low-Grade Gliomas
- The Biologic and Prognostic Role of Replicative and Oncogene Induced Senescence
- Targeting Cancer Stem Cells in Pediatric Fibrillary Astroctyoma
- Molecular JPA Study
Functional engagement and effect of RAF-targeted therapies in glioma
Award: $180,000 over 2 years (2020-2022)
Principal Investigators: Dr. Karisa Schreck, Assistant Professor of Neurology, Johns Hopkins University-School of Medicine
An accurate understanding of drug penetration, target inhibition in the brain, and prognostic biomarkers is lacking in PLGA. This is due in part to the limitations of obtaining serial biopsies from patients with brain tumors. Detailed genomic characterization over the past decade has revealed that, while PLGA is a distinct entity, it shares some molecular drivers with pediatric HGG (pHGG) and adult HGG (aHGG). A common driver in PLGA is dysregulation of the RAS signaling pathway via activating BRAF-fusions or point mutations in p.V600E. Implementation of RAF and MEK inhibitors (RAFi/MEKi) against these oncogenes has had some successes in PLGA, but very little is known about blood-brain barrier penetration, target inhibition in the brain, combination with other modalities, and optimal duration of therapy. Moreover, effective biomarkers of response are lacking, making clinical trials challenging to conduct given the long natural history of this disease and lack of prognostic intermediaries. propose to determine RAFi/MEKi penetration and target engagement in non-enhancing and enhancing brain tumor tissue as a surrogate for penetration into PLGA. Through the ongoing clinical trials run by our multi-institutional team, we are acquiring pre-/post- RAFi/MEKi brain tumor specimens in order to answer critical questions for PLGA drug delivery and treatment. We will determine intra-tumoral drug concentrations, functional ERK inhibition, and correlation with response to treatment. We will also identify a kinome signature for treatment sensitivity or resistance using pre-/post- treatment specimens and serial blood samples.
The David Andrysiak Tissue Harvesting Clinical Research Assistant at the Dana Farber Cancer Institute
Award: $132,000 over 2 years (2019-2021)
Principal Investigators: Dr. Keith Ligon, Associate Professor Pathology, Harvard Medical School, Associate Pathologist/Neuro-Pathologist, Brigham and Women’s Hospital, Dana-Farber Cancer Institute
This CRA position will work within the clinical research program and support the research team in the overall conduct of clinical trials using Good Clinical Practice under the auspices of the Principal Investigator. The CRA will be responsible for the primary data collection and management of patient clinical information as it pertains to participation in clinical trials. They will ensure timely collection of protocol-related samples including shipment to outside entities as required. The individual will maintain regulatory binders and ensure study compliance with all state, federal, and IRB requirements. The individual may be responsible for IRB protocol submissions (amendments, continuing reviews, and minimal risk protocols). This individual may also screen patients for protocol eligibility, obtain informed consent, and register study participants with the Office of Data Quality (ODQ). They must understand the required basic principles of human research subject protection. The individual must work independently under general supervision.
Human iPSC PLGA Models for Drug Discovery
Award: $300,000 over 3 years (2019-2022)
Principle Investigators: Dr. David Gutmann, The Washington University in St. Louis
Pediatric low-grade astrocytomas (PLGAs) are benign brain tumors that have proven difficult to maintain as cell lines in vitro or as patient-derived xenografts in vivo. These obstacles reflect numerous critical features that distinguish PLGAs from their malignant counterparts. First, these tumors have low proliferative indices and frequently undergo senescence. Second, PLGAs are highly dependent on trophic support from non-neoplastic (stromal) cells in the tumor microenvironment, such as microglia and lymphocytes. Third, these tumors likely arise from a limited number of progenitor populations. Lastly, many PLGAs, especially those located within midline structures, are not biopsied or resected. Because of these barriers, there are few successful human PLGA models for preclinical drug identification, therapeutic agent testing, and biomarker discovery. Leveraging human induced pluripotent stem cell engineering, we have successfully generated tractable human PLGA models for basic science investigation and preclinical application. The overarching goal of this project is to develop and characterize a series of human PLGA models that reflect the genetic diversity of these brain tumors in children.
Optimizing Outcomes in PLGG Survivorship Study
Award: $364,000 over 3 years (2019-2023)
Principle Investigators: Dr. Tobey Macdonald, Children’s Hospital of Atlanta; Dr. Krista Hardy, Children’s National Medical Center, Dr. Tricia King, Georgia State University Medical Center
Pediatric low grade gliomas (PLGG) are the most common childhood brain cancer. Although there are higher survival rates and less severe cognitive complications relative to other pediatric brain tumors, the cognitive outcomes among PLGG are variable and disruption in cognitive abilities and everyday functioning may be subtle in some PLGG survivors. Therefore, it is essential to identify changes in cognition as early as possible so that interventions can be initiated quickly in order to optimize long-term outcomes. Unfortunately, due to better outcomes on average in PLGG, fewer children are routinely referred for monitoring of neurocognitive outcomes over time. The technology for computer-based assessment of neuropsychological functioning has only recently become widely available. it is crucial to establish a reliable, valid, and efficient screening battery in PLGG that is sensitive to subtle neurocognitive changes and impairments in order to improve the quality of care available in standard practice of PLGG. Our first aim is to examine performance on computerized measures of processing speed, attention, and executive function using NIH Toolbox and Cogstate. We also will obtain concurrent reliability and sensitivity data with gold-standard measures of performance of these constructs, and parent report of attention, executive and adaptive abilities in everyday functioning, as well as important contextual information on sleep, fatigue, physical activity, and household material hardship. Second, it is critical to understand the genetic predisposition of individuals with PLGG that may impact cognitive outcomes after treatment for PLGG. Using whole genome sequencing of patient DNA, we plan to conduct host genome wide analyses, disease-associated genome variant profiles, as well as targeted SNP analyses in order to identify the SNPs associated with neurocognitive vulnerabilities (e.g. sustained attention difficulties), and SNPs associated with neuroinflammation following brain tumor treatment. In sum, integration of computerized measures with traditional measures of neurocognitive functioning fits within a problem-prevention model that emphasizes universal monitoring of children over time with minimal burden and cost. The model is designed to identify children with emerging problems before significant functional impairments develop, and to respond to the call for risk-based approaches to survivorship care. McCabe and colleagues recently commented that, “Although tailoring follow-up survivorship care based on risk for adverse outcomes is widely considered to be the way forward,” few studies evaluating this approach have been published, and “none considered other aspects of risk such as psychosocial adjustment and risk of long-term or late-effects of treatment” (p 809). Data provided by the proposed study also have the potential to permit development and implementation of treatment strategies for at-risk children that can be administered before the onset of functional cognitive impairments.
The recent progress in both molecular understanding and the exciting preliminary results of targeted therapies in pediatric low-grade gliomas (PLGG) created both hope for a new era in front of us but also highlighted urgent issues that will be required to be addressed in the near future to optimize and ensure progress in the field.
The international meeting supported by the PLGA foundation in Padua highlighted examples of both the former and the latter.
Perhaps the most significant step forward was achieved by 2 reports on BRAF-V600E PLGG. An international collaboration funded in part by the PLGA Foundation and led by the SickKids and St. Jude groups confirmed that these tumors confer extremely poor outcomes and do not respond to current therapies. In parallel, early data from a prospective trial on these BRAF- V600E tumors using targeted inhibitor led by Dr. Kieran from Boston suggest extremely high response not previously seen in these tumors.
In contrast, specific challenges areas included:
- The need for a universal classification of PLGG for both outcome analysis and clinical trials
- The need to consolidate and synergize future clinical targeted therapeutics supported by pharma
- The need to develop and agree on robust clinical outcome measures for the short and long-term goals.
In order to address the first and most burning issue, a subcommittee of experts from the European Union (EU) and North America started plans to enable such a classification. The major obstacle to such a project is lack of consensus on molecular and pathological tests used among all centers. Specifically, lack of morphological and some mutation analysis in the EU group and lack of methylation arrays as a classification tool in the North American group.
Currently, the largest comprehensive database combining tissue, molecular analysis with long term outcome (>30 years) exist in Ontario, Canada and the St. Jude databases.
With current support of the PLGA Fund, an ambitious project between these centers and other US centers is being carried out to finalize the molecular classification using RNAseq and genome sequencing. However, without parallel methylation array analysis of all tumors, no comparison and classification with the EU will be possible.
To address this issue, we plan to undertake a stepwise approach:
We plan to initially address the first, and most urgent subtype of PLGG, the BRAF-V600E PLGG. We already assembled a cohort of 280 tumors with the mutation. Sequencing and specific copy number analysis were already done on all these PLGG.
Here we plan to finalize this proof of principle testing by performing 850k Methylation arrays on all these tumors. In order to further classify tumors with the EU group, we will also analyze the BRAF PLGG that transformed to high grade gliomas (n=30, Mistry et al, JCO 2015).
After gathering this information, parallel data from the EU tumors will be reanalyzed to see whether molecular classification can add to the current clinical morphological classification of this type of PLGG. This initial step is key as it will serve as a platform for future work including:
- It will inform both current and future clinical trials with BRAF V600E inhibitors.
- It will form the basis of comparative clinical, pathological and molecular analysis for future efforts on other subtypes of PLGG.
This detailed study, conducted by Dr. Denise Sheer from Queen Mary/University of London and others, focuses on DNA methylation and gene expression to improve researchers’ understanding of the biology of pilocytic and diffuse astrocytomas. Pilocytic Astrocytomas were found to have a distinctive signature at 315 CpG sites, of which 312 were hypomethylated and 3 were hypermethylated. Genomic analysis revealed that 182 of these sites are within annotated enhancers. The signature was not present in diffuse astrocytomas, or in published profiles of other brain tumors and normal brain tissue. These findings highlight novel genetic and epigenetic differences between pilocytic and diffuse astrocytoma, in addition to well described alterations involving BRAF, NYB and FGR1.
This award is made up of three distinct projects at Johns Hopkins Medical Center with Dr. Eric Raabe, Dr. Charles Eberhart, and Dr. Fausto Rodriguez.
- Using human neural stem cells to create genetically accurate models of LGG: Researchers have shown that they can take normal human brain cells and introduce into these cells the genetic changes that they find in LGG. Although they can model three of the six subtypes of LGG, the cells do not grow for enough time to allow researchers to use them for drug screen. The lack of long-term growth suggests that researchers need to refine their models. As a proof of principle, they did create a model that has activation of a common driver in PLGA (the MAP kinase pathway), and they found that the drug trametinib, which is currently in clinical trials for pediatric LGG, can suppress the growth of the research team’s engineered cells. This result shows that their models behave as the team hoped, validating their approach. The next step is to combine the known drivers of LGG with suppression of epigenetic modifiers that were recently demonstrated to be the end-result of cellular senescence. Researchers hypothesize that this approach will allow the normal cells to tolerate the drivers of pediatric LGG – thereby creating a panel of genetically accurate human cells that will allow the research team to find new drugs to help children with LGG.
- Models of pediatric LGG which grow robustly and allow the study of tumor biology and drug testing are desperately needed. In prior work from multiple groups, including the research team’s own, tumor-derived cells have stop growing over time, limiting researchers’ ability to study them. Researchers are currently trying to bypass these limitations using genetic methods, i.e. knocking down tumor suppressor genes and/or introducing oncogenes that facilitate the growth of these tumors. An alternative approach that this project’s researchers are currently developing with their collaborators is known as conditionally reprogrammed cells (CRC) using specific culture conditions previously applied to study many epithelial cancers, which they are now applying to cells derived from primary pediatric LGG with promising initial results. There has been great success in growing fastidious cells using CRC, and they anticipate that this approach will allow them for the first time to grow primary LGG cells in culture.
- Recent studies suggest that in addition to BRAF, other signaling pathways are operational in LGG and other low-grade gliomas in children. This project’s researchers have already identified mTOR and NOTCH as frequently active in these tumors, and these pathways may represent additional therapeutic targets in aggressive tumors. They are currently dissecting in detail the status of the NOTCH and mTOR pathways and their relation to BRAF in tumors. They will determine the mTOR and p16INK4a expression in a COG cohort of low grade glioma tumors as part of a comprehensive COG biology study. They have previously demonstrated efficacy of mTOR and NOTCH monotherapy in LGG, and now propose to test combination therapy in LGG models in vitro and in vivo to find if they can synergistically stop the growth of LGG cell lines.
Pediatric low grade gliomas possess the dichotomy of excellent (greater than 90%) short term overall survival with very low (less than 40%) progression-free survival leading to the following major clinical challenges: Multiple recurrences resulting in accumulation of toxic therapies, significant but extremely variable long term morbidity resulting in late mortality, and multiple pathological subgroups lumped together resulting in lack of specific and targeted therapies. In this project, in order to address these issues, Dr. Uri Tabori and colleagues at Sick Kids of Toronto hypothesize that uncovering RAS/MAPK alterations in all PLGG subtypes as well as secondary events in these cancers will enable novel molecular risk stratification of PLGG. This novel classification will guide current and future targeted therapies which are becoming available for these tumors.
Principal Investigator Dr. Lindsey Hoffman, Cincinnati Children’s Hospital, in collaboration with the Dana Farber Cancer Institute, Nationwide Children’s Hospital in Columbus and the Hospital for Sick Children in Toronto, will be exploring the genomic chafes between matched primary and progressive, recurrent or malignantly transformed PLGGs to guide the use of molecularly targeted therapies.
This position works within the Pediatric Neuro-Oncology Program at the Dana-Farber/Children’s Hospital Cancer Center as well as the Center for Neuro-Oncology at Dana-Farber Cancer Center, the Neurosurgery and Neuropathology Departments at Brigham and Women’s Hospital and Children’s Hospital Boston to facilitate tissue banking at these hospitals. Tissue banking is the storage of patient’s tumor tissue, blood, and other specimens collected at the time of surgery or during other clinical collections for use in future research and clinical trials that the patient may choose to participate in. The main goals of this position are to increase the number of patients consented to tissue banking, facilitate the banking of specimens at the time of surgery, and help ensure that all pathology review required as part of clinical trials is completed.
Building on an initial grant awarded in 2013 focused on the development of human neural stem cell models of PLGA, this study focuses on further exploration in defining and accumulating neural stem cell models for PLGA brain tumors. The central hypothesis of this proposal is that suppression of oncogene-induced senescence in human neural stem cells will allow these cells to tolerate constitutive activation of the RAS/BRAF/MAP kinase pathway, leading to increased growth in vitro and tumorigenicity in vivo. These models will be used to screen for new drug targets that can decrease the growth of PLGA by attacking specific pathways.
This proposal fills a critical unmet need for a pediatric population with few other therapeutic alternatives and addresses an important problem in PLGG therapy, namely, how to best target dysregulated components within signaling pathways. This study (PNOC001) will elucidate mechanisms by which the most common genetic aberrations in PLGGs influence responses to novel, promising, translatable agents and will enable the next generation of clinical trials in which rational drug combinations are administered to appropriate patients in hypothesis-driven studies. This proposal steps beyond the usual approach of testing agents empirically in response-based trials. It utilizes a novel clinical trial statistical design to establish if specific molecular features are predictive markers of response to a targeted agent and establishes a new paradigm for PLGGs in which tumor tissue is acquired from each child in order to identify biomarkers of response. Funding support for the trial provides for the trial’s implementation and continued patient accrual across PNOC’s 15 member clinical trial consortium. Funding for the trial by PLGA fund at PBTF thus supports the robust accrual into an important clinical trial and enables children from all areas of the country to have access to a novel, directed treatment for PLGGs.
A three-year funding grant was approved to hire a dedicated Clinical Research Assistant with dedicated responsibilities for increasing the number of brain tumor tissue samples available for research purposes. The main goals of this position is to increase the number of pediatric patients who consent to tissue banking, facilitate the banking of specimens at the time of surgery, and help ensure that all pathology review required as part of clinical trials is completed. Tissue banking is the storage of patient’s tumor tissue, blood, and other specimens collected at the time of surgery or during other clinical collections for use in future research and clinical trials that the patient may choose to participate in. This person will also be responsible for coordinating all required pathology reviews done at Dana-Farber Cancer Institute as part of a patient’s participation in Neuro-oncology clinical trials. This position will work within the Pediatric Neuro-Oncology Program at the Dana-Farber/Children’s Hospital Cancer Center as well as the Center for Neuro-Oncology at Dana-Farber Cancer Center, the Neurosurgery and Neuropathology Departments at Brigham and Women’s Hospital and Children’s Hospital Boston to facilitate tissue banking at these hospitals. Without brain tumor tissue samples, researchers have little hope of finding more effective treatments and a cure for kids battling brain tumors. Investing in this aspect of the research agenda will ensure that rapid scientific progress can be made.
Pediatric diffuse astrocytomas are rare but represent a major clinical problem in pediatric neuro-oncology due to their heterogeneous pathology and unpredictable clinical behavior. Unlike adult gliomas researchers’ understanding of the molecular mechanisms which drive tumorigenesis within pediatric low grade gliomas are largely unknown. Recent genomic studies by the Dana Farber Cancer Institute identified several new copy number aberrations which appear to represent the first definitions of new subclasses within this disease which may be useful for targeting therapy or predicting tumor behavior.
Principal Investigator Dr. Keith Ligon proposed to further accelerate understanding the biology of normal MYBL1 andMYBL1tr in brain development and pediatric disuse astrocytomas while also establishing MYBL1tr as a biomarker, seeking to do this through two specific aims: construction of a transgenic mouse model expressing MYBL1tr in the brain and evaluation of the outcomes of patients found to have MYBL1 using IHC and bioinformatics approaches.
Pediatric low grade glioma (PLGG) is the most common pediatric brain tumor. While many patients do well, others have a more aggressive disease and need chemotherapy, radiation, or repeat surgery. Although there are numerous candidate drugs that could be tried in PLGG, there are no genetically accurate human cell models of pediatric low grade gliomas for testing of new therapeutics, so there is no way to screen these drugs before starting clinical trials in children. The solution: use human neural stem cells, the cells that this project’s researchers believe give rise to pediatric brain tumors, to create accurate pre-clinical models of PLGG.
Principal investigator Dr. Eric Raabe at Johns Hopkins Medical Center had previously shown that they can take human neural stem cells and introduce activating mutations in BRAF, the most commonly altered gene in PLGG (Raabe et al, Clinical Cancer Research, 2011). These cells grow well in the beginning, but then stop growing and undergo senescence. This process occurs in non-aggressive PLGG tumors in patients. However, aggressive PLGG do not express senescence markers. These researchers believe that increased expression of stem cell genes prevents senescence and allows aggressive PLGG to tolerate activated BRAF. Examination of aggressive low-grade glioma also shows that activation of the mTOR/AKT pathway defines the highest risk PLGG group (Rodriguez et al, Acta Neuropathol. 2011). mTOR and BMI1 can cooperate in other model systems to prevent senescence. They believe that a combination of mTOR activation and the stem cell factor BMI1 will suppress the senescence caused by BRAF and allow human neural stem cells to grow indefinitely and form low-grade glioma tumors in mice.
While the Childhood Brain Tumor Tissue Consortium (CBTTC) biorepository, housed at CHOP, encompasses all brain tumor types, this study supported by PLGA Fund at PBTF (in partnership with the Why Not Me? Foundation) advances the genetic and molecular characterization of WHO grade II, Diffuse Fibrillary Astrocytomas. This is a targeted PLGA research study that will not only inform about one type of PLGA tumor, but many others as well. This project not only accomplishes goals that will impact the scientific understanding about these tumor types, it also creates a full academic collaboration uniting numbers of centers of medical excellence in the world. Not only will the study results be shared with the participating CBTTC consortium members, they will also be shared by the PLGA Research Program at the Dana Farber Cancer Institute and the Boston and Beijing Genome Institute, China.
This study at University of Texas M.D. Anderson Cancer Center, led by principal investigator Dr. Kwong-Kwok Wong, will investigate different methods to immortalize JPA primary cells which have limited growth potential. Cell culture method will involve the expressing of telomerase gene into JPA primary cells with limited growth potential. Over-expression of telomerase has previously shown to increase the life span of human cells. Additionally, researchers will attempt to inject fresh JPA tumor tissue into SCID mice which are severely immunodeficient to investigate whether JPA tumor cells can be propagated inside the brain of the SCID mice. The successful development of these resources will allow researchers to perform various pre-clinical trials of various therapeutic strategies in the future. We recognize the Brain Tumor Society (BTS) Boston for their support on this project.
This study, led by principal investigator Dr. Jeffrey Leonard at Washington University, is evaluating three growth characteristics of JPA that might offer clues for research. First, JPA is primarily a disease of childhood. Second, JPAs behave differently when they occur in different parts of the brain. Third, JPAs grow slowly and often stop growing spontaneously, possibly because JPAs cannot bypass the ‘biological clock’ that stops non-cancer cells from growing indefinitely. Researchers will implant JPA cells taken from children undergoing surgical removal of their tumor into the brains of mice. They will determine if these cells grow preferentially when they are implanted into the brains of very young mice in places that correspond to the original location of the tumor in the patient, and if so, why. Researchers will also put telomerase, a gene that bypasses the ‘biological clock’ into JPA cells and see if this allows tumor growth in mice brains. This project could identify proteins or genes that are important for JPA growth that could be used as targets for drugs or therapies to cure JPA. We recognize the Brain Tumor Society (BTS) Boston for their support on this project.
A collaborative project conducting the first truly comprehensive genomic, genetic and proteomic analysis of JPAs led by Dr. David Gutmann and Dr. Tobey MacDonald at Washington University. This project will apply cutting edge bioinformatics techniques to proven genetic, genomic and proteomic analyses which have helped lead to the development of “targeted therapeutics” in a number of adult cancers. A Kid’s Brain Tumor Cure recognizes the Brain Tumor Society (BTS) Boston for their support on this project.
In a collaborative initiative between St. Jude Children’s Research Hospital and University of London, this project led by principal investigator Dr. David Ellison is a comprehensive study of grade II LGGs with a view to deriving a molecular diagnostic/stratification system and identifying novel markers for the development of targeted therapies. This strategy involves:
- Assessment and analysis of DNA/RNA from grade II LGGs for genome-wide CNAAs, subgroup gene expression/miRNA profiles, aberrant DNA methylation, signaling pathway analysis and specific candidate gene sequencing
- Search for mutations by paired end/cDNA sequencing
- Validation of molecular abnormalities on further FFPE samples and comparison with other LGGs and glioneuronal tumors
This project is a one-year study to provide an opportunity for both St. Jude and University of London to assess the potential of further collaboration to advance scientific understanding of LGG, particularly WSO II diffuse astrocytoma.
Much excitement in the low-grade astrocytoma field has been generated by the discovery of frequent mutations in a protein kinase known as BRAF. However, these BRAF mutations can account for only approximately one third of these pediatric tumors. Dr. Chuck Stiles and the PLGA program at Dana-Farber is focusing on genetic lesions that underlie the remaining two thirds of these tumors. Towards this end, this project’s researchers are creating a dedicated core facility for a technology known as Chromatin Immune Precipitation Sequencing ( ChIP/Seq). The ChIP/Seq method identifies potentially druggable genetic targets for DNA-binding proteins known as transcription factors. The ChIP method will be used to identify genetic targets for three transcription factors plus the Olig2 transcription factor which may play an even more pervasive role in pediatric LGAs.
In the fullness of time, small molecule inhibitors of BRAF may be used for the treatment of BRAF mutant pediatric LGAs. However, multiple protein kinases have been shown to be co-activated in high-grade adult gliomas, and this is likely to be the case in BRAF-transformed pediatric astrocytomas as well. Complimentary signaling pathways are both an obstacle and an opportunity for targeted therapy strategies. An RNAi screening core allows Dr. Chuck Stiles and others at Dana Farber Cancer Institute to conduct a kinome-wide genetic screen for additional druggable protein kinases that cooperate with BRAF to dysregulate the proliferation of normal neural progenitor cells. In addition, RNAi screening complements DNA sequencing as a route to knowledge about other kinds of genes (e.g., GTP-binding proteins, transcription factors) that might underlie these tumors.
In addition to supporting a doctorate level scientist to create mouse models of low-grade astrocytoma and to conduct entry-level tests on these cells for drugs that may benefit children with LGAs, this project led by Dr. Chuck Stiles at Dana Farber Cancer Institute takes the next steps in in testing cells for drugs outside the culture dish.
This study by Dr. Chuck Stiles at Dana Farber Cancer Institute will perform a proof of concept study to determine the optimal strategy for comprehensively characterizing somatic genetic events in individual tumors with a focus on grade II pediatric astrocytoma. The research team anticipates that these studies will determine the important oncogenes and tumor suppressor genes that drive pediatric low-grade glioma development. They also anticipate that an understanding of the molecular pathways disrupted by these mutations will guide the development of rational therapeutics for this disease. If successful, it will enable rapid follow-up with an extended characterization of larger numbers of tumors to identify the recurrent events that cause this disease.
A major roadblock hindering investigations into the various types of PLGA is the lack of frozen tissue or renewable tumor models such as cell lines and xenografts. Several factors have contributed to this. First, such tumors are rare, and have not been a research priority at most institutions. Second, surgical resections are often small, and the limited tissue available has gone to pathology for diagnosis, with little or none reserved for research. Finally, because of their relatively indolent growth, it has been difficult to develop cell line or xenograft models. This project by Charles G. Eberhart M.D., Ph.D., Kenneth Cohen M.D., Eli Bar Ph.D., and Peter Burger M.D., describes a strategy designed to harvest tissue from the majority of PLGA and other pediatric brain tumors resected at Johns Hopkins to overcome these barriers through the commitment of dedicated personnel; better-integration between neurosurgery, neuropathology and neurooncology; and the utilization of improved laboratory technologies enabling the establishment of cell lines and xenografts.
Pediatric Low Grade Astrocytomas (PLGA) are a heterogeneous group of generally slow-growing glial neoplasms. Most common are the largely non-infiltrative pilocytic/pilomyxoid astrocytomas; infiltrating WHO grade II fibrillary astrocytomas represent a second, less common type of PLGA. Relatively little is known about the genetic alterations that differentiate grade II fibrillary astrocytomas from other PLGA, or cause any of these neoplasms to form. However, the molecular biology and clinical behavior of grade II fibrillary astrocytomas arising in children seems to be different from that observed in adult cases. This project, led by Charles G. Eberhart M.D., Ph.D., Peter Burger M.D. and Eli Bar Ph.D., has two aims built on the researchers’ recent identification of a chromosomal change involving the BRAF oncogene in 17 of 25 pilocytic astrocytomas examined: 1) identify BRAF mutations and gene fusions in pediatric grade II fibrillary astrocytoma and 2) perform oligonucleotide array CGH analysis of pediatric grade II fibrillary astrocytoma.
During the last decade, researchers have gained significant preclinical and clinical experience with immunotherapy for adult gliomas, and propose to extend these insights to the treatment of childhood gliomas, based on the research team’s observation of substantial similarities between these tumors in their expression of glioma-associated antigens (GAAs). Principal investigator Dr. Ian Pollack and colleagues at Children’s Hospital of Pittsburgh propose the use of a GAA-based vaccine cocktail, combined with an immunoadjuvant (poly-ICLC), for children with progressive low-grade gliomas. They hypothesize that vaccine-based immunotherapy will not only prove safe for the treatment of pediatric gliomas, but will also demonstrate activity as assessed by clinical, radiologic, and immunologic parameters. Their clinical study and biological correlative analyses will represent the first application of a multipeptide epitope vaccine-based strategy to a pediatric glioma cohort, providing fundamental data for assessing safety, and clinical and immunological efficacy, of immunotherapeutic strategies in the pediatric tumor context.
Pilocytic astrocytomas (PA), the most common childhood brain tumor, is classified into 2 groups: those that are resected and do not recur (non-progressors), and those that recur early and need further treatment, progressors. There is little that distinguishes these patients at diagnosis, a fact which leads to uncertainty regarding the need for further treatment on the part of the physician and uneasiness and worry about the long-term outcome for their children on the part of the parent. A pilot study at the University of Texas Southwestern Medical Center to generate comprehensive molecular profiles of patients’ PA tumors produced exciting preliminary data showing distinct differences. This study, led by principal investigator Elizabeth Maher, MD, PhD, aims to identify novel markers that can predict progressive disease and, equally important, identify novel targets for new drug development for this important childhood disease.
The goal of this project, led by principal investigator Xiao-Nan Li, MD, PhD, Texas Children’s Hospital-Baylor College of Medicine, is to develop and characterize a panel of primary tumor-based orthotopic xenograft mouse models of pediatric low-grade glioma for broad distribution and use in understanding the biology and testing of novel therapies. Using surgical protocols that have successfully achieved greater than 70% (20 models from 28 specimens) tumor take rate in malignant pediatric brain tumors, researchers aim to develop 4-5 transplantable orthotopic xenograft models through direct implantation of 20-25 fresh surgical specimens of low grade gliomas into anatomically matched locations in mouse brains. Detailed characterization of the xenograft tumors will be performed to make sure they faithfully replicate the biology of the original patient’s tumor, and to identify all genetic abnormalities. The research team will also examine if cancer stem cells play a role in determining the xenograft forming capabilities by correlating cancer stem cell frequencies in patient tumors with their tumor take rate.
In this proposal, principal investigator Michael K. Cooper, MD, and colleagues at Vanderbilt University Medical Center seek to better define the pediatric glioma subtypes in which the Hedgehog signaling pathway is activated and to determine whether the delivery of Hedgehog signaling inhibitors will halt the growth of these human gliomas in an animal model. This is based on researchers’ previous work which identified compounds that inhibit Hedgehog signaling and determined that the Hedgehog pathway is activated in stem cells in some types of adult gliomas. If successful, these preclinical findings will constitute an important component for developing a novel therapeutic strategy for malignant gliomas and a basis for patient selection.
In May 2007, PLGA Fund at PBTF funded the establishment of the first dedicated PLGA research program at the Dana Farber Cancer Institute. The initial $2 million grant helped concentrate resources on research into pediatric low-grade brain tumors in order to discover new and improved targeted therapies that don’t risk impairing children’s bodies and minds. This is believed to be the first coordinated research effort committed to this specific type of tumor worldwide. This flagship program, under the direction of Charles Stiles, PhD, and Mark Kieran, MD, PhD, drew resources, including personnel and technology, from Dana-Farber’s pediatric neuro-oncology program, the Department of Neurobiology at Harvard Medical School, Children’s Hospital Boston, and the Broad Institute of MIT and Harvard. Since its founding more than 10 years ago, the program has advanced the study of PLGA tumors through genomics, drug development, and tumor micro-environment research, as well as clinical trials and tissue banking initiatives. Learn more about the program at https://danafarberplga.org.
This study, led by principal investigators Dr. David Gutmann and Dr. Tobey MacDonald of Washington University, represents a collaborative project that builds upon a 2006 project funded by Brain Tumor Society (BTS) Boston. The 2006 project resulted in the first truly comprehensive genomic, genetic and proteomic analysis of juvenile pilocytic astrocytomas (JPAs). This new project will focus on pediatric fibrillary astrocytomas (PFA) as it continues to employ multiple complementary high-throughput technologies to identify key molecular genetic changes (DNA, RNA and protein) and growth control pathways that represent potential molecular targets for future therapeutic drug design. This approach, leading to “targeted therapeutics,” has had great success in a number of adult cancers. Unfortunately, unlike some of the other common childhood tumors, PFA has not been subjected to the same rigorous and comprehensive molecular analysis that constitutes the necessary first step for the development of targeted therapeutics. No single study has analyzed a sufficiently large enough sample size, and more importantly, no investigation has concurrently studied the DNA, RNA and corresponding protein expression of each individual tumor to make definitive and statistically valid conclusions regarding the molecular basis of PFA.
This study will evaluate three growth characteristics of JPA that might offer clues for research. First, JPA is primarily a disease of childhood. Second, JPAs behave differently when they occur in different parts of the brain. Third, JPAs grow slowly and often stop growing spontaneously, possibly because JPAs cannot bypass the ‘biological clock’ that stops non-cancer cells from growing indefinitely. Researchers led by principal investigator Dr. Jeffrey Leonard of Washington University will implant JPA cells taken from children undergoing surgical removal of their tumor into the brains of mice. They will determine if these cells grow preferentially when they are implanted into the brains of very young mice in places that correspond to the original location of the tumor in the patient, and if so, why. They will also put telomerase, a gene that bypasses the ‘biological clock’ into JPA cells and see if this allows tumor growth in mice brains. This project could identify proteins or genes that are important for JPA growth that could be used as targets for drugs or therapies to cure JPA. We recognize the Brain Tumor Society (BTS) Boston for their support on this project.
This study will investigate different methods to immortalize JPA primary cells which have limited growth potential. Cell culture method will involve the expressing of telomerase gene into JPA primary cells with limited growth potential. Over-expression of telomerase has previously shown to increase the life span of human cells. Additionally, researchers led by principal investigator Dr. Kwong-Kwok Wong of University of Texas M.D. Anderson Cancer Center will attempt to inject fresh JPA tumor tissue into SCID mice which are severely immunodeficient to investigate whether JPA tumor cells can be propagated inside the brain of the SCID mice. The successful development of these resources will allow researchers to perform various pre-clinical trials of various therapeutic strategies in the future. We recognize the Brain Tumor Society (BTS) Boston for their support on this project.
This study will apply the prognostic markers in childhood high-grade gliomas to analyze low-grade gliomas. Researchers led by principal investigator Dr. Ian F. Pollack, Children’s Hospital of Pittsburgh, University of Pittsburgh, will evaluate a series of hypothesis-based markers linked with glioma progression in previous studies, such as MGMT status, proliferation index and genetic alterations. These results would be amenable to comparison with results from high-throughput allelotyping. Researchers will evaluate 100 “favorable-risk” (e.g., grossly resected) tumors in parallel with 100 “higher-risk” (unresectable brainstem and diencephalic) lesions. This analysis should have sufficient statistical power to identify meaningful prognostic associations, and would provide new insights into biological correlates of prognosis in pediatric gliomas and therapeutic targets to improve the chances of curing these tumors. We recognize the Brain Tumor Society (BTS) Boston for their support on this project. UPDATE: This study resulted in a published paper in the Brain Pathology Journal, September 2009.
This study led by principal investigator Dr. Uri Tabori, Hospital for Sick Children, will study why some PLGA tumors stop growing. Using this alternative research strategy, researchers will build on previous results that demonstrated that a mechanism that controls tumor growth arrest, defined as senescence, predicts outcome in PLGA. With the collaboration between three of the leading pediatric neuro-oncology centers in North America, researchers plan to expand the team’s preliminary findings and to determine the pathways that control senescence in PLGA. Upon completion of this project, they will be able to better predict which patients are unlikely to have tumor progression (and can thus be spared from current toxic therapies), and they will uncover novel targets as therapeutic options for PLGA. Furthermore their findings will provide a framework for a new understanding of astrocytoma behavior in children.
The ultimate goal of this proposal by principal investigators Dr. David H. Rowitch, Dr. C. David James, and Dr. Graeme Hodgson, Ph.D. of the University of California, San Francisco is to change the landscape of pediatric grade II glioma (fibrillary astrocytoma) research by investigating the biological regulation of cancer stem cells. The three specific aims of this program are as follows: 1) investigate the function of OLIG2-positive stem cells in pediatric low-grade glioma, 2) develop novel mouse orthotopic models of low-grade glioma, and 3) identity genes that cause diffuse low-grade astrocytomas (DLGAs) and test the efficacy of small inhibitory nucleic acids (siNA) that target these genes in preclinical models of DLGAs.
This study by Dr. KK Wong at MD Anderson Cancer Center 1) analyzes the gene expression profiles in 40-60 cases of subtotally resected JPAs located at the midline region to test whether midline located JPA also forms two subgroups with one group more aggressive, and (2) identifies prognostic markers that can predict the likelihood of progression in subtotally resected JPAs using statistical methods. Dr. Wong submitted his study to the NIH and was granted funding; however, the funding was not sufficient to cover the entire sample size. This would have required Dr. Wong to decrease his sample size, thus jeopardizing the significance of the results. The incremental funding necessary to keep the study intact was funded by funds raised by Fightjpa.org families for the Childhood Brain Tumor Foundation, who conducted a special peer review to confirm the viability of the study. The PLGA Foundation recognizes the Childhood Brain Tumor Foundation for their support of this program.
A collaborative project led by principal investigators Dr. David Gutmann and Dr. Tobey MacDonald at Washington University to conducting the first truly comprehensive genomic, genetic and proteomic analysis of JPAs. This project applies cutting edge bioinformatics techniques to proven genetic, genomic and proteomic analyses which have helped lead to the development of “targeted therapeutics” in a number of adult cancers. A Kid’s Brain Tumor Cure recognizes the Brain Tumor Society (BTS) Boston for their support on this project.