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Principal Investigator: Lukas Chavez
Organization: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
Fiscal Year: 2024
Award: $617,669
Funding agency: National Institute of Neurological Disorders and Stroke
The overall objective of this proposal is to investigate circular extrachromosomal DNA (ecDNA) as a potential
driver of intratumoral heterogeneity and treatment resistance in medulloblastoma, the most common pediatric
malignant brain tumor. Intratumoral heterogeneity is one of the leading determinants of therapeutic resistance
and treatment failure and one of the main reasons for poor overall survival in cancer patients. However, the
functional relevance of ecDNA as a driver of tumor heterogeneity and treatment resistance in medulloblastoma
has hardly been studied. To analyze the clinical impact of ecDNA in the different molecular subgroups of
medulloblastoma, we assembled a multi-institutional cohort of Whole Genome Sequencing data from 468
medulloblastoma patient samples. Using novel computational methods for the detection and reconstruction of
ecDNA, we found ecDNA in 82 patients (18%) and observe that the presence of ecDNA is associated with
significantly poorer outcomes. In addition, we find that individual medulloblastoma tumors often harbor multiple
variants of ecDNA, each containing different amplified oncogenes along with co-amplified non-coding
regulatory DNA (‘enhancers’). Based on our preliminary results, we propose the central hypothesis that ecDNA
drives intratumoral heterogeneity and treatment resistance in high-risk medulloblastoma patients. The central
hypothesis will be tested through the following three specific aims: To investigate the molecular evolution of
ecDNA as a potential driver of treatment resistance (Aim 1); To evaluate combinatorial therapies targeted
against mechanisms of ecDNA formation and clustering to reduce treatment resistance (Aim 2); To probe
medulloblastoma tumor-dependencies by functional inhibition of coding and non-coding regulatory DNA co-
amplified on ecDNA (Aim 3). The research proposed in this application has technical, conceptual, and
biological innovations, including the analysis of ecDNA on the single-cell level using novel imaging and
multiome single-nucleus sequencing methods in medulloblastoma tumors and in patient-derived xenograft
(PDX) models. The proposed research is significant, because the current standard treatment for children with
medulloblastoma causes developmental disorders, neurological damage, and secondary metastases. Novel
therapeutic approaches are urgently needed. Our approach will test the impact of standard-of-care treatments
on the molecular evolution of ecDNA and functionally test novel combination treatments targeted against
ecDNA genesis and clustering. These preclinical studies have the potential to uncover novel mechanisms by
which ecDNA contributes to the pathogenesis of medulloblastoma and to identify new scientific leads for the
development of improved treatments. We expect that our studies will expose the contribution of ecDNA
variants to the emergence of therapy resistance, reveal their selection advantages, validate recently described
properties of ecDNA and their therapeutic susceptibilities, and identify novel tumor-dependency genes
amplified on ecDNA in some of the most aggressive medulloblastoma tumors.
Terms: <0-11 years old><BET bromodomain inhibitor><BET inhibitor><BETi><Biological><Biopsy><Bromodomain and Extra-Terminal motif inhibitor><Bromodomains and extra-terminal domain inhibitor><CRISPR><CRISPR/Cas system><Cancer Genes><Cancer Patient><Cancer-Promoting Gene><Cancers><Cell Body><Cells><Chemotherapy and Radiation><Chemotherapy and/or radiation><Child><Child Youth><Childhood Malignant Brain Tumor><Children (0-21)><Children's Hospital><Circular DNA><Clinical><Clustered Regularly Interspaced Short Palindromic Repeats><Code><Coding System><Combined Modality Therapy><Computing Methodologies><DNA><DNA Damage Repair><DNA Repair><DNA dependent protein kinase catalytic subunit><DNA-PKcs><Data><Data Banks><Databanks><Deoxyribonucleic Acid><Dependence><Development><Disease><Disease Progression><Disorder><Enhancers><Functional RNA><Functional dependence><Gene Amplification><Gene Transcription><Genes><Genetic Transcription><Human><Image><In Vitro><Individual><Institution><Intratumoral heterogeneity><Investigation><MYCN><MYCN gene><Malignant Neoplasms><Malignant Tumor><Mediating><Medulloblastoma><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Tumor><Methods><Mission><Modern Man><Molecular><Molecular Analysis><Molecular Evolution><Monitor><Multimodal Therapy><Multimodal Treatment><NHEJ><NIH><NMYC><NMYC Gene><National Institutes of Health><Neoplasm Metastasis><Nervous System Injuries><Nervous System Trauma><Nervous System damage><Neurological Damage><Neurological Injury><Neurological trauma><Non-Coding><Non-Coding RNA><Non-Homologous End Joining><Non-homologous DNA End Joining><Non-translated RNA><Noncoding RNA><Nonhomologous DNA End Joining><Nonhomologous End Joining><Nontranslated RNA><Oncogene Products><Oncogene Proteins><Oncogenes><Oncoproteins><Outcome><PARP Inhibitor><PARP-1 inhibitor><PARPi><PDX model><Pathogenesis><Patient derived xenograft><Patients><Pediatric Hospitals><Pediatric Malignant Brain Tumor><Poly(ADP-ribose) Polymerase Inhibitor><Poly(ADP-ribose) polymerase 1 inhibitor><Predisposition><Prevention><Primary Neoplasm><Primary Tumor><Process><Proliferating><Property><Public Health><RNA Expression><Relapse><Research><Resistance><Role><Sampling><Secondary Neoplasm><Secondary Tumor><Single-Nucleus Sequencing><Subgroup><Susceptibility><Testing><Therapeutic><Transcription><Transforming Genes><Treatment Efficacy><Treatment Failure><Tumor Biology><Tumor Cell><Tumorigenicity><United States National Institutes of Health><Unscheduled DNA Synthesis><Untranslated RNA><Variant><Variation><Work><biologic><bromodomain extra-terminal inhibitor><cancer genomics><cancer metastasis><chemo/radiation therapy><chemotherapy and radiotherapy><childhood brain cancer><cohort><combination therapy><combinatorial><combined modality treatment><combined treatment><computational methodology><computational methods><computer based method><computer methods><computing method><data depository><data repository><data set repository><dataset repository><detection method><detection procedure><detection technique><developmental><developmental disease><developmental disorder><entire genome><experiment><experimental research><experimental study><experiments><extrachromosomal DNA><full genome><genome sequencing><heterogeneity in tumors><high risk><human disease><imaging><improved><in vivo><inhibitor><innovate><innovation><innovative><intervention efficacy><intra-tumoral heterogeneity><intratumor heterogeneity><kids><malignancy><multi-modal therapy><multi-modal treatment><multiomics><multiple omics><natural gene amplification><neoplasm/cancer><neoplastic cell><neurotrauma><new therapeutic approach><new therapeutic intervention><new therapeutic strategies><new therapy approaches><new treatment approach><new treatment strategy><noncoding><novel><novel therapeutic approach><novel therapeutic intervention><novel therapeutic strategies><novel therapy approach><oncogenomics><panomics><patient derived xenograft model><pediatric brain cancer><pre-clinical study><preclinical study><radiation or chemotherapy><reconstruction><resistance to therapy><resistant><resistant to therapy><sNuc-Seq><single nucleus RNA-sequencing><single nucleus seq><single-nucleus RNA-seq><snRNA sequencing><snRNA-seq><social role><standard care><standard of care><standard treatment><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment><therapeutic efficacy><therapeutic resistance><therapeutic target><therapy efficacy><therapy failure><therapy resistant><treatment resistance><tumor><tumor cell metastasis><tumor growth><tumor heterogeneity><whole genome><youngster>