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Principal Investigator: Nathan A Dahl
Organization: UNIVERSITY OF COLORADO DENVER
Fiscal Year: 2024
Award: $189,896
Funding agency: National Institute of Neurological Disorders and Stroke
PROPOSAL SUMMARY
Diffuse intrinsic pontine gliomas (DIPGs) are aggressive brainstem tumors in children with no curative therapies
available. DIPGs are canonically driven by recurrent mutations in the histone 3 gene (H3K27M). This substitution
imparts broad dysregulation of the histone post-translational modifications (PTMs) that regulate the recruitment
and initiation of transcriptional machinery. Processive transcription, or the mechanics of RNA Pol II as it actively
transcribes across chromatin, is both dependent on and actively propagates chromatin states such as dynamic
accessibility and transcription-associated PTMs (tPTMs). Disorders of transcription dynamics have
demonstrated pathogenic roles in cancer development, and inhibition of transcription machinery is an effective
therapy in these models. We have recently shown that the H3K27M mutation activates regulators of
transcriptional elongation, including CDK9. We have demonstrated that inhibition of CDK9-dependent
transcriptional elongation is an effective therapy in DIPG, but the contribution of processive transcription to DIPG
oncogenic transformation is unknown. The overall hypothesis of this proposal is that the H3K27M mutation
promotes CDK9-dependent nascent transcription, which in turn contributes to both the establishment of an
oncogenic chromatin state as well as the adaptive response to standard-of-care radiation therapy. Using a
combination of CRISPR-edited model systems, patient derived cultures, and both patient-derived xenograft and
syngeneic engineered mouse models, we will test this hypothesis by 1) defining the role of processive
transcription in H3K27M-mediated oncogenesis, 2) determining the impact of CDK9 inhibition on processive
transcription, and 3) characterizing the role of transcriptional induction in response to ionizing radiation.
Successful completion of the proposal will allow us to comprehensively map the impact of the H3K27M mutation
on the nascent transcriptional landscape. This data will enable us to define a novel transcriptional framework for
understanding DIPG’s chromatin-mediated oncogenesis, and it will demonstrate how exploiting this
transcriptional dependence may be leveraged to improve the patient benefit derived from radiation therapy.
The proposed career development plan leverages these studies to provide advanced training in the conduct of
rigorous hypothesis-driven research, the molecular study of transcriptional regulation, and representative pre-
clinical cancer modeling. The mentorship team reflects nationally-recognized senior scientists who possess both
focused expertise in these areas of study as well as a strong commitment to my career development. The training
plan outlines how I will refine my expertise through a combination of didactic course work, focused workshops,
national meetings, and mentorship guidance. Collectively, this training platform will facilitate my transition to
independence as a basic-translational researcher with a long-term goal of applying novel chromatin- and
transcription-based strategies to improve patient outcomes in DIPG.
Terms: <ATAC sequencing><ATAC-seq><ATACseq><Apoptosis><Apoptosis Pathway><Area><Assay><Assay for Transposase-Accessible Chromatin using sequencing><Attenuated><Bioassay><Biologic Models><Biological><Biological Assay><Biological Models><Brain Stem Neoplasms><Brain Stem Tumors><Brainstem Neoplasms><Brainstem Tumors><CRISPR><CRISPR approach><CRISPR based approach><CRISPR method><CRISPR methodology><CRISPR technique><CRISPR technology><CRISPR tools><CRISPR-CAS-9><CRISPR-based method><CRISPR-based technique><CRISPR-based technology><CRISPR-based tool><CRISPR/CAS approach><CRISPR/Cas method><CRISPR/Cas system><CRISPR/Cas technology><CRISPR/Cas9><CRISPR/Cas9 technology><Cancer Model><CancerModel><Cancers><Cas nuclease technology><ChIP Sequencing><ChIP-seq><ChIPseq><Childhood Malignant Brain Tumor><Childhood Neoplasm><Childhood Tumor><Chromatin><Chromatin Structure><Clustered Regularly Interspaced Short Palindromic Repeats><Clustered Regularly Interspaced Short Palindromic Repeats approach><Clustered Regularly Interspaced Short Palindromic Repeats method><Clustered Regularly Interspaced Short Palindromic Repeats methodology><Clustered Regularly Interspaced Short Palindromic Repeats technique><Clustered Regularly Interspaced Short Palindromic Repeats technology><Curative Surgery><DIPG><DNA Damage><DNA Damage Repair><DNA Injury><DNA Polymerase II><DNA Polymerase epsilon><DNA Repair><DNA-Dependent DNA Polymerase II><Data><Dependence><Development><Development Plans><Diagnosis><Diffuse intrinsic pontine glioma><Disease><Disorder><Educational workshop><Engineering><Enhancers><Fractionated radiotherapy><Functional RNA><Gene Action Regulation><Gene Expression><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Gene Transcription><Genes><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Goals><H3 K27M mutant><H3 K27M mutation><H3K27M mutant><H3K27M mutation><Histones><In Vitro><Ionizing Electromagnetic Radiation><Ionizing radiation><Link><Malignant Neoplasms><Malignant Tumor><Maps><Mechanics><Mediating><Mentorship><Mice><Mice Mammals><Model System><Modeling><Molecular><Murine><Mus><Mutation><Non-Coding><Non-Coding RNA><Non-Polyadenylated RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><Oncogenesis><Oncogenic><PDX model><PRO-seq><Pathogenicity><Patient derived xenograft><Patient outcome><Patient-Centered Outcomes><Patient-Focused Outcomes><Patients><Pediatric Malignant Brain Tumor><Pediatric Neoplasm><Pediatric Tumor><Pol II><Post-Translational Modification Protein/Amino Acid Biochemistry><Post-Translational Modifications><Post-Translational Protein Modification><Post-Translational Protein Processing><Posttranslational Modifications><Posttranslational Protein Processing><Precision Run-On Sequencing><Precision nuclear run-on sequencing><Programmed Cell Death><Protein Modification><RNA><RNA Expression><RNA Gene Products><Radiation Induced DNA Damage><Radiation Induced Genotoxicity><Radiation therapy><Radiation-Ionizing Total><Radiotherapeutics><Radiotherapy><Recurrence><Recurrent><Research><Ribonucleic Acid><Role><Senior Scientist><Testing><Therapeutic><Time><Training><Transcription><Transcription Elongation><Transcription Initiation><Transcription Regulation><Transcriptional Control><Transcriptional Regulation><Translations><Unscheduled DNA Synthesis><Untranslated RNA><Work><Workshop><anti-tumor effect><antitumor effect><assay for transposase accessible chromatin followed by sequencing><assay for transposase accessible chromatin seq><assay for transposase accessible chromatin sequencing><assay for transposase-accessible chromatin with sequencing><attenuate><attenuates><biologic><career development><chemotherapy><childhood brain cancer><chromatin immunoprecipitation-sequencing><clinical effect><clinical relevance><clinically relevant><curative intervention><curative therapeutic><curative therapy><curative treatments><developmental><effective therapy><effective treatment><genome mutation><improved><in vivo><inhibitor><inhibitor drug><inhibitor therapeutic><inhibitor therapy><ionizing output><malignancy><mechanic><mechanical><meeting><meetings><mouse model><murine model><neoplasm/cancer><noncoding><novel><oncohistone><patient derived xenograft model><patient oriented outcomes><pediatric brain cancer><phase 1 trial><phase I trial><pre-clinical><preclinical><radiation damage to DNA><radiation treatment><radiation-induced DNA breaks><recruit><response><social role><standard of care><synergism><translation><translational investigator><translational researcher><translational scientist><treatment with radiation><tumorigenesis><tumors in children>