Single-cell Gene Expression and Cytosine Modification Profiling in Pediatric Central Nervous System Tumors
Lay Summary: Single-cell gene expression profiling of pediatric central nervous system (CNS) tumors holds great potential to further our understanding of carcinogenesis, augment prognostic indicators, and identify rational therapeutic targets. Whereas the genomic characteristics of these tumors are fairly well-defined in aggregate, the extent to which cellular variation is associated with carcinogenesis and clinical outcomes is largely unknown. We will profile single nuclei gene expression in 34 brain tumor specimens from 29 unique individuals with a diagnosis of ependymoma, glioma, or embryonal CNS tumor with substantial follow-up time, as well as nontumor brain tissue from four pediatric controls. We will compare gene expression landscapes between tumor and nontumor control, among tumor types, and compare between tumor variation using five tumors with matched specimens. Pediatric brain tumors are rare and single nucleus expression profiles from such a diverse group of diagnoses has not been studied to our knowledge. We will capture and measure gene expression in 5000 single nuclei and conduct bulk RNA sequencing. Molecular classifications of CNS tumors have identified subgroups which predict response to treatment. In addition, we will compare epigenetic modification profiles collected on these samples with their gene expression profiles to further both cell type deconstruction methods, as well as investigate functional aspects of epigenetic gene regulation. The data and results from this study are expected to reveal an abundance of information about pediatric CNS tumors with value for the broader scientific community.
Lay Summary Project Goal: Our proposed study leverages single-cell resolution data on pediatric central nervous system (CNS) tumors from a clinically well-annotated cohort with substantial follow-up time to enrich our knowledge of cancer origins and discover new therapeutic targets. Historically, pediatric gliomas were thought to resemble those in adults; however, molecular studies have demonstrated distinct pathways altered in pediatric disease. While advances in precision medicine for adult glioblastomas have been identified, pediatric neuro-oncology has seen fewer breakthroughs. Each tumor is host to a complex mixture of cells which can have an impact on prognosis and is expected to be one of the major reasons behind treatment failure. At a time when treatment decisions are increasingly based on molecular profiling of biopsy specimens, it is important to understand how representative a single sample from a tumor can be. A high percentage of CNS tumors in this population are caused by altered developmental pathways. Epigenetic patterns that we are already measuring in these tumors are known to be reset during human development, and we have the experience that will allow us to deeply examine developmental origins of cancer formation by combining data in-hand with data we propose to collect here. Single nucleus gene expression sequencing is an established approach we will use here as our human tumor samples are archived and frozen. By comparing tumor samples to non-tumor pediatric brain tissue, we will more readily discover rational therapeutic targets. As pediatric brain tissue is difficult to obtain, this grant provides an opportunity to contribute to the atlas of the nervous system from ages 1 to 18, when cortical development is most rapid. Importantly, the patients we propose to study have been followed for clinical outcomes for several years, allowing us to ask questions not only of tumor formation but of tumor progression and recurrence.