Tumor DNA in CSF and novel modeling decode breast cancer - brain metastases

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 DESCRIPTION (provided by applicant): Tumor DNA in CSF and novel modeling decode breast cancer brain metastases Project Summary DESCRIPTION: Advances in the treatment of cancer metastatic to the central nervous system (CNS) require paradigm shifts in diagnostic and scientific tools, with faithful models recapitulating the human disease. I am developing an innovative, less invasive method to identify brain tumor mutations and track how the genetic spectrum of tumors metastatic to the CNS changes over time and with therapy. Tumor cellular and cell-free DNA (cfDNA) acts as a fingerprint, allowing detection of genetic alterations that mark the variation and progression of disease. Tumor DNA in cerebral spinal fluid (CSF) will suggest targeted therapies based on the mutations contained in solid and leptomeningeal (LM) breast cancer metastases within the brain. Newly identified tumor mutations in CSF will detail how brain metastases acquire advantageous mutations in response to therapy. Mutations consistent with LM spread of disease will unveil the underlying pathophysiology of this brain metastasis subtype, and suggest effective, targeted therapies. Solid and LM metastases to the brain from breast cancer are woefully understudied, in part due to a lack of cell culture and animal xenograft models that reliably reflect the human disease. I will create a novel, translatable, xenograft model, involving the intracerebral transplantation of primary cultures of breast cancer cells derived directly from human brain metastases. These primary, human brain metastases-specific tools will allow for novel drug screens and validation of genetic targets identified through sequencing of tumor DNA in CSF. Specific Aim 1: To create a method of identifying and characterizing brain tumor-specific mutations in the CSF of patients with solid and LM breast cancer brain metastases, in CSF I will: a) sequence tumor cellular and cfDNA for known mutations in the primary breast tumor, and determine the mutant fraction, b) apply whole exome sequencing to brain tumor DNA to identify additional mutated genes, and c) develop a cancer sequencing panel consisting of known, targetable mutations in breast cancer. Specific Aim 2: To determine how breast cancer primary tumors, solid brain tumor metastases, and leptomeningeal metastases differ in tumor biology and response to medical therapy, I will utilize novel primary cell culture and intracranial xenograft models from breast cancer CNS metastases to validate tumor mutations identified in CSF and screen therapeutics. Summary: The proposed aims are complimentary yet not reliant on each other, and if successful in combination have substantial potential to exponentially advance our understanding of one of the most common cancers to metastasize to the CNS. Our findings would propose potential therapeutic avenues to improve treatment for these patients. Identifying and following the brain tumor DNA fingerprint in patient CSF will ultimately enable more sophisticated, personalized, and targeted therapies. Our translational study will revolutionize the recognition and treatment of solid and LM metastases, and deepen our understanding of metastatic cancer progression. Testing hypotheses of novel therapeutics for brain metastases requires more specific, rapid, and translatable cell culture and animal models. By developing cell lines and implanting mouse xenograft models intracranial with human breast cancer brain tumors we can test therapeutics and advance our understanding of solid and LM CNS tumors. I am a practicing neurosurgeon, in the early stage of my career, with a clinical practice focused on the surgical treatment of patients with brain tumors. My laboratory focuses on the basic science of neuro-oncology, with a project focus to directly impact patient care and unveil new areas of study in brain tumor biology. I care for brain tumor patients in the operating room and in the clinic, striving in the laboratory to understand the genetic and epigenetic mechanisms that drive tumor genesis in the CNS. This mentored training award is crucial to protect my research time and allow me to further develop my laboratory focus on cellular and cfDNA in CSF, and to advance a working model for established intracranial metastases. My department chair has provided me with 50% protected research time, and I am fully committed to this project.