Integrative Bioinformatic and Experimental Investigation of the Mechanisms of Brain Metastatic Adaptation

Cancer metastasis alters many of the processes that are necessary for tumorigenesis to facilitate successful metastases.However, a global analysis of the transcriptome landscape of the metastatic tumor has not been well studied.In my analysis, I compared the primary tumor to the brain metastatic tumor to identify the occurring functional transcriptome changes.I further identified the changes that are unique to the brain metastatic process. I finally analyzed the gene expression pattern that occurs between the colonization stage and outgrowth metastatic stage.This analysis provides a global view of the brain metastatic process starting from the primary tumor to early colonization stage and finally to the overt late stage brain metastatic tumor.In conjunction with the analysis of the metastatic tumor, I also conducted a global analysis of the surrounding microenvironment.I first compared the primary tumor and brain metastatic microenvironments for their respective gene expression changes.Furthermore, I compared the surrounding microenvironment during the early and late stages of brain metastases.This global analysis provides one of the first global views of the transcriptome landscape of the brain microenvironment during the entire metastatic process.

My global analysis of both the tumor and stroma provide insights into many aspects of the metastatic process.To further investigate these insights, I focused on the role of metabolism in the brain metastatic process.Based on a distinct metabolic transcriptome profile in brain metastases compared to their primary tumor counterparts, I hypothesized that metabolic transcriptome shifting during metastatic evolution is crucial for metastatic success to the brain. Here I show that the expression of the GABA metabolic pathway mediator glutamate decarboxylase 1 (GAD1) is significantly up-regulated. Down-regulation of DNA methyltransferase 1 (DNMT1) induced by the brain microenvironment results in decreased GAD1 promoter methylation and subsequent up-regulation of GAD1 expression. I utilized the Peredox biosensor coupled with time-lapse imaging to monitor the cytosolic NADH:NAD⁺ equilibrium in tumor cells. Knocking down of GAD1 abolishes the capability of tumor cells to utilize extracellular glutamine. Repurposing of a neurological drug, vigabatrin, results in a significant decrease in brain metastasis incidence. Taken together, my results demonstrated that brain microenvironment-specific metabolic shifting through GAD1 promoter demethylation contributes to the context-dependent cellular metabolic adaption and facilitate brain metastasis outgrowth.