Jason W. Locasale - US grants

DESCRIPTION (provided by applicant): Cancers are diseases of uncontrolled cell growth in which cells acquire mutations that lead to cell proliferation outside of the context of normal tissue development. Molecular advances over the past 30 years have characterized many of the signal transduction pathways and gene transcription networks that are altered during cancer progression. Aberrant regulation of these networks invariably results in gross alterations of the metabolic network. Differences in the metabolism of glucose in tumors compared to that of normal tissue have been noted for over 70 years; yet, the origins, consequences, cancer specificities, and the principles of intervention are poorly understood. Our understanding of cancer cell metabolism is challenged by the enormous complexity of the interaction between metabolic pathways and the genetic aberrations that alter these pathways. Advances will require new technologies and conceptual frameworks, such as high-throughput metabolomics, a technique that aims to quantify within a single measurement, a large number of small-molecules within cells and tissues, and mathematical models that can parse the effects of many simultaneous interactions. Investing such effort has the potential to fundamentally alter our understanding of basic cancer biology and lead to innovative therapies. My proposed research focuses on this central problem of cancer cell growth and development and utilizes the application of computational methods rooted in systems biology in conjunction with the use high-throughput technologies such as mass spectrometry-based metabolomics to understand mechanisms that lead to unregulated growth and altered metabolism in cancer cells and primary tumors. During my postdoctoral work, I discovered two novel metabolic pathways in cells undergoing rapid proliferation and tumor development. These studies combined metabolomics technology with techniques I acquired in my postdoctoral training involving cell biology, biochemistry and genetics. One pathway involves an alternate route of glucose uptake that decouple catabolic glucose metabolism with energy metabolism. The other involves the diversion of glycolytic flux into anabolic metabolism through a glycolytic intermediate. Further genetic studies established that this pathway is selected for in the development of human cancer. I will continue these projects during the remainder of my postdoctoral training in the mentored phase. This work will allow me to establish an independent research program involving using systems biology techniques to investigate define biological problems in understanding the role of glucose metabolism in cancer. My previous training in systems biology and current training in a leading cancer biology and signal transduction lab provides a skill-set that is uniquely suited to approach this problem.

? DESCRIPTION (provided by applicant): Cancer cells adapt their metabolism to achieve the requirements of uncontrolled proliferation, survival, and long-term maintenance. Serine, glycine, and one carbon (SGOC) metabolism integrates nutritional status from amino acids, glucose and vitamins, and generates diverse outputs, such as the biosynthesis, the maintenance of redox status and the substrates for methylation reactions. We have recently found that cancer cells divert a relatively large amount of flux from glucose into de novo serine metabolism leading to the deregulation of one carbon metabolism. Here we will build upon findings we have made that have identified newfound roles for one carbon metabolism in cancer pathogenesis. We will carry out an integrated computational and experimental analysis to investigate the diversity of functions within the metabolic network involving one carbon metabolism in cancer. In aim 1, we will characterize the serine and one carbon gene expression network in tumor tissues. We reconstruct the network of genes that encode enzymes that metabolize serine. We will overlay TCGA data onto the serine metabolic network to assess its expression in cancer. We will analyze the cancer context of the network by comparing expression of network components across normal tissues, different cancer tissues, histological subtypes, and mutational statuses. In aim 2, we will carry out a flux analysis and metabolomics of one carbon metabolism in cancer cells. We will capitalize on a metabolomics platform our lab has developed and we have developed a method for 13C serine flux analysis. We will expand on these methods and then exploit these capabilities to measure the diversity of serine flux across different cancer cells. I aim 3, we will evaluate the relationship between one carbon metabolism and anti-metabolite chemotherapy. We will consolidate our findings and relate them in the context of clinically available pharmacological agents that target enzymes in the SGOC network. We will next model the metabolomics response of cells treated with different agents.

? DESCRIPTION (provided by applicant): Metastasis of cancer cells from the primary site to distant organs is a major cause of cancer-related death, as current chemotherapies are largely ineffective against metastasis. Recent data from the PIs' lab suggest that colorectal cancer (CRC) cells may undergo remarkable metabolic reprogramming after they metastasize to liver, which is the most common site for CRC metastasis. This discovery makes the conceptual argument that altered metabolism may contribute to metastatic phenotypes. The proposed study will use an integrative systems approach to understand metabolic reprogramming of CRC liver metastasis. Primary and liver tumors from an in vivo CRC metastasis model will be profiled by RNA-seq and high-resolution, liquid chromatography-mass spectrometry (LC-MS) based metabolomics. Integrated network analysis of the transcriptome and metabolome will identify altered metabolic pathways in CRC metastases. The findings will be corroborated by an extensive clinical biobank that contains a large collection of CRC liver metastases. Based on the integrative systems analysis, this study will then explore the hypothesis that manipulation of metabolic reprogramming will interfere with growth of CRC liver metastasis. Preliminary data suggest that targeting dysregulated metabolism, which includes inhibition of enzymes and restrictive diets, can interfere with growth of liver metastases more than frontline chemotherapy can in animal models. Since metastatic tumor cells have to adapt to their new microenvironment, targeting metabolic reprogramming of metastasis may be a viable approach for multiple cancer types and a significant percentage of the patient population.

Nutrient availability (i.e. diet) can affect metabolic pathways and determine the requirements of cancer cell metabolism to as large a degree as the metabolic genes that are reprogrammed in tumors. Previous work from us and others has shown that 1.) methionine availability affects one carbon cycle flux, DNA and histone methylation and thus epigenetic programming, 2.) dietary methionine restriction promotes metabolic health and extends insect and mammalian lifespan, two anti-cancer phenotypes, 3.) deletions of genes that affect methionine metabolism in tumors render them susceptible. Nevertheless, how this dietary factor (and diet in general) can influence cancer outcome is largely unknown. Our preliminary data shows that methionine restriction delays tumor growth in colorectal cancer patient derived xenograft (CRC PDX) models and sensitizes a genetically engineered mouse sarcoma model to radiation. These findings led us to propose an investigation to define the mechanisms underlying these phenotypes. We will consider the following aims. In aim 1 we seek to identify molecular determinants of sensitivity to methionine restriction. We will employ a metabolomics approach using a metabolite profiling platform and flux analysis method our laboratory has developed to investigate the metabolic changes in cancer cells that are induced by methionine restriction. We will next investigate the epigenetic role that methionine metabolism in tumor growth. The outcome will determine the metabolic and epigenetic adaptations that are modulated through dietary methionine metabolism. In aim 2, we will determine why the sarcomas are resistant to methionine restriction but respond to dietary methionine restriction and radiation in a synergistic manner. The outcome will define the metabolic and epigenetic mechanisms that occur in order to resist dietary manipulation of methionine metabolism but leads to a synergy effect of dietary methionine restriction and radiation. In aim 3, we will determine the role of methionine availability from diet in methylthioadenosine phosphorylase (MTAP)-deleted cancers. MTAP is an enzyme essential for the methionine salvage pathway and recent studies have shown that deletions in MTAP confer additional dependencies on methylation reactions. The outcome, using MTAP, dietary methionine, and methionine metabolism as a model system will characterize the metabolic interaction between dietary methionine and MTAP deletion and lead to a newfound understanding of the interaction between genetics and environment, particularly diet and nutrition in mediating cancer outcome.