MYC oncogene regulation of the intersection between proteins, lipids and metabolic networks

Changes in cell metabolism are regarded as one of the hallmarks of cancer. Increasing our knowledge of oncogene regulation of metabolic pathways is of key importance to the development of novel cancer therapies. Metabolites provide substrates to build new cells and energy to drive this process. Additionally metabolites are used in the post-translational modification of proteins and these modifications can regulate protein function and targeting to sites of activation and signaling pathway initiation. Such sites include lipid rafts, which provide an essential platform for protein-protein interactions at the plasma membrane. The synthesis of these rafts provides a important link between metabolic programs and cell signaling networks. Ongoing work in our laboratory is focused on determining the role of the oncogene c-MYC in the regulation of this interconnected metabolite-lipid-protein network. 

Topics under investigation:

• The lipid raft proteome during MYC regulated cell cycle entry.
• Tumor progression and regulation by metabolic, transcriptome and miRNA networks.
• Biochemical microscopy of the tumor and microenvironment during tumor progression.
• Bioactive lipids and signaling during cell cycle and in the tumor microenvironment.

Metabolic characterization of locally advanced breast cancers resistant to neoadjuvant therapy

Molecular subtypes of breast cancer provide the rationale for tailored therapies. Triple-negative, or basal-like, breast cancers are treated with combinations of standard cytotoxic chemotherapies. Dynamic FDG-PET assays pre-therapy have demonstrated an association of high glucose uptake/blood flow ratios with poor responses to neoadjuvant therapy. Triple-negative breast cancer cell lines are highly glycolytic, with activation of HIF-1 under normoxic conditions. Our analysis of microarray data from tumor biopsy specimens for patients undergoing neoadjuvant therapy for triple-negative tumors identified an immune response signature consistent with M2 macrophages, an anti-inflammatory and pro-tumorigenic subtype. Metabolic products from tumor cells, such as lactic acid, can polarize tumor-associated macrophages to a M2 phenotype, potentially linking the FDG-PET results with the tumor immune micro-environment. We are attempting to repolarize tumor-associated macrophages toward M1 phenotypes using metabolic inhibitors of fatty acid oxidation, a metabolic pathway required for M2 polarization, in syngeneic tumor models. 

Metabolic features of naïve and primed embryonic stem cells 

Embryonic stem cells (ESCs) are derived from transient pluripotent cell populations in the embryonic epiblast, and are divided into naïve and primed states based on their similarity to pre- and post-implantation phenotypes, respectively. In collaboration with Hannele Ruohola-Baker and Carol Ware at the UW Institute for Stem Cell and Regenerative Medicine, we identified striking metabolic differences between naïve and primed ESCs, with a loss of respiratory capacity in primed cells due to transcriptional downregulation of mitochondrial electron transport chain complexes. We have recently shown that naïve and primed ESCs exhibit opposite sensitivities to acetaldehyde, a metabolic byproduct implicated in Fanconi anemia. Fanconi anemia is associated with a DNA repair defect for interstrand DNA crosslinks, and recently, defective mitophagy. Both naïve and primed ESCs produce endogenous acetaldehyde, with primed ESCs producing lower amounts, but having higher levels of acetaldehyde-DNA adducts. We are using this model to investigate mechanisms of differential sensitivity, metabolic sources and mitochondrial targets for acetaldehyde to advance our understanding of Fanconi anemia and fetal alcohol syndrome pathogenesis.

Functional genomics of a transmissible cancer in Tasmanian Devils

Devil Facial Tumor Disease is a clonally derived allograft tumor of Schwann cell origin that is spreading through the Tasmanian Devil population, threatening its extinction. Immune evasion appears to be important for transmissibility, as devil tumors lack MHC expression due to epigenetic downregulation of antigen-processing molecules. We have characterized bioenergetic metabolism in devil tumor cell lines, and observed selective dependence on pentose phosphate pathway, fatty acid synthesis, and anaplerotic pathways. We are developing a genome-scale devil CRISPR-Cas9 library, which will be tested in pools to identify genes required for suppressing MHC expression on the cell surface.

Identifying metabolic vulnerabilities in glioblastoma stem cells

In collaboration with Patrick Paddison, we have been screening glioblastoma stem cell lines, in comparison to normal neural stem cells for metabolic vulnerabilities, using shRNA and CRISPR/Cas9 functional genomics approaches (Paddison lab) and a unique library of 260 enzyme inhibitors for 62 metabolic pathways (Hockenbery lab). These cell lines can be grown in serum-free, defined media as monolayers and retain tumor-specific genetic and epigenetic features over long periods. Uling the two complementary screening approaches, we have identified metabolic pathways required for survival of mesenchymal vs. proneural subtypes of glioblastoma, as well as GBM vs. neural stem cell lines. Current efforts involve metabolomic validation of these dependencies, and investigation of the role of specific driver mutations in generating unique metabolic vulnerabilities.