Lecture Summaries | Cellular Metabolism and Cancer: Nature or Nurture? | Biology

Course lecture summaries.
WEEK #	TOPICS	LECTURE SUMMARIES
1	Introduction to the Course	This first class is an introduction to the course. After getting to know each other, we will describe the syllabus, goals and expectations of the course. We will also discuss course logistics, schedule meeting times and due dates. We will provide an overview of the course and discuss the different diseases we will explore. We will also discuss strategies for reading the primary scientific literature. At the end of the class, we will introduce the topic (aerobic glycolysis and the Warburg effect) and papers for our first full class next week.
2	An Introduction to Cancer Metabolism: The Warburg Effect	Optional Background: An Introductory Lecture on the Hallmarks of Cancer (First 3 minutes) In the 1920s it was observed that cancer cells exhibit altered metabolism compared to normal cells. This observation was made by Otto Warburg, a German biochemist. He found that unlike normal cells, cancer cells have increased glucose uptake and increased secretion of lactate. Most normal cells display this behavior only under oxygen deprivation. Why tumors have this behavior and if it could be targeted to slow cancer growth were problems not explored for decades. The first of our papers from this week comes from Gerty and Carl Cori, contemporaries of Warburg whose scientific partnership illuminated much of carbohydrate metabolism. We will see how they pushed Warburg’s observations outside the Petri dish. The second paper describes how in 2008 the field of cancer metabolism was reinvigorated following the discovery that cancer cells express a specific isoform of a key metabolic enzyme, pyruvate kinase M2 (PKM2).
3	Role of Mitochondrial Function in Tumor Cell Growth	After Warburg made his discoveries regarding increased aerobic glycolysis, he further hypothesized that cancer cells displayed this behavior because of dysfunctional mitochondria: cells could not further oxidize glucose-derived pyruvate in the TCA cycle but instead converted the pyruvate to lactate for secretion. While Warburg’s observation of cancer aerobic glycolysis has been repeatedly upheld, his hypothesis that dysfunctional mitochondria explained this observation has not been supported. We will read literature this week that challenges this hypothesis and argues that cancer cells require mitochondrial function. Why do proliferating cancer cells require mitochondria if they do not utilize much pyruvate in the TCA cycle (which takes place in the mitochondria) and instead use pyruvate to make lactate, which is secreted? We will read a recent paper that uses genetics and biochemical tracing approaches to answer this question.
4	Amino Acid Metabolism	One widely held hypothesis in the field of cancer cell metabolism is that the high flux through glycolysis exhibited by rapidly proliferating cancer cells means that glucose is used to synthesize new cell biomass. However, our first paper shows that amino acids, not glucose, account for the majority of biomass in proliferating mammalian cells, highlighting an important role for amino acids in cancer cell metabolism. Our second paper looks at a specific amino acid synthesis pathway, the serine synthesis pathway, and its role in supporting cancer cell metabolism. Although serine and the amino acid glycine can be interconverted in cells via either loss or gain of a carbon (also referred to as a “one-carbon unit”), the authors found that serine, but not glycine, is important for proliferation because of the contribution of these one-carbon units to nucleotide synthesis.
5	Nucleotide and Lipid Metabolism	Nucleotides and lipids are classes of macromolecules that must be synthesized by proliferating cancer cells. Cancer cells need deoxyribonucleotides to duplicate their genome to divide, and they also have a higher demand for lipids so that they can synthesize membranes to build a new cell. How does the reprogrammed glucose metabolism of cancer cells support the increased biosynthesis of nucleotides and lipids? The first paper describes how loss of PKM2 shifts cells towards increased glucose oxidation, resulting in the decreased utilization of glucose to synthesize nucleotides and subsequent impairment of proliferation. These data suggest that one of the roles of aerobic glycolysis might be to support nucleotide synthesis. The second paper explores a cancer drug in development that targets the enzyme acetyl-CoA carboxylase, which is required for cells to synthesize fatty acids. This drug inhibits fatty acid synthesis in lung cancer cells and impairs the growth of lung tumors in vivo, demonstrating that fatty acid synthesis is a potential metabolic vulnerability for cancer cells.
6	Mutations in Isocitrate Dehydrogenase and the Discovery of a Neomorphic Activity	Recently, cancer genome sequencing efforts identified a unique and novel oncogenic mutation driving many gliomas, a form of brain cancer. Mutations in the key TCA cycle enzyme isocitrate dehydrogenase (IDH), which converts isocitrate to alpha-ketoglutarate, were found to occur with high frequency in glioma. How does IDH mutation promote gliomas? The first paper for this week shows that the mutant IDH1 enzyme loses oxidative enzymatic activity and suggests that mutant IDH could act to suppress the activity of wild-type IDH enzymes. The second paper offers a different explanation and finds that mutant IDH1 and IDH2 have a novel reductive activity that converts alpha-ketoglutarate to a novel metabolite called 2-hydroxyglutarate (2HG). This new enzymatic activity is referred to as a neomorphic activity.
7	2-hydroxyglutarate: The First Oncometabolite?	2-HG, to which we were introduced last week, quickly was termed an “oncometabolite,” given its association with tumor-causing IDH mutations. This concept suggested that 2-HG itself was capable of transforming cells into cancerous cells. However, whether 2-HG is sufficient for cellular transformation is unclear. Even less clear is how 2-HG might cause cellular transformation. One mechanism that has been proposed is that 2-HG inhibits alpha-ketoglutarate-dependent enzymes that function as tumor suppressors. The first paper shows that 2-HG can inhibit histone lysine demethylases (enzymes that remove methyl groups from lysine residues in histone proteins). Histone methylation is known to regulate gene expression epigenetically, meaning that this process activates or inactivates genes without changing the DNA sequence itself. This paper was among the first to show that IDH mutations affect gene expression via epigenetic regulation of histone methylation. The second paper describes enasidenib, a drug in development that blocks 2-HG production by targeting the IDH mutant enzymes. Interestingly, in clinical trials with this drug, a few patients relapsed and gained clinical resistance to enasidenib, and the mechanism of resistance was traced to a novel IDH mutation that allowed 2-HG production even under enasidenib treatment. These papers highlight the oncogenic function of 2-HG and exemplify current clinical efforts to target this oncometabolite for cancer therapy.
8	Field Trip—Visit to Agios	We will take a field trip to a company translating cancer metabolism findings (from the papers we have read!) into patient therapeutics. Agios is a biotechnology company founded by Dr. Lewis Cantley, Dr. Tak Mak, and Dr. Craig Thompson. We have read papers from the laboratories of Drs. Cantley and Thompson. These investigators realized potential for translating the basic biology underlying tumor metabolism for cancer therapeutics and banded together to form Agios. Initial work has involved developing IDH inhibitors and pyruvate kinase activators, both of which are now in phase I clinical trials. We will tour the research space and facilities to observe how the research is done and hear a presentation from an Agios scientist describing how his/her research could benefit people afflicted with cancer and inborn errors of metabolism.
9	Oncogenes and Metabolism: How Genetic Changes Alter Cancer Metabolism	Thus far, we have mostly discussed how cancer cells differ from their normal counterparts when it comes to glucose utilization. However, tumor cells grow in a complex mixture of nutrients, including amino acids, lipids, proteins and other molecules. Do tumor cells also utilize other nutrients to their proliferative advantage? These two papers discuss the “alternative carbon source” – glutamine – and its usage by cancer cells. The first paper describes how activation of the RAS oncogene causes cells to be reliant on glutamine for survival. These studies were done in vitro using cultured cells, vastly simplifying nutrient tracing. The second paper uses mouse models of MYC oncogene-induced liver and lung cancers. This work found that MYC-induced tumors in the liver but not in the lung utilize glutamine. These studies highlight that oncogenes themselves do not direct cancer cell metabolism, but rather that there is interplay between the oncogene and the tissue where the tumor arises. Further, these studies demonstrate there are many differences between in vitro and in vivo cancer cell metabolism we are just beginning to appreciate.
10	Context Matters! How Tissue Environment Alters Cancer Cell Metabolism	As we discussed in our previous classes, much of the renewed interest in cancer cell metabolism over the past 10 years has been centered on observations that genetic alterations in metabolic genes or oncogenes drive metabolic changes in cancer cells. However, recent findings have illuminated how nutrient utilization by tumors depends not only on genotype but also on environmental factors, such as the tissue in which a tumor is located and the physiological levels of metabolites available to a tumor. This has become particularly evident from studies showing that the metabolism of cancer cells in lab tissue culture conditions often do not mirror the metabolism of tumors in an in vivo context. The first paper describes how the utilization of glutamine by lung cancer cells changes depending on whether they are grown in a petri dish versus in a mouse. This finding has important implications for the development of therapeutic strategies that target glutamine metabolism. The second paper describes the development of a tissue culture medium that more closely mimics the physiological levels of metabolites in human plasma. Culturing cancer cells in this medium has broad effects on cellular metabolism, and interestingly, increased levels of uric acid found in human plasma that increases the resistance of cancer cells to 5-fluorouracil, a chemotherapy that is commonly used in the clinic. These studies highlight the importance of studying tumor metabolism in the appropriate in vivo context and of developing better tissue culture models that mirror the in vivo tumor microenvironment.
11	Metabolic Interactions of Stroma Cells and Cancer	Tumors are composed of a heterogeneous mix of cell types, including cancer cells and stromal cells such as macrophages, fibroblasts, and immune cells. How these cells interact to support tumor growth is poorly understood. Symbiotic metabolic interactions among these different cell types have been reported in various cancers. Studies of bulk tumor metabolism fail to capture information about heterogeneity with regard to different cell types. However, this information is critical to understand tumor metabolism because environmental context, differences in nutrient use among different cell populations, and metabolic cooperation among different cell types can all influence tumor phenotypes. Today’s papers highlight two metabolites, alanine and asparagine, that are produced in stromal cells and might support the growth of cancer cells. The first paper examines the role of autophagy, the process of degradation and recycling of components within the cell, and alanine secretion by tumor stromal cells to support the growth of pancreatic cancer. The second paper shows that loss of the scaffolding/adaptor protein p62 in the stroma leads to resistance to glutamine deprivation, ultimately resulting in asparagine production by the stroma that supports prostate cancer growth.
12	Impact of Diet on Tumor Metabolism and Progression	Changes in whole-body metabolism and systemic nutrient availability by dietary factors are another important part of a tumor’s metabolic environment that can dictate nutrient utilization by cancer cells. Although diet has long been appreciated to contribute to cancer risk and progression, a better molecular understanding of how diet modulates nutrient availability and utilization by cancer cells is limited. Recent studies have sought to apply our biochemical understanding of cancer cell metabolism towards examining how certain diets affect tumor progression. The first paper explores whether the dependence of certain cancer cells on the amino acids serine and glycine, which we discussed in an earlier session, can be exploited from a dietary perspective by administering tumor-bearing animals with a serine/glycine-free diet. The second paper describes a potential mechanism for how the ketogenic diet, which has recently received much attention in popular culture, might be used effectively in combination with an existing cancer therapy to treat various tumor types. Studies like these might begin to provide patients with more rigorous scientific guidance for incorporating diet and nutrition into cancer therapy.
13	Oral Presentations and Final Discussion	Following the oral presentations, we will have a final discussion about what we have learned about metabolism and its role in disease, as well as about where we think the field will be going next. In addition, we will complete evaluation forms and discuss those sections of the course that were most informative and those that need improvement.