Modeling, Targeting Acetyl-CoA Metabolism in Breast Cancer

Institution: The Burnham Institute for Medical Research
Investigator(s): Chen Yang, Ph.D. -
Award Cycle: 2006 (Cycle 12) Grant #: 12FB-0100 Award: $90,000
Award Type: Postdoctoral Fellowship
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease

Initial Award Abstract (2006)
Tumor cell metabolism is distinct from that of normal cells. Unlike non-transformed cells, tumor cells stimulate growth through increased glycolysis despite low pH and hypoxic conditions. Hypoxia precipitates overexpression of many genes of glycolysis, ultimately stimulating key metabolites that may be used as tumor markers. For example, glycolysis drives fatty acid synthesis though a central metabolic precursor, acetyl-CoA. Increased levels of fatty acid synthase (FAS) in breast cancer tissues indicate poor prognosis and implicate FAS as a possible drug target. Quantitative modeling of the acetyl-CoA metabolic sub-network will elucidate further fundamental distinctions between mammary epithelia and mammary carcinoma regulation and identify novel therapeutic targets in breast cancer.

We propose that hypoxic exposure leads to an increased rate of glycolysis through sequential, quantifiable stimulation of associated enzymes and transcription factors. Consequently, comprehensive quantification of metabolic flux from glycolysis to fatty acid synthesis in hypoxic mammary carcinoma cells could reveal unexplored critical control points suitable for clinical breast cancer drug development.

Our aims are:
#1. Assess metabolic pathways, individual reactions and enzymes, whichcomprise an acetyl-CoA subnetwork in mammary carcinoma cells.
#2. Build a quantitative metabolic model of the acetyl-CoA sub-network tointerpret and reconcile cancer specific alterations of metabolism in terms ofrespective metabolic fluxes.
#3. Predict, prioritize, and validate potential therapeutic targets based on acetyl-CoA network modeling.

Mammary carcinoma cell lines will be fed 13C-labeled glucose to construct a flux model of cellular carbon flow. Using both 2D NMR and GC/LC-MS, we will characterize labeling patterns, fluxes and pools of key metabolites involved in up to 50 biochemical reactions spanning the range of glycolysis to fatty acid synthesis. Experimental data will be coordinated with functional genomics techniques to construct an accurate quantitative model of carbon flux and identify cancer-specific metabolic aberrations. We will select 10–15 potential drug targets based on key distinctions between mammary epithelia and mammary carcinoma metabolic flux. RNAi knockdown will validate potential targets and measure subsequent effects on metabolic flux, growth rate, and cell death.

Discovering molecular marker–based targets is crucial to developing individualized, less toxic breast cancer treatment. This integrative study will be the first to identify novel therapeutic breast cancer targets using 2D NMR and GC/LC-MS techniques to measure metabolite fluxes associated with the hypoxia and glycolytic shift. We propose that unique control points in hypoxia-adapted cells, resulting from increased glycolytic rate through sequential quantifiable stimulation of associated enzymes and transcription factors in the acetyl-CoA pathway, can be identified and validated for therapeutic benefit.

Final Report (2008)
Understanding specifics of breast cancer metabolism could greatly facilitate our understanding of this disease and the development of new therapies aimed at selective killing of tumor cells. Unlike normal cells, cancer cells grow uncontrollably, require increased energy, and withstand low pH and hypoxic (low oxygen) conditions. Using continual glycolysis (anaerobic metabolism of glucose)as a primary energy source is a cancer-specific process that differentiates normal from cancerous cells. We studied unique control points in breast tumor cells, stemming from hypoxic selection that leads to an increased rate of glycolysis, can be exploited to develop anticancer drugs.

We developed a model of breast cancer cell metabolism by measuring fundamental energy usage in the acetyl CoA network. Acetyl-CoA is a central metabolite that connects glycolysis to fatty acid synthesis. I quantified the metabolism in both normal and breast cancer cells using 13C isotope labeling followed by two-dimensional nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS) analysis. The obtained information was then used to pinpoint tumor-specific metabolism and characterize the metabolic changes that occur during cancer development. This approach allowed me to select a set of prospective drug targets. The impact upon tumor metabolism, growth rate, and cell death by intercepting these targets was validated using RNA interference (RNAi), a proven molecular technique.

In the future, I will continue using metabolomics (study of genetic patterns in cell metabolism) using a “systems biology” approach to improve our understanding of breast cancer and our ability to diagnose, cure and prevent this deadly disease.

Symposium Abstract (2007)
Comparative metabolic profiling of cancerous and normal cells improves our understanding of the fundamental mechanisms of tumorigenesis and opens new opportunities in target and drug discovery. We are developing a novel methodology of comparative metabolome analysis that integrates the information about both metabolite pools and fluxes associated with a large number of key metabolic pathways in model cancer and normal cell lines. The data were acquired using [U-13C]glucose labeling followed by two-dimensional NMR and GC-MS techniques and analyzed using isotopomer (i.e., an isomer that differs in the position of its isotopic substitution positions) modeling approach. Significant differences revealed between breast cancer and normal human mammary epithelial cell lines are consistent with previously reported phenomena, such as upregulation of fatty acid synthesis. Additional changes established for the first time in this study expand a remarkable picture of global metabolic rewiring associated with tumorigenesis and point to new potential diagnostic and therapeutic targets.

Central carbon metabolism in the progression of mammary carcinoma.
Periodical:Breast Cancer Research and Treatment
Index Medicus: Breast Cancer Res Treat
Authors: Richardson AD, Yang C, Osterman A, Smith JW.
Yr: 2008 Vol: 110 Nbr: 2 Abs: Pg:297-307

Profiling of central metabolism in human cancer cells by two-domensional NMR, GC-MS analysis, and isotopomer modeling
Index Medicus: Metabolomics
Authors: Yang C, Richardson AD, Osterman A, and Smith JW
Yr: 2008 Vol: 4 Nbr: 1 Abs: Pg:13-29