REGULATION OF METABOLISM BY THE ONCOPROTEIN C-MYC by Lia Rae Edmunds Biochemistry, Washington and Jefferson College, 2008 Submitted to the Graduate Faculty of Molecular Genetics and Developmental Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2015 UNIVERSITY OF PITTSBURGH MOLECULAR GENETICS AND DEVELOPMENTAL BIOLOGY This dissertation was presented by Lia Rae Edmunds It was defended on November, 2015 and approved by Eric S. Goetzman, Ph.D., Medical Genetics Robert M. O’Doherty, Ph.D., Endocrinology Bennet Van Houten, Ph.D., Molecular Genetics and Developmental Biology Dissertation Advisor: Edward V. Prochownik, M.D., Ph.D., Pediatric Hematology/Oncology ii Copyright © by Lia Rae Edmunds 2015 iii REGULATION OF METABOLISM BY THE ONCOPROTEIN C-MYC Lia Rae Edmunds, Ph.D. University of Pittsburgh, 2015 c-Myc (hereafter Myc), a transcription factor that regulates a variety of cellular functions including growth and differentiation, is deregulated in many different types of cancers. Myc regulates the Warburg effect and oncogenic biosynthesis, but also many aspects of metabolism, believed to be a pivotal point of transformation. Myc is known to control glycolysis and glutaminolysis but little is known about the interplay between glucose, amino acid, and fatty acid oxidation. We hypothesize Myc integrates glucose, amino acid, and fatty acid utilization for energy, and either loss- or gain-of-function will disrupt metabolic homeostasis. Loss of Myc in rat fibroblasts elicits a severe energy deficit, including diminished acetyl-coA levels, to which they respond by enhancing FAO and lipid uptake and storage. Using an in vivo model, we found murine hepatocytes respond to Myc ablation with a milder phenotype. They display metabolic defects, including reduced respiratory chain capacity and an increased metabolic rate when fed a high-fat diet. Additionally, hepatocytes had major lipid defects including transcriptional deregulation, lipid accumulation and increased FAO. Reduced ATP in Myc KO fibroblasts constitutively activates AMPK, a protein which limits anabolism for catabolism, leading us to hypothesize AMPK may play a role in Myc deregulated phenotypes. We found AMPK controls mitochondrial structure and function in conjunction with Myc over-expression, via redox state, electron transport chain (ETC) capacity, and TCA cycle dehydrogenases. Additionally, AMPK KO cells demonstrate transcriptional and translational differences and differential responses in regulating glycolysis, which results in iv metabolite dysfunction, when exposed to Myc over-expression. Thus, AMPK is critical to supporting metabolic pathways in response to Myc deregulation. To ascertain if Myc plays a role in hepatic proliferative capacity, we turned to a mouse model of hereditary tyrosinemia. We definitively proved that Myc is not required for prolonged hepatocyte proliferation, even in direct competition with Myc-replete hepatocytes. Proliferating KO hepatocytes were associated with a pro-inflammatory environment that correlated with worsening lipid accumulation and lipid oxidation-mediated liver damage, a phenotype reminiscent of non-alcoholic fatty liver-like disease. Throughout this work, we reveal Myc-regulated metabolism is vital for maintaining lipid homeostasis and energy production, but dispensable for sustained hepatic proliferation. v TABLE OF CONTENTS PREFACE ................................................................................................................................... XV CHAPTER 2 ACKNOWLEDGEMENTS ...................................................................... XV CHAPTER 3 ACKNOWLEDGEMENTS ...................................................................... XV CHAPTER 4 ACKNOWLEDGEMENTS .................................................................... XVI ABBREVIATIONS .......................................................................................................... XVI 1.0 INTRODUCTION ........................................................................................................ 1 1.1 TUMOR METABOLISM ................................................................................... 3 1.2 MYC AND METABOLIC REPROGRAMMING ........................................... 4 1.3 MYC AND FATTY ACID METABOLISM ..................................................... 5 1.4 AMPK AND MYC ............................................................................................... 8 1.5 MYC AND PROLIFERATION ....................................................................... 11 2.0 C-MYC PROGRAMS FATTY ACID METABOLISM AND DICTATES ACETYL COA ABUNDANCE AND FATE ............................................................................ 15 2.1 INTRODUCTION ............................................................................................. 15 2.2 RESULTS ........................................................................................................... 18 2.2.1 Uptake and oxidation of fatty acids by KO cells......................................... 18 2.2.2 Differential utilization of fatty acids ............................................................ 20 2.2.3 Neutral Lipid Accumulation in KO cells ..................................................... 22 vi 2.2.4 AMPK is Myc-responsive ............................................................................. 26 2.2.5 KO cells maximize their accumulation of acetyl CoA by increasing its production and decreasing its utilization for purposes other than TCA cycle utilization .................................................................................................................... 29 2.3 DISCUSSION ..................................................................................................... 32 2.4 EXPERIMENTAL PROCEDURES ................................................................ 37 2.4.1 Cell culture ..................................................................................................... 37 2.4.2 14C-palmitate and 14C-octanoate uptake and β-oxidation studies ............. 37 2.4.3 Incorporation of 3H-palmitate, 14C-octanoate and 14C-acetate into lipids 38 2.4.4 Enzyme assays ................................................................................................ 39 2.4.5 Visualization and quantification of neutral lipids ...................................... 40 2.4.6 Immunoblotting ............................................................................................. 41 2.4.7 RNA isolation and real time qRT-PCR ....................................................... 41 2.4.8 Acetyl CoA assays .......................................................................................... 43 3.0 C-MYC AND AMPK CONTROL CELLULAR ENERGY LEVELS BY COOPERATIVELY REGULATING MITOCHONDRIAL STRUCTURE AND FUNCTION ................................................................................................................................. 45 3.1 INTRODUCTION ............................................................................................. 45 3.2 RESULTS ........................................................................................................... 47 3.2.1 AMPK is necessary for Myc-stimulated mitochondrial biogenesis and function ....................................................................................................................... 47 3.2.2 Transcriptional and enzymatic profiling reveals co-operativity between Myc and AMPK in modulating metabolic function ................................................ 52 vii 3.2.3 Differences in mitochondrial proteomes of WT and KO MEFs ............... 57 3.2.4 Differential redox states of WT and KO cells ............................................. 59 3.2.5 AMPK influences Myc-mediated re-programming of steady-state metabolites .................................................................................................................. 60 3.3 DISCUSSION ..................................................................................................... 66 3.3.1 Mitochondrial responses to Myc over-expression are AMPK-dependent 66 3.3.2 Co-operativity between Myc and AMPK in determining cellular redox state ......................................................................................................................... 70 3.3.3 Changes in PK and PDH as a potential mechanism for metabolite differences between WT and KO MEFs .................................................................. 71 3.3.4 Cross-talk between Myc and AMPK ........................................................... 72 3.4 EXPERIMENTAL PROCEDURES ................................................................ 74 3.4.1 Cell culture ..................................................................................................... 74 3.4.2 Quantification of glycolysis, Oxphos and ATP levels ................................. 75 3.4.3 Measurements of mitochondrial mass and reactive oxygen species ......... 76 3.4.4 Blue native gel electrophoresis and electron transport chain assays ........ 76 3.4.5 RNA extraction and real-time qRT-PCR analysis ..................................... 78 3.4.6 Immunoblotting ............................................................................................. 80 3.4.7 Mitochondrial oxidoreductase assays .......................................................... 81 3.4.8 Enrichment and Tryptic Digestion of MEF Mitochondrial Proteins ......