Copyright by Shannon Renee Sweeney 2020 The Dissertation Committee for Shannon Renee Sweeney Certifies that this is the approved version of the following dissertation: Elucidating metabolic vulnerabilities to improve outcomes in pediatric precursor B-cell acute lymphoblastic leukemia Committee: Stefano Tiziani, Supervisor Dean R. Appling Jennifer S. Brodbelt John DiGiovanni Marina Y. Konopleva Elucidating metabolic vulnerabilities to improve outcomes in pediatric precursor B-cell acute lymphoblastic leukemia by Shannon Renee Sweeney Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin May 2020 Dedication To my parents for always believing I was exceptional and inspiring me to prove them right. To my sisters – Lauren for keeping me grounded, Erin for making me want to fly – together you have taught me innumerable lessons. Thank you for teaching me how to mediate, negotiate, and above all, choose my battles. And to Nicholas, you make me better; none of this would have been possible without you. Acknowledgements I will be forever grateful and indebted to the many people who have guided me with endless encouragement and unwavering support. The most incredible tribe of brilliant women – Dr. Nathalie Muñoz, Dr. Maria José Romo Palafox, Dr. Gloria Cecilia Galván, Dr. Lauren D. Mangini, Dr. Deborah Salvo Domínguez, and soon to be doctors, Diana E. Gutierrez Lopez and Amy R. Nichols. It took me a while to find you, but in the end, your timing was impeccable. My lab family – Dr. Renu Pandey, Xiyuan Lu, Jennifer Chiou, Meghan Collins, Paul Gries, and Lavender Hackman. Thank you for sharing your gifts and being on this journey with me. Dr. Enrique Sentandreu, thank you for mentoring me long beyond our time together at the bench. Your guidance has been one of the greatest gifts. Dr. Alessia Lodi, thank you for your insightful observations, computational magic, and ability to visualize data so beautifully. To my committee members, I acknowledge that truly none of this is possible without you; thank you for sharing your precious time and insights with me. Last, but certainly not least, deepest gratitude to my advisor, Dr. Stefano Tiziani, for endlessly encouraging me to find my passion and realize my potential. v Abstract Elucidating metabolic vulnerabilities to improve outcomes in pediatric precursor B-cell acute lymphoblastic leukemia Shannon Renee Sweeney, PhD The University of Texas at Austin, 2020 Supervisor: Stefano Tiziani Cancer continues to be the leading cause of disease-related death in children. Improving treatment protocols and outcomes for pediatric leukemia patients is of critical importance as acute lymphoblastic leukemia (ALL) accounts for 25% of all childhood cancers. ALL five-year relative survival rates have improved significantly in recent decades. However, many survivors suffer severe chronic physiological and psychological health problems, as well as poor social and economic outcomes. These consequences exemplify the continuing need to develop targeted, less toxic alternative therapeutics. Metabolomics, an emerging tool for precision medicine, can be used to analyze intracellular and extracellular environments, metabolic response to treatment, and pathway regulation in order to expand our understanding of the molecular mechanisms that drive pediatric cancer biology and identify and evaluate novel therapeutics. This study applied metabolomics approaches to precursor B-cell ALL (BCP-ALL) which accounts for 80% of ALL cases in children and adolescents. First, high-throughput screening (HTS) was used to identify a synergistic combination of non-toxic therapeutic alternatives to chemotherapy. Metabolomics and metabolic flux analyses of dimethylaminoparthenolide (DMAPT) and vi shikonin (SHK) in BCP-ALL showed changes in amino acid, antioxidant, TCA cycle, and nucleotide metabolism. The shunting of glycolytic intermediates and glutaminolysis- related metabolites to support proliferation was inhibited by DMAPT and SHK leading to apoptosis in BCP-ALL cells. Second, bone marrow-derived leukemia cells were collected from pediatric BCP-ALL patients at diagnosis. Stratifying patients by cytogenetic anomalies yielded unique metabolic profiles. Aberrations at the IGH locus are associated with poor outcomes, but no clear therapeutic targets have been identified. Assessment of individual metabolites indicated that amino acids, amino acid-related compounds, and some sugars were more abundant in patients with IGH locus aberrations. Phosphatidylcholines, phosphatidylethanolamines, and polar compounds involved in lipid metabolism were also increased, while nucleotides, diglycerides, and triglycerides were decreased in the IGH group. Pathway interrogation confirmed metabolic dysregulation. HTS indicated IGH mutant sensitivity to HSP, proteasome, mTOR, and HDAC inhibitors. Together, these analyses indicate the flexibility and utility of metabolomics to elucidate the underlying biology of pediatric leukemia and evaluate novel therapeutics to improve quality of life and long-term outcomes for childhood leukemia patients and adult survivors. vii Table of Contents List of Tables ..................................................................................................................... xi List of Figures ................................................................................................................... xii Chapter 1: Introduction ........................................................................................................1 1.1 Cancer ...................................................................................................................1 1.2 Pediatric cancer .....................................................................................................3 1.3 Leukemia ..............................................................................................................4 1.3.1 Background ............................................................................................4 1.3.2 Urgent need to improve long-term outcomes for pediatric leukemia survivors ....................................................................................................5 1.3.3 Risk stratification has reduced pediatric leukemia mortality .................6 1.3.4 Leukemia is characterized by significant genetic alterations ................7 1.4 Cancer as a disease of aberrant metabolism .........................................................8 1.5 Metabolomics......................................................................................................10 1.5.1 The short history of metabolomics ......................................................10 1.5.2 Nuclear magnetic resonance spectroscopy ..........................................12 1.5.3 Mass spectrometry ...............................................................................14 1.5.4 Technological advancements ...............................................................17 1.5.5 Integration of clinical parameters and metabolic profiling ..................18 Chapter 2: Identification of a synergistic combination of dimethylaminoparthenolide and shikonin alters metabolism and inhibits proliferation of pediatric precursor B- cell acute lymphoblastic leukemia ...............................................................................20 2.1 Abstract ...............................................................................................................20 2.2 Introduction .........................................................................................................21 2.3 Materials and methods ........................................................................................23 viii 2.3.1 Reagents and chemicals .......................................................................23 2.3.2 Cell culture ...........................................................................................24 2.3.3 High-throughput screening ..................................................................25 2.3.4 Combination screening ........................................................................26 2.3.5 Ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS) analysis ...............................................................................27 2.4 Results .................................................................................................................30 2.4.1 Natural product library (NPL) screening .............................................30 2.4.2 Metabolomics and metabolic flux analysis ..........................................35 2.5 Discussion ...........................................................................................................45 Chapter 3: Stratification of pediatric leukemia patients by combining clinical parameters and metabolic signatures to identify exploitable pathway dysregulation for a personalized therapeutic approach ......................................................................49 3.1 Abstract ...............................................................................................................49 3.2 Introduction .........................................................................................................50 3.3 Materials and methods ........................................................................................52 3.3.1 Reagents and