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Mass Spectrometry-Based Characterization, Quantitation, and Repair Investigations of Complex Dna Lesions

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Mass Spectrometry-Based Characterization, Quantitation, and Repair Investigations of Complex Dna Lesions MASS SPECTROMETRY-BASED CHARACTERIZATION, QUANTITATION, AND REPAIR INVESTIGATIONS OF COMPLEX DNA LESIONS A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Arnold Groehler IV IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Dr. Natalia Y. Tretyakova, Advisor March 2018 © Arnold Scott Groehler IV 2018 Acknowledgements As my time as a graduate student comes to an end, I must express my sincere thanks and gratitude to all the people who helped me during the process. First and foremost, I would like to thank my advisor, Dr. Natalia Tretyakova, for her constant support and guidance over the last six years. As an aspiring professor, Dr. Tretyakova’s dedication to helping her students succeed and produce quality science was inspiring. I would also like to thank Dr. Colin Campbell for his mentorship in biology and constant support during my graduate career. I am also grateful to Dr. Daniel A. Harki and Dr. Rodney L. Johnson for agreeing to serve as my thesis committee members and for their valuable feedback and suggestions. I would also like to express my thanks to all the Tretyakova and Campbell group members for their mentorship, contributions, and discussions. Dr. Susith Wickramaratne, Dr. Dewakar Sangaraju, Dr. Srikanth Kotapati, Dr. Teshome Gherezghiher, and Dr. Delshanee Kotandeniya for their mentorship during the first years of my graduate work. Abby Hoffman, Joshua Schmidt, Dominic Najjar, Lisa Chesner, Dr. Suresh Pujari, and Daeyoon Park, whose contributions and support were crucial to completing my projects. And all current and past members of the Tretyakova laboratory for their helpful suggestions and contributions throughout the past six years. Furthermore, I would like to thank all the collaborators who contributed to my projects. My sincere thanks to Dr. Yuichi Machida, Dr. Reeja Maskey, Dr. Mary Garry, Qinglu Li, Stefan Kren, Maggie Robledo-Villafane, Dr. Deborah Ferrington, and Dr. Ashis Basu for performing experiments and/or generous donation of tissues for my thesis projects. I am also very thankful to Brock Matter, Dr. Peter Villalta, Xun Ming, and i Yingchun Zhao for their help and expertise in mass spectrometry method development and troubleshooting. Furthermore, I would like to thank Robert Carlson for his help with preparing figures for my publications, presentations, and thesis. Last but not least, I would like to thank my family and friends, especially my incoming classmates for their unconditional support and encouragement. I could not have achieved such a great accomplishment without all of you in my life. ii Abstract DNA is constantly under the threat of damage by various endogenous and exogenous agents, leading to the structural modification of nucleobases (DNA adducts). These DNA adducts can range from smaller nucleoside monoadducts and exocyclic adducts, to the helix distorting and super-bulky DNA-DNA cross-links and DNA-protein cross-links. If not repaired, DNA adducts can inhibit crucial biological processes such as DNA replication, leading to adverse consequences such as mutagenesis and carcinogenesis. Therefore, understanding the atomic connectivity, extent of formation, and repair of DNA adducts is crucial to fully elucidating the biological consequences of the adduct. DNA-protein cross-links (DPCs) are ubiquitous, super-bulky DNA lesions that form when proteins become irreversibly trapped on chromosomal DNA. The structural complexity of cross-linking and the diversity of proteins susceptible to DPC formation represents significant challenges to studying the biological consequence of these adducts. In the first part of the thesis, we identified the protein constituents, structural characterized and quantified, and investigated the repair mechanism of bis-electrophile (Chapter 2) and reactive oxygen species (ROS, Chapters 3 and 4)-induced DPCs. In Chapter 2, we investigated DPC formation after exposure to N,N-bis-(2- chloroethyl)-phosphorodiamidic acid (phosphoramide mustard, PM) and N,N-bis-(2- chloroethyl)-ethylamine (nornitrogen mustard, NOR), the two biologically active metabolites of the antitumor agent cyclophosphamide. A mass spectrometry-based proteomics approach was employed to characterize the protein constituents of PM- and NOR-mediated DNA-protein cross-linking in human fibrosarcoma (HT1080) cells. HPLC- iii ESI+-MS/MS analysis of proteolytic digests of DPC-containing DNA from NOR-treated cells revealed a concentration-dependent formation of N-[2-[cysteinyl]ethyl]-N-[2-(guan- 7-yl)ethyl]amine (Cys-NOR-N7G) conjugates, confirming that it cross-links cysteine thiols of proteins to the N-7 position of guanines in DNA. A sensitive and accurate Cys- NOR-N7G isotope dilution tandem mass spectrometry assay was developed to quantify PM-induced DPC formation and repair in mammalian cells proficient or deficient in a DNA repair pathway. In Chapters 3, we employed the model of left anterior descending artery ligation/reperfusion surgery in rat to show that ischemia/reperfusion injury is associated with the formation of hydroxyl radical-induced DNA-protein cross-links (DPCs) in cardiomyocytes. Mass spectrometry based experiments revealed that these conjugates were formed by a free radical mechanism and involved thymidine residues of DNA and tyrosine side chains of proteins (dT-Tyr). Quantitative proteomics experiments utilizing Tandem mass tags (TMT) revealed that radical-induced DPC formation increase after LAD- ligation/reperfusion compared to the control sham surgery. Using the developed dT-Tyr nanoLC-ESI+-MS/MS assay, we investigated the role of the metalloprotease Spartan (SPRTN) in the repair of radical-induced DPCs (Chapter 4). Analysis of the brain, liver, heart, and kidneys of wild type (SPRTN+/+) and hypomorphic (SPRTN f/-) mice revealed a 1.5 – 2-fold increase in dT-Tyr in the hypomorphic mice, providing direct evidence that Spartan plays a role in the repair of radical-induced DPCs. Finally, we investigated the formation of formamidopyrimidine (FAPy) adducts after exposure to 3,4-epoxybutene, an epoxide metabolite of the known carcinogen 1,3- butadiene (Chapter 5). We successfully synthesized and structurally characterized a novel iv BD-induced DNA adduct EB-FAPy-dG, and developed a sensitive isotope dilution tandem mass spectrometry assay for its detection in vitro and in cells. To our knowledge, this is the first report of a BD-induced FAPy adduct, and future studies will examine whether BD- induced FAPy adducts In summary, during the course of this Thesis, we utilized mass spectrometry-based proteomics techniques to identify the proteins susceptible to PM- and ROS-induced DPC formation. After structurally characterizing the atomic connectivity of these adduces, we developed sensitive and accurate isotope dilution tandem mass spectrometry assays to perform absolute quantitation of PM- and ROS-induced DPC formation in cells and tissues. These assays were further utilized to begin investigating the repair mechanism of DPCs in cells and tissues, including providing direct evidence that the metalloprotease Spartan is involved in the repair of radical-induced DPCs. Finally, we detected EB-FAPy-dG formation in vitro and in vivo, the first evidence of 1,3-butadiene induced formamidopyrimidine formation. v TABLE OF CONTENTS ACKNOWLEDGEMENTS……………………………………………………...…….... i ABSTRACT……………………………………………………...…………………....... iii LIST OF TABLES ……………………………………………………...…………....... xii LIST OF SCHEMES.…………………………………………………….…….…........ xii LIST OF FIGURES.……………………………………………………………….…. xvii LIST OF ABBREVIATIONS....................................................................................... xxv 1. INTRODUCTION………………………………………..……………………... 1 1.1. DNA damage and its biological consequences…………………………..1 1.1.1. Structural modifications of DNA..................................................... 1 1.1.2. DNA modifying agents………………………………………….... 1 1.1.3. DNA repair mechanisms………………………………………... 17 1.1.4. Biological consequences of DNA damage…………...…....…….. 28 1.2. 1,3-Butadiene induced DNA damage…………...………….....….…… 30 1.2.1. Overview of 1,3-butadiene……………………………………… 30 1.2.2. Metabolism of 1,3-butadiene…………………………...….…..... 30 1.3. N6-(2-Deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4- oxo-formamidopyrimidine (FAPy) adducts…………...…...………… 38 1.3.1. Formation of FAPy adducts……………………...…………..….. 38 1.3.2. Biological consequences of FAPy adducts…………………….... 41 1.3.3. Repair of FAPy adducts….…………………………………….... 45 1.4. DNA-protein cross-links……….…………………….………………... 46 vi 1.4.1. Formation of DPCs in cells…………………………………….... 46 1.4.2. Biological consequences of DPCs…………………..................... 52 1.5. DPC-inducing agents studied in this thesis……………………............ 56 1.5.1. Reactive oxygen species……………………………………….... 56 1.5.2. ROS-induced DPCs……………………………………………... 56 1.5.3. ROS-induced DPC formation following myocardial infarction/reperfusion………………………………...….…….... 57 1.5.4. Phosphoramide mustard and nornitrogen mustard......................... 58 1.6. Characterization of DPCs....................................................................... 60 1.6.1. Biophysical identification techniques……............................….... 60 1.6.2. DPC isolation techniques………………………………………... 62 1.6.3. Structural characterization of cross-linking…...……………….... 66 1.6.4. Mass spectrometry-based proteomics………………………….... 67 1.6.5. Quantitative proteomics of DPCs………...…………….……….. 72 1.7. Mechanism(s) of DPC repair………………………………………….. 77 1.8. Thesis
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