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Whole Genome Expression in Hmbl +/+ Mice Examining The Whole Genome Expression in Mice Containing a Human Mannose Binding Gene (hMBL): Examining the Immunological Role of Monoclonal Antibody (mAb) 3F8 In Attenuating Myocardial Ischemia-Reperfusion Injuries By William Brian Gorsuch A Dissertation Submitted to Rutgers, The State University of New Jersey School of Health Related Professions In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Department of Health Informatics Biomedical Informatics Program October 2014 ii TABLE OF CONTENT ABSTRACT................................................................................................................................ v ACKNOWLEDGMENTS ..........................................................................................................vii LIST OF TABLES .....................................................................................................................ix LIST OF FIGURES ................................................................................................................... x ABREVIATIONS ......................................................................................................................xii CHAPTER 1 INTRODUCTION ................................................................................................. 1 1.1 Statement of The Problem .................................................................................... 1 1.2 Background of the Problem ................................................................................... 2 1.3 Goals, Objectives and Research Questions ......................................................... 3 CHAPTER II LITERATURE REVIEW ....................................................................................... 5 2.1 Ischemia-Reperfusion Injuries ............................................................................... 5 2.2 Myocardial Ischemia-Reperfusion Injuries (MI/R) ................................................. 5 2.3 The Complement System and Lectin Pathway ..................................................... 6 2.4 Historical Perspectives of MBL Research in MI/R Injuries .................................... 8 2.5 MBL Knowledge Discovery in Current Models of MI/R Injury ............................... 9 2.6 Complement and Drug-Target Elucidation in MI/R Injuries ................................. 11 2.7 mAb 3F8 .............................................................................................................. 13 2.8 MBL Genetics ...................................................................................................... 14 2.9 Whole Genome Microarray ................................................................................. 17 2.10 Whole Genome Microarray in Cardiovascular Disease .................................... 21 2.11 Epitope Knowledge Discovery ........................................................................... 22 2.12 hMBL Epitope Discovery For 3F8: Stahl Lab Research .................................... 23 STATEMENT OF HYPOTHESIS ............................................................................................ 25 CHAPTER III METHODS AND MATERIALS ......................................................................... 26 3.1 Mice ..................................................................................................................... 26 iii 3.2 Experimental MI/R Model .................................................................................... 32 3.3 Measurement of Infarct Size and Area At Risk (AAR) ......................................... 34 3.4 Real Time Polymerase Chain Reaction For Microarray Assessment ................. 37 3.41 RNA Extraction and Purification ........................................................................ 37 3.42 RNA Quality Assessment .................................................................................. 37 3.43 Primers .............................................................................................................. 37 3.44 cDNA Library Development ............................................................................... 38 3.45 Quantitative Polymerase Chain Reaction ......................................................... 38 3.5 Processing of Microarray Data and Limma ......................................................... 39 3.6 Molecular Modeling ............................................................................................. 41 3.61 Homology Modeling ........................................................................................... 41 3.62 Structure Alignment ........................................................................................... 42 CHAPTER IV RESULTS ........................................................................................................ 44 4.1 Mice Genotyping .................................................................................................. 44 4.2 Measurement of Infarct Size and AAR Results ................................................... 44 4.3 Microarray Gene Expression Results .................................................................. 48 4.4 Gene Set Enrichment Analysis ............................................................................ 52 4.5 Quantitative Polymerase Chain Reaction ............................................................ 59 4.6 Molecular Modeling ............................................................................................. 63 CHAPTER V DISCUSSION .................................................................................................... 71 CONCLUSION ........................................................................................................................ 84 REFERENCES ....................................................................................................................... 85 iv Whole Genome Expression in Mice Containing a Human Mannose Binding Gene (hMBL): Examining the Immunological Role of mAb 3F8 In Attenuating Myocardial Ischemia-Reperfusion Injuries William Brian Gorsuch Rutgers Biomedical and Health Sciences ABSTRACT During a myocardial ischemic event, acute occlusion sets in motion cell necrosis and myocardial tissue injury referred to as a myocardial ischemia-reperfusion (MI/R) injury. The resultant injury is triggered by an immunological response of which a major contributor involves the complement cascade of innate immune system involving mannose binding lectin (MBL). Few anti-complement therapeutics however have been approved for clinical use. Those studies to date have involved extensive whole genome expression in murine models of MI/R injury to assist in drug target elucidation. Studies performed have examined genomic traits and expression of mouse MBL (mMBL), which is not one hundred percent homologous to human mannose binding lectin (hMBL). In this study, novel hMBL+/+ mice treated with a novel mAb 3F8 were protected from MI/R injury as measured by area at risk and myocardial infarct staining when compared to control mice. Whole genome expression with the use of microarray was performed between hMBL mice undergoing MI/R treated with either a novel recombinant mAb 3F8 or mAb 1C10 as control. Mice treated with mAb 3F8 compared to mice treated with 1C10 revealed a significant down regulation in uncharacterized genes of the lncRNA family. Molecular modeling was used to study the three dimensional structural characteristics of mAb 3F8 recognition of hMBL. Within the hinge region of hMBL three possible locations were identified for the mAb 3F8 epitope for hMBL. These structurally similar locations offer possible insight into the ability of mAb 3F8 in protecting against MI/R injuries. These findings v will assist in better understanding the genomic role hMBL in MI/R, the ability of a novel murine mAb 3F8 to modulate those effects and aide in continued drug target elucidation. vi ACKNOWLEDGEMENTS I wish to thank a number of people who aided me in my research on mAb 3F8. I would like to give special mention to Dr. Masayuki Shibata and Dr. Greg Stahl. Dr. Greg Stahl from the Center for Experimental Therapeutics and Reperfusion Injury, Harvard Institutes of Medicine, Brigham and Women’s Hospital Department of Anesthesiology, Perioperative and Pain Medicine, has been my research mentor from the beginning of my masters degree and all throughout my dissertation, serving as my dissertation advisor and committee chair. Dr. Stahl’s enormous generosities in the use of his facilities have allowed me to gain experience in many laboratory techniques and learn from the many scientists on his research team. Dr. Stahl has been one of the most influential mentors and supporters of my academic and research work. The opportunities, generosity and support he has shown have changed my life. Dr. Shibata from Rutgers Biomedical and Health Science School of Health Related Professions, Department of Health Informatics and Biomedical Informatics Program, has not only been my academic advisor and dissertation committee member but also a continued force of significant support and guidance during difficult times. Without Dr. Shibata’s mentorship I would have never succeeded. He has challenged and taught me the true art of critical scientific thinking and problem solving. I would like to acknowledge my other dissertation committee members. Dr. John Quackenbush and Dr. Gwendolyn Mahon. Dr. Quackenbush from the Computational Biology and Functional Genomics Laboratory at the Dana Farber Cancer
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