LOSS of INVERSIN CONTRIBUTES to RENAL CYSTIC DISEASE THROUGH ALTERED CELLULAR PROCESSES and DECREASED SODIUM TRANSPORT in RENAL EPITHELIAL CELLS by Nalini H
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LOSS OF INVERSIN CONTRIBUTES TO RENAL CYSTIC DISEASE THROUGH ALTERED CELLULAR PROCESSES AND DECREASED SODIUM TRANSPORT IN RENAL EPITHELIAL CELLS by Nalini H. Kulkarni A Dissertation Submitted to the Faculty of Purdue University In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy Department of Biological Sciences Indianapolis, Indiana May 2017 ii THE PURDUE UNIVERSITY GRADUATE SCHOOL STATEMENT OF DISSERTATION APPROVAL Dr. Bonnie L. Blazer-Yost, Chair Department of Biological Sciences Dr. Cynthia V. Stauffacher Department of Biological Sciences Dr. Rosamund C. Smith Department of Biological Sciences Dr. Simon J Atkinson Department of Biological Sciences Dr. Nicolas F. Berbari Department of Biological Sciences Approved by: Dr. Stephen K. Randall Head of the Departmental Graduate Program iii Dedication This dissertation is dedicated to all the people in my life who have been a positive force for guidance and support during this entire process. I would like to thank my parents Hanumantha Rao and Sunanda Bai for all that they have done for me over my lifetime. You have been a constant source unconditional love and support. Thanks to my Uncle Late Narayana Kulkarni for his constant encouragement and faith in me. Most importantly, thanks to my husband, Prahalad for his love and endless support. I am very thankful for your patience and care. I want to thank my two beautiful children, Neha and Keshav for making my everyday an absolute joy. iv ACKNOWLEDGMENTS At the outset, I extend my heartfelt thanks to my mentor and committee chair, Dr. Bonnie Blazer-Yost for giving me the opportunity to work in her laboratory, providing guidance and constructive feedback during the course of this investigation. I express my sincere gratitude to my committee member Dr. Rosamund Smith for her constant encouragement, guidance and support over the years. Thanks to my committee member Dr. Cynthia Stauffacher for her valuable time and patience. I also thank my other committee members Dr. Simon Atkinson and Dr. Nicolas Berbari for their time and suggestions. I would like to thank Dr. Tao Wei for providing bioinformatics assistance and helpful discussions. My thanks to Dr. Amy Usborne for providing histology support. Finally, I would like to thank the Lilly Graduate Research Advanced Degrees program for funding, time and support. v TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ........................................................................................................... ix ABSTRACT ....................................................................................................................... xi CHAPTER1: INTRODUCTION ........................................................................................ 1 An overview of renal cystic diseases ...................................................................... 1 Dominant forms of inherited renal cystic diseases ................................................. 3 Recessive forms of inherited polycystic kidney disease ......................................... 5 Type II nephronophthisis (NPHP2) ...................................................................... 11 Animal models of NPHP2 .................................................................................... 12 Mouse inversin ...................................................................................................... 13 Inversin in development ........................................................................................ 16 Inversin role in cilia of mature renal epithelial cells ............................................. 18 Mechanism of cyst growth and expansion ............................................................ 19 Research presentation and summary ..................................................................... 21 CHAPTER 2: TRANSCRIPTOME ANALYSIS OF inv/inv MICE KIDNEYS.............. 25 Introduction ........................................................................................................... 25 Materials and methods .......................................................................................... 27 Results ................................................................................................................... 32 Discussion ............................................................................................................. 69 CHAPTER 3: LOSS OF INVERSIN DECREASES TRANSEPITHELIAL SODIUM TRANSPORT IN MURINE RENAL CELLS OF THE CORTICAL COLLECTING DUCT ................................................................................................................................ 78 Introduction ........................................................................................................... 78 Materials and methods .......................................................................................... 81 Results ................................................................................................................... 87 Discussion ........................................................................................................... 111 vi CHAPTER 4: TRANSCRIPTOME ANALYSIS OF INVERSIN-DEPLETED RENAL EPITHELIAL CELLS: COMPARSION OF IN VITRO WITH IN VIVO ARRAY DATA .............................................................................................................. 116 Introduction ......................................................................................................... 116 Materials and Methods ........................................................................................ 118 Results ................................................................................................................. 123 Discussion ........................................................................................................... 156 CONCLUSIONS............................................................................................................. 162 REFERENCES ............................................................................................................... 165 APPENDIX ..................................................................................................................... 204 VITA ............................................................................................................................... 238 PUBLICATIONS ............................................................................................................ 240 vii LIST OF TABLES Table 1: Types of inherited renal cystic diseases in humans .............................................. 2 Table 2: Genetic heterogeneity and overlap of NPHP, Senior-Loken, Joubert and Meckel-Gruber syndrome ................................................................................................... 9 Table 3: Kidneys in NPHP2 have overlapping features with NPH and ADPKD ............. 10 Table 4: List of primer-probe sets for validation of array findings by real-time quantitative PCR ............................................................................................................... 30 Table 5: GO biological process terms considered significantly enriched for the genes regulated in inv/inv mice kidneys compared to wild-type ...................................... 37 Table 6: GO cellular component terms considered significantly enriched for the genes regulated in inv/inv mice kidneys compared to wild-type ...................................... 41 Table 7: GO molecular function terms considered significantly enriched for the genes regulated in inv/inv mice kidneys compared to wild-type ...................................... 42 Table 8: Immune/inflammatory genes upregulated in inv/inv mice kidneys .................... 47 Table 9: Regulation of genes affecting cell cycle progression and proliferation in inv/inv mice kidney ........................................................................................................... 52 Table 10: Regulation of genes representing a decrease in apoptosis and increase in cell survival in inv/inv mice kidneys ............................................................................. 55 Table 11: Genes associated with development altered in inv/inv mice kidneys ............... 57 Table 12: Downregulation of genes that affect migration and trafficking in inv/inv mice kidneys ......................................................................................................... 59 Table 13: Regulation of genes affecting Na+ reabsorption and Na+-dependent transporters in inv/inv mice kidneys ................................................................................. 62 Table 14: Regulation of genes affecting organic anion and cation transporters and acid-base balance in inv/inv mice kidneys ................................................................. 65 Table 15: Genes associated with metabolic pathways altered in inv/inv mice kidneys .... 67 Table 16: Sequences of siRNA targeting mouse Invs ....................................................... 83 Table 17: Sequences of shRNA constructs targeting mouse Invs..................................... 84 viii Table 18: Percent levels of inversin knockdown with different doses of inversin shRNA lentiviral particles in mCCD cells compared to NTC ......................................... 93 Table 19: Percent inversin knockdown in stable clones and non-targeting