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[Thesis Title Goes Here] Understanding Pathways Regulating Liver versus Pancreas Fate Decision and beta-cell Regeneration A Dissertation Presented to The Academic Faculty by Jin Xu In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in Biology in the School of Biological Sciences Georgia Institute of Technology August 2017 Copyright © 2017 by Jin Xu Understanding Pathways Regulating Liver versus Pancreas Fate Decision and beta-cell Regeneration Approved by: Dr. Chong Shin, Advisor Dr. Francesca Storici School of Biological Sciences School of Biological Sciences Georgia Institute of Technology Georgia Institute of Technology Dr. Alfred Merrill Dr. Yury Chernoff School of Biological Sciences School of Biological Sciences Georgia Institute of Technology Georgia Institute of Technology Dr. Young Jang School of Biological Sciences Georgia Institute of Technology Date Approved: July 17, 2017 ACKNOWLEDGEMENTS I would like to extend my deepest gratitude to my advisor Dr. Chong Shin for her invaluable guidance. My success would not have been possible without the continuous support and nurturing of her. I am also grateful to my committee members, Dr. Francesca Storici, Dr. Alfred Merrill, Dr. Yury Chernoff, and Dr. Young Jang for their insightful questions and discussions on my thesis proposal and for reviewing this dissertation. I also wish to thank my parents and my friends for their unconditional support and love. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................... IV LIST OF FIGURES ......................................................................................................... VII SUMMARY .................................................................................................................. XI CHAPTER 1 INTRODUCTION .......................................................................................... 1 1.1 PATHWAYS IN NORMAL DEVELOPMENT OF LIVER AND PANCREAS ........................ 2 1.2 PATHWAYS IN PANCREATIC Β-CELL REGENERATION ............................................... 4 1.3 DIABETES AND THE LOSS OF FUNCTIONAL Β-CELLS ................................................. 5 1.4 ZEBRAFISH AS A MODEL ORGANISM FOR DEVELOPMENTAL/REGENERATION STUDIES AND CHEMICAL TESTING .................................................................................. 6 1.5 CONCLUSION ............................................................................................................. 7 CHAPTER 2 BMP2B SIGNALING ACTIVATES FOUR AND A HALF LIM DOMAINS 1B (FHL1B) TO REGULATE THE LIVER VERSUS PANCREAS FATE DECISION .......................... 9 2.1 ABSTRACT .................................................................................................................. 9 2.2 INTRODUCTION ....................................................................................................... 11 2.3 METHODS AND MATERIALS .................................................................................... 14 2.4 RESULTS .................................................................................................................. 22 2.4.1 fhl1b is a target of the Bmp2b pathway .......................................................... 22 2.4.2 Loss-of-function and gain-of-function studies of fhl1b ................................... 34 2.4.2.1 Loss of fhl1b promotes pancreatic cells specification and compromises liver specification ...................................................................................................................... 34 2.4.2.2 Decreased fhl1b activity augments induction of pancreatic endocrine cells ....... 47 2.4.2.3 Increased fhl1b activity suppresses specification of pancreatic cells and induces liver ................................................................................................................................... 53 2.4.3 Fhl1b as a major effector of Bmp signaling determines the fate of the endodermal progenitors into liver versus pancreas ................................................. 57 2.4.3.1 Fhl1b regulates the patterning and subsequent fate of the medial and lateral endodermal progenitors ................................................................................................... 57 2.4.3.2 Relationship between Bmp2b, Fhl1b, and Id2a in fate choice of liver versus pancreas ............................................................................................................................ 67 2.5 CONCLUSION ........................................................................................................... 72 v 2.6 DISCUSSION ............................................................................................................. 74 CHAPTER 3 SIGNALING PATHWAYS PROMOTING Β-CELL REGENERATION .................. 77 3.1 ABSTRACT ................................................................................................................ 77 3.2 INTRODUCTION ....................................................................................................... 79 3.3 METHODS ................................................................................................................ 83 3.4 RESULTS .................................................................................................................. 89 3.4.1 Modulation of fhl1b activity regulates the capacity of β-cell regeneration .... 89 3.4.2 Identification of TBK1/IKKε inhibitors as enhancers for β-cell regeneration in zebrafish .................................................................................................................... 99 3.4.3 TBK1/IKKε inhibitors specifically promote β-cell proliferation ...................... 105 3.4.3.1 Repression of TBK1/IKKε increases β-cell regeneration by primarily promoting their proliferation ........................................................................................................... 105 3.4.3.2 TBK1/IKKε inhibition selectively accelerates proliferation of β-cells.................. 111 3.4.3.3 Repression of TBK1/IKKε enhances β-cell replication via cAMP activation ........ 116 3.4.4 TBK1/IKKε inhibition augments β-cell function and proliferation in mammalian systems .................................................................................................................... 119 3.5 CONCLUSION ......................................................................................................... 127 3.6 DISCUSSION ........................................................................................................... 127 CONCLUSION AND DISCUSSION ................................................................................ 131 REFERENCES ............................................................................................................. 134 vi LIST OF FIGURES Figure 2.1 Scheme for the preparation of performing expression profiling to identify Bmp2b downstream genes. ...................................................................................... 23 Figure 2.2 Strategy for the identification of Bmp2b downstream genes potentially associated with the liver versus pancreas fate decision. ......................................... 25 Figure 2.3 Confirmation of fhl1b expression from microarray results ............................. 26 Figure 2.4 The expression pattern of fhl1b during early development. ........................... 28 Figure 2.5 fhl1b is a target of the Bmp2b pathway. ......................................................... 30 Figure 2.6 Fhl1 is the mouse ortholog of zebrafish fhl1b. ................................................ 32 Figure 2.7 Fhl1 is consistently expressed in the liver during mouse embryonic development. ............................................................................................................ 33 Figure 2.8 Specificity of fhl1b morpholinos. ..................................................................... 33 Figure 2.9 Loss of fhl1b activity expands expression of pancreatic gene domain and compromises expression of liver gene domain. ....................................................... 33 Figure 2.10 Loss of fhl1b activity enhances induction of pancreatic cells and compromises liver specification. .............................................................................. 38 Figure 2.11 Loss of Fhl1b activity phenotypes are not caused by p53 induced apoptosis. ................................................................................................................................... 40 Figure 2.12 The reduced liver cell number in fhl1b depletion is not caused by p53 induced apoptosis. .................................................................................................... 41 Figure 2.13 Cell death does not contribute to the reduction of liver size upon fhl1b depletion. .................................................................................................................. 42 vii Figure 2.14 fhl1b mRNA injection rescues the effect of fhl1b MO knockdown. .............. 43 Figure 2.15 Cas9/gRNAs induces indels in the fhl1b locus in zebrafish. .......................... 45 Figure 2.16 Decreased fhl1b activity augments induction of pancreatic endocrine cells.48 Figure 2.17 Decreased fhl1b activity augments induction of both dorsal and ventral insulin cells. ............................................................................................................... 50 Figure 2.18 Decreased fhl1b activity
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