Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Spring 5-15-2019 The Role of IFRD1 in the Recruitment and Function of Reserve Stem Cells in Regeneration and Cancer Mark Anthony Lewis Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Lewis, Mark Anthony, "The Role of IFRD1 in the Recruitment and Function of Reserve Stem Cells in Regeneration and Cancer" (2019). Arts & Sciences Electronic Theses and Dissertations. 1861. https://openscholarship.wustl.edu/art_sci_etds/1861 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Molecular and Cellular Biology Dissertation Examination Committee: Jason C. Mills, Chair David DeNardo Blair Madison Deborah Rubin Ting Wang The Role of IFRD1 in the Recruitment and Function of Reserve Stem Cells in Regeneration and Cancer by Mark Lewis A dissertation presented to The Graduate School of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2019 St. Louis, Missouri © 2019, Mark Lewis Table of Contents List of Figures ................................................................................................................................ iv List of Tables ................................................................................................................................. vi Acknowledgments......................................................................................................................... vii Abstract ........................................................................................................................................ viii Chapter 1: Introduction ................................................................................................................... 1 1.1 Emergence of Paligenosis ................................................................................................ 1 1.2 Parallells between Apoptosis and Paligenosis .................................................................3 1.3 IFRD1 review ....................................................................................................................5 1.4 Paligenosis and GI Disease ............................................................................................13 1.5 IFRD1 review..................................................................................................................20 1.6 Figures.............................................................................................................................21 1.7 References .......................................................................................................................27 Chapter 2: Regenerative proliferation of differentiated cells by mTORC1-dependent paligenosis (manuscript) ...................................................................................................................................36 2.1 Introduction .....................................................................................................................36 2.2 Results .............................................................................................................................38 2.3 Discussion ......................................................................................................................49 2.4 Materials and Methods ....................................................................................................55 2.5 Figures.............................................................................................................................61 2.6 References .......................................................................................................................93 Chapter 3: Increased IFRD1 Expression in Human Colon Cancers Predicts Reduced Patient Survival (manuscript)...................................................................................................................104 3.1 Introduction ...................................................................................................................104 3.2 Methods.........................................................................................................................106 3.3 Results ...........................................................................................................................108 3.4 Discussion .....................................................................................................................110 3.5 Figures...........................................................................................................................113 3.6 References .....................................................................................................................122 Chapter 4: IFRD1 promotes survival and proliferation in the conserved cellular regeneration program (paligenosis) by suppressing p53 (manuscript in submission) ......................................125 4.1 Summary .......................................................................................................................125 4.2 Introduction ...................................................................................................................126 4.3 Results and Discussion .................................................................................................128 4.4 Conclusions ...................................................................................................................138 4.5 Figures...........................................................................................................................140 ii 4.6 Methods.........................................................................................................................166 4.7 References .....................................................................................................................171 Chapter 5: Future Directions ........................................................................................................175 5.1 Summary .......................................................................................................................175 5.2 Future Directions ..........................................................................................................176 5.3 Conclusions ...................................................................................................................184 5.4 Figures...........................................................................................................................185 5.5 References .....................................................................................................................189 Curriculum Vitae .........................................................................................................................192 iii List of Figures Figure 1.1: Metaplasias in Stomach and Pancreas ........................................................................21 Figure 1.2: Schematic of Paligenosis .............................................................................................23 Figure 1.3: Identification of IFRD1 ..............................................................................................24 Figure 1.4: In silico screen of paligenosis genes ..........................................................................25 Figure 1.5: Schematic of nucleolar stress .....................................................................................26 Figure 2.1: Changes in mTORC1 during paligenosis ...................................................................61 Figure 2.2: Injury induced proliferation in the stomach and pancreas .........................................62 Figure 2.3: mTORC1 in gastric tumorigenesis .............................................................................63 Figure 2.4: GSEA and cell cycle gene analysis ............................................................................64 Figure 2.5: Upregulation of lysosomal and autophagic machinery during paligenosis ................65 Figure 2.6: Lysosomes are required for proliferation ...................................................................66 Figure 2.7: Schematic of paligenosis ............................................................................................68 Figure S2.1: GSEA of SPEM, cell cycle and rapamycin sensitive genes .....................................69 Figure S2.2: Time course of LAMP1 activity during paligenosis ................................................71 Figure S2.3: Cerulein treated GNPTAB-/- mice demonstrate aberrant histology .........................72 Figure S2.4: Apoptosis during paligenosis in the stomach and pancreas .....................................73 Figure EV2.1: pS6 as a marker for mTORC1 activity ..................................................................78 Figure EV2.2: Paligenosis in liver and kidneys .............................................................................80