The Role of the Cytoskeleton in Pluripotent Stem Cell Differentiation

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The Role of the Cytoskeleton in Pluripotent Stem Cell Differentiation THE ROLE OF THE CYTOSKELETON IN PLURIPOTENT STEM CELL DIFFERENTIATION AN ABSTRACT SUBMITTED ON THE 21ST DAY OF AUGUST, 2013 TO THE DEPARTMENT OF BIOMEDICAL ENGINEERING OF THE SCHOOL OF SCIENCE AND ENGINEERING AT TULANE UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY BY ___________________________ EMMA T. PINEDA FORTIN APPROVED: ___________________________ TABASSUM AHSAN, Ph.D. (COMMITTEE CHAIR) __________________________ WALTER LEE MURFEE, Ph.D. __________________________ DAMIR KHISMATULLIN, Ph.D. ABSTRACT An understanding of the pathways responsible for differentiation in pluripotent stem cells (PSCs) would accelerate their translation to medical therapies. Specifically, studies that identify criteria for the better design of experiments targeting certain phenotypes would allow for the generation of cell sources adequate for transplantation. In this dissertation, we aimed at elucidating the role of the cytoskeleton in the spontaneous differentiation of PSCs in two dimensional (2D) and three dimensional (3D) microenvironments. First, we quantified the expression of the cytoskeleton in ESCs, iPSCs, and the iPSC source phenotype, showing that there were indeed differences in the expression of microfilaments and certain intermediate filaments among all three phenotypes. Next, we found that there were inherent differences in ESC differentiation when cultured in 2D and 3D microenvironments. Lastly, alterations in the cytoskeleton were found to decrease mesodermal differentiation in 3D culture, while increase both mesodermal and endodermal differentiation in 2D culture. Taken together, we identified the cytoskeleton as a regulator of differentiation to the mesodermal and endodermal lineages in both 2D and 3D culture. THE ROLE OF THE CYTOSKELETON IN PLURIPOTENT STEM CELL DIFFERENTIATION A DISSERTATION SUBMITTED ON THE 21ST DAY OF AUGUST, 2013 TO THE DEPARTMENT OF BIOMEDICAL ENGINEERING OF THE SCHOOL OF SCIENCE AND ENGINEERING AT TULANE UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY BY ___________________________ EMMA T. PINEDA FORTIN APPROVED: ___________________________ TABASSUM AHSAN, Ph.D. (COMMITTEE CHAIR) __________________________ WALTER LEE MURFEE, Ph.D. __________________________ DAMIR KHISMATULLIN, Ph.D. ACKNOWLEDGEMENTS I am grateful towards the Department of Biomedical Engineering at Tulane University for allowing me to pursue my scientific career. I would especially like to thank my advisor, Dr. Taby Ahsan for helping me grow and become a better scientist and thinker. I also want to thank all of the members of the STEM cell lab through the years, undergraduates, high school students, and graduates. Thank you in particular, to Dr. Kristen Lynch and Dr. Russell Wolfe for all the good times and laughter. I would like to thank my committee members Dr. Lee Murfee and Dr. Damir Khismatullin for their support, as well as the entire BME faculty. A big thanks to the BME staff, Lorrie McGinley, Megan Ohar, John Sullivan, and Cindy Stewart who made everything work smoothly. I would like to thank my parents, Angel & Guadalupe, my brother Angel, sisters Denise and Marcela, and my nephew Santiago for their love and constant support. Special thanks to Abuelita for her prayers and candles. Lastly, I thank my boyfriend Brendan who always believes in me! ii TABLE OF CONTENTS Chapter 1: Introduction ...................................................................................... 1 Chapter 2: Background ...................................................................................... 7 2.1 Defining Pluripotency and iPSCs................................................................. 7 2.2 Germ Lineage Commitment in vivo: Gastrulation ...................................... 11 2.2.1 Physical Force Regulation in vivo ....................................................... 13 2.3 In vitro Differentiation Models .................................................................... 13 2.4 Directed Differentiation .............................................................................. 16 2.5 The Microenvironment and Differentiation ................................................. 17 2.6 Mechanotransduction ................................................................................ 18 2.6.1 Cytoskeleton: A Continuous Mechanical Link to the Nucleus ............. 19 2.7 Actomyosin Contractility in Pluripotency and Differentiation ...................... 23 Chapter 3: Cytoskeletal Protein Characterization of Induced Pluripotent Stem Cells ......................................................................................................... 28 3.1 Abstract ..................................................................................................... 28 3.2 Introduction ............................................................................................... 29 3.3 Materials & Methods .................................................................................. 31 3.3.1 Pluripotent Cell Expansion .................................................................. 31 3.3.2 Embryoid Body Differentiation ............................................................. 32 3.3.3 Phase Microscopy ............................................................................... 32 3.3.4 Gene Expression................................................................................. 32 3.3.5 Protein Expression .............................................................................. 33 iii 3.3.6 Statistical Analysis .............................................................................. 34 3.4 Results ...................................................................................................... 34 3.4.1 Pluripotent stem cell morphology differed in ESCs and iPSCs ........... 34 3.4.2 Transcription factors of pluripotency were expressed similarly or at lower levels in iPSCs ................................................................................... 36 3.4.3 iPSCs expressed microfilaments and integrin α5 at a higher level than ESCs ............................................................................................................ 38 3.4.4 Embryoid Bodies from iPSCs and ESCs had similar levels of microfilaments, intermediate filaments, and microtubules at Day 6 ............. 42 3.5 Discussion ................................................................................................. 44 Chapter 4: Differentiation Patterns of Embryonic Stem Cells in Two versus Three Dimensional Culture .............................................................................. 49 4.1 Abstract ..................................................................................................... 49 4.2 Introduction ............................................................................................... 50 4.3 Materials and Methods .............................................................................. 52 4.3.1 Expansion of Mouse Embryonic Stem Cells ....................................... 52 4.3.2 Two and Three Dimensional Differentiation Systems.......................... 53 4.3.3 Gene Expression Analysis .................................................................. 54 4.3.4 Statistical Analysis .............................................................................. 55 4.4 Results ...................................................................................................... 57 4.4.1 Cell Growth in Differentiation Systems ................................................ 57 4.4.2 Pluripotency and Germ Lineage Differentiation .................................. 58 4.4.3 ESC Differentiation Patterns ............................................................... 60 4.4.4 Functional Gene Groupings ................................................................ 63 4.4.5 Matrix Remodeling .............................................................................. 67 4.5 Discussion ................................................................................................. 70 4.6 Acknowledgements ................................................................................... 75 iv Chapter 5: Actin and myosin II modulate mesodermal commitment of embryonic stem cells in 3D ............................................................................. 79 5.1 Abstract ..................................................................................................... 79 5.2 Introduction ............................................................................................... 80 5.3 Materials and Methods .............................................................................. 81 5.3.1 Embryoid Body Culture ....................................................................... 81 5.3.2 Microscopy .......................................................................................... 82 5.3.3 Gene Expression................................................................................. 82 5.3.4 Protein Expression .............................................................................. 83 5.3.5 Statistical Analysis .............................................................................. 83 5.4. Results ..................................................................................................... 84 5.4.1 CYTO-D and BLEBB altered cell and EB size .................................... 84 5.4.2 Inhibitor treatment decreased commitment to the mesodermal
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