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Transcriptomic Analysis of Cortical Versus Cancellous Bone in Response to Mechanical Loading and Estrogen Signaling

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Transcriptomic Analysis of Cortical Versus Cancellous Bone in Response to Mechanical Loading and Estrogen Signaling TRANSCRIPTOMIC ANALYSIS OF CORTICAL VERSUS CANCELLOUS BONE IN RESPONSE TO MECHANICAL LOADING AND ESTROGEN SIGNALING A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Natalie H Kelly January 2017 © 2017 Natalie H Kelly TRANSCRIPTOMIC ANALYSIS OF CORTICAL VERSUS CANCELLOUS BONE IN RESPONSE TO MECHANICAL LOADING AND ESTROGEN SIGNALING Natalie H Kelly, Ph. D. Cornell University 2017 Osteoporosis is a skeletal disease characterized by low bone mass that often results in fracture. Mechanical loading of the skeleton is a promising approach to maintain or recover bone mass. Mouse models of in vivo loading differentially increase bone mass in cortical and cancellous sites. The molecular mechanisms behind this anabolic response to mechanical loading need to be determined and compared between cortical and cancellous bone. This knowledge could enhance the development of drug therapies to increase bone formation in osteoporotic patients. After developing a method to isolate high-quality RNA from marrow- free mouse cortical and cancellous bone, differences in gene transcription were determined at baseline and at two time points following mechanical loading of wild-type mice. Cortical and cancellous bone exhibited different transcriptional profiles at baseline and in response to mechanical loading. Enhanced Wnt signaling dominated the response in cortical bone at both time points, but in cancellous bone only at the early time point. In cancellous bone at the later time point, many muscle-related genes were downregulated. Decreased bioavailable estrogen levels are a major cause of bone loss in postmenopausal women. Estrogen signaling through estrogen receptor alpha (ERa) has been found to be particularly important in regulating bone mass and the skeletal response to mechanical loading. We recently showed that mice lacking ERa in osteoblasts and osteocytes (pOC-ERaKO) had an increased adaptive response to mechanical loading, particularly in cancellous bone. The molecular mechanisms of functional adaptation to load in the context of decreased estrogen signaling are not fully elucidated, particularly in cortical versus cancellous sites. We examined transcription in cortical versus cancellous bone of tibiae from littermate control (LC) and pOC- ERaKO mice. pOC-ERaKO mice had a blunted transcriptional response to mechanical loading in cortical bone compared to littermate controls, but had an increased response in cancellous bone. This work demonstrates the importance of examining cortical and cancellous bone separately, and that next-generation sequencing is a powerful tool for discovering the complete transcriptional mechanisms responsible for mechanical loading-related bone anabolism. BIOGRAPHICAL SKETCH Natalie Hillhouse Kelly was born in Wadsworth, Illinois in 1983. She graduated from Zion Benton Township High School and attended Case Western Reserve University. In 2006 she completed her Bachelor of Science degree in Biomedical Engineering with a concentration in orthopaedic biomaterials, including a one-year cooperative education experience at DePuy Orthopaedics. While at CWRU, she was captain of the Fighting Gobies ultimate frisbee team for 4 years and competed regionally. Upon graduation, Natalie published 13 peer-reviewed journal articles as a research engineer at the Hospital for Special Surgery in the Department of Biomechanics. In 2010, she entered the Biomedical Engineering PhD program at Cornell University, earning her Master of Science in 2014. While in graduate school, Natalie began running competitively, qualified for the Boston marathon twice, and completed a total of four marathons. In August 2016, she received her Doctorate of Philosophy degree in Biomedical Engineering. While at Cornell, Natalie received a prestigious three-year NSF Graduate Research Fellowship and the Robert and Helen Appel Fellowship in Biomedical Engineering. She was also honored with the Harold M. Frost Young Investigator award from the American Society of Bone and Mineral Research. She served on the New Investigators Mentoring Committee and the Annual Meeting Committee of the Orthopaedic Research Society. v I dedicate this work to Bome and G’ampa Kelly vi ACKNOWLEDGMENTS I am extremely grateful to all of the individuals who assisted me both professionally and personally on my PhD journey. I want to thank my committee chair, Dr. Marjolein van der Meulen for her guidance throughout my career and her mentorship. My committee members Dr. John Schimenti and Dr. Jan Lammerding provided advice and encouragement. Furthermore, Dr. Schimenti graciously allowed me to conduct most of my research in his laboratory. Dr. F. Patrick Ross was practically my fourth committee member and was instrumental to the design and interpretation of this work. Many fellow scientists and colleagues provided technical advice and personal support. I would like to thank my undergraduate mentor Dr. Clare Rimnac for encouraging me to apply to the Hospital for Special Surgery, and to Dr. Timothy Wright for hiring me and inspiring me to pursue a PhD. I would also like to thank all of the members of the van der Meulen lab, past and present. In particular, Drs. Maureen Lynch, Katie Melville and Frank Ko taught me many technical skills and provided advice in the early years of graduate school. Thank you to Funmi Adebayo for being my main sounding board and allowing me to vent on our near weekly coffee dates. Dr. Adrian McNairn taught me molecular biology, and fed me cookies along the way. Many thanks to Judy Thoroughman, Marcia Sawyer, and Belinda Floyd for all of their administrative support. I am grateful for my classmates and friends who always offered a supportive ear, especially the POB crew: Drs. Liz Wayne, Sara Che, Young Hye Song, Karin Wang, and Stephanie Lindsey, and John Foo and Fredrik Thege. vii Several core facilities at Cornell University provided extensive assistance in my experiments. The Biotechnology Resource Center provided technical expertise, sequencing, and computational resources. Dr. Peter Schweitzer, and Jennifer Mosher assisted in experimental design, taught me technical skills, and performed sequencing. Dr. Jen Grenier of the RNA sequencing core provided invaluable technical expertise on RNA isolation. Dr. Qi Sun assisted me with bioinformatics techniques to analyze my data. I would like to thank the dedicated staff of the Cornell Center for Animal Resources and Education who make our animal work possible. My time in Ithaca would not have been the same without my running and polo communities. I appreciate the many miles covered with my Wednesday morning ladies, particularly Melissa Weiner, Lesley Middleton, Katie Stettler, and Ellie Pell. I am grateful to Cornell University polo for teaching me the sport of kings, and to the entire Wednesday night polo group. My family and loved ones shared in my triumphs and setbacks equally and were unwavering in their support. My sister, Dr. Felice Kelly, is not only my best friend and confidant, she is also an incredible scientist who contributed to my research. Finally, I owe everything to my parents Jack and Kathleen Kelly. They raised me with a curiosity of the world around me and the belief that anything is achievable if you’re willing to work for it. Funding for this work was provided by the National Institutes of Health grants R01-AG028664 and R21-AR064034. I was honored to receive a three-year Graduate Research Fellowship from the National Science Foundation, and the Robert and Helen Appel Fellowship in Biomedical Engineering from the Hospital for Special Surgery and Cornell University. viii TABLE OF CONTENTS Biographical Sketch .................................................................................................. v Dedication ................................................................................................................. vi Acknowledgments ................................................................................................... vii Table of Contents .................................................................................................... ix List of Figures .......................................................................................................... xii List of Tables .......................................................................................................... xiv Chapter 1: Introduction...........................................................................1 1.1 Cortical and Cancellous Bone ............................................................... 1 1.2 Osteoporosis ............................................................................................ 4 1.3 Bone Mechanosensitivity ....................................................................... 7 1.4 Signaling in Bone Response to Mechanical Loading ......................... 9 1.5 Differential Gene Expression Following in vivo Mechanical Loading .................................................................................................. 21 1.6 Aims ........................................................................................................ 25 1.7 References .............................................................................................. 29 Chapter 2: A Method For Isolating High Quality RNA From Mouse Cortical and Cancellous Bone ............................................................. 41 2.1 Introduction ..........................................................................................
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