University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Interplay Between P53 and Epigenetic Pathways in Cancer Jiajun Zhu University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biology Commons, Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Zhu, Jiajun, "Interplay Between P53 and Epigenetic Pathways in Cancer" (2016). Publicly Accessible Penn Dissertations. 2130. https://repository.upenn.edu/edissertations/2130 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2130 For more information, please contact [email protected]. Interplay Between P53 and Epigenetic Pathways in Cancer Abstract The human TP53 gene encodes the most potent tumor suppressor protein p53. More than half of all human cancers contain mutations in the TP53 gene, while the majority of the remaining cases involve other mechanisms to inactivate wild-type p53 function. In the first part of my dissertation research, I have explored the mechanism of suppressed wild-type p53 activity in teratocarcinoma. In the teratocarcinoma cell line NTera2, we show that wild-type p53 is mono-methylated at Lysine 370 and Lysine 382. These post-translational modifications contribute ot the compromised tumor suppressive activity of p53 despite a high level of wild-type protein in NTera2 cells. This study provides evidence for an epigenetic mechanism that cancer cells can exploit to inactivate p53 wild-type function. The paradigm provides insight into understanding the modes of p53 regulation, and can likely be applied to other cancer types with wild-type p53 proteins. On the other hand, cancers with TP53 mutations are mostly found to contain missense substitutions of the TP53 gene, resulting in expression of full length, but mutant forms of p53 that confer tumor-promoting “gain-of-function” (GOF) to cancer. In the second section of my dissertation, I have investigated the mechanism of this GOF property by examining genome-wide p53 binding profiles in multiple cancer cell lines bearing p53 mutations. This reveals an epigenetic mechanism underlying mutant p53 GOF. Various GOF p53 mutants bind to and upregulate genes including MLL1, MLL2, and MOZ, leading to genome-wide changes of histone modifications. These studies also demonstrate a critical functional role of the MLL pathway in mediating mutant p53 GOF cancer phenotypes, and that genetic or pharmacological perturbation of MLL function can achieve specific inhibition of GOF p53 cell proliferation. Overall, studies described in this dissertation demonstrate the crosstalk between p53 signaling and chromatin regulatory pathways, contribute to our knowledge of p53 cancer biology with respect to epigenetic regulation, and in the long term suggest new therapeutic opportunities in targeting cancers according to their p53 mutational status. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Shelley L. Berger Keywords cancer, chromatin, epigenetics, genomics, p53 Subject Categories Biology | Cell Biology | Molecular Biology This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/2130 INTERPLAY BETWEEN p53 AND EPIGENETIC PATHWAYS IN CANCER Jiajun Zhu A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2016 Supervisor of Dissertation ______________________ Shelley L. Berger , Ph.D. Daniel S. Och University Professor Graduate Group Chairperson ______________________ Daniel S. Kessler, Ph.D. Associate Professor of Cell and Developmental Biology Dissertation Committee: Roger A. Greenberg, M.D., Ph.D., Associate Professor of Cancer Biology Gerd A. Blobel, M.D., Ph.D., Professor of Pediatrics F. Bradley Johnson, M.D., Ph.D., Associate Professor of Pathology and Laboratory Medicine Xiaolu Yang, Ph.D., Professor of Cancer Biology To my parents, Sudan Li and Feili Zhu For their love and support ii ACKNOWLEDGMENT First and foremost, I owe my deepest gratitude to my thesis advisor Dr. Shelley L. Berger, for her unreserved support and mentorship throughout my graduate studies. Her enthusiasm for scientific discoveries and immense knowledge across research fields have guided me along the way of becoming an independent scientist. I am also thankful for the vibrant laboratory environment Shelley has created. I appreciate collaboration as well as friendship with all past and present members in the Berger lab. Special thanks to Morgan A. Sammons, who since my rotation in the Berger lab has led my journey in formulating scientific questions and conducting experiments; Zhixun Dou, who is always passionate for science and inspiring to me, has offered enormous intellectual and technical ideas and assistance to me; Greg Donahue, without whom it would be impossible for me to learn any of the powerful computational skills that have helped my research projects tremendously. It is also my honor to be under the mentorship of a fantastic thesis committee, Drs. Roger A. Greenberg, Gerd A. Blobel, F. Bradley Johnson, and Xiaolu Yang. They have been inspiring and suggestive with their own knowledge and experiences, and supportive towards building up my own career. I would like to extend my appreciation to collaborators outside the Berger lab. Dr. Michael A. Tainsky for generously sharing the Li-Fraumeni Syndrome cells; Drs. Cheryl H. Arrowsmith and Xianxin Hua for kind support, enabling me to utilize MLL1 pharmacological inhibitors; and Dr. iii Ali Shilatifard for access to MLL1 cDNA plasmids. Without these and all other collaborative efforts, I could not have achieved anything in my graduate studies. I also want to acknowledge the Cancer Biology program in the Cell and Molecular Biology graduate group. The relaxing yet interactive and critical scientific environment, and the efficient and helpful administrative efforts all make it a big warm family based on which my graduate life has been more colorful and fruitful. There are far more people and support I am grateful for. I apologize to those names I could not list due to a limited space. But I wish to convey my thankfulness all the same, and I do appreciate them being along with me in the journey, with great moments I will always memorize. iv ABSTRACT INTERPLAY BETWEEN p53 AND EPIGENETIC PATHWAYS IN CANCER Jiajun Zhu Thesis advisor: Shelley L. Berger, Ph.D. The human TP53 gene encodes the most potent tumor suppressor protein p53. More than half of all human cancers contain mutations in the TP53 gene, while the majority of the remaining cases involve other mechanisms to inactivate wild-type p53 function. In the first part of my dissertation research, I have explored the mechanism of suppressed wild-type p53 activity in teratocarcinoma. In the teratocarcinoma cell line NTera2, we show that wild-type p53 is mono-methylated at Lysine 370 and Lysine 382. These post-translational modifications contribute to the compromised tumor suppressive activity of p53 despite a high level of wild-type protein in NTera2 cells. This study provides evidence for an epigenetic mechanism that cancer cells can exploit to inactivate p53 wild-type function. The paradigm provides insight into understanding the modes of p53 regulation, and can likely be applied to other cancer types with wild-type p53 proteins. On the other hand, cancers with TP53 mutations are mostly found to contain missense substitutions of the TP53 gene, resulting in expression of full length, but mutant forms of p53 that confer tumor- promoting “gain-of-function” (GOF) to cancer. In the second section of my dissertation, I have investigated the mechanism of this GOF property by examining genome-wide p53 binding profiles in multiple cancer cell lines bearing p53 mutations. This reveals an epigenetic mechanism underlying mutant p53 GOF. Various GOF p53 mutants bind to and upregulate genes including MLL1, MLL2, and MOZ, leading to genome-wide changes of histone modifications. These studies v also demonstrate a critical functional role of the MLL pathway in mediating mutant p53 GOF cancer phenotypes, and that genetic or pharmacological perturbation of MLL function can achieve specific inhibition of GOF p53 cell proliferation. Overall, studies described in this dissertation demonstrate the crosstalk between p53 signaling and chromatin regulatory pathways, contribute to our knowledge of p53 cancer biology with respect to epigenetic regulation, and in the long term suggest new therapeutic opportunities in targeting cancers according to their p53 mutational status. vi TABLE OF CONTENTS Dedication ......................................................................................................................... ii Acknowledgement ........................................................................................................... iii Abstract ..............................................................................................................................v Table of contents ............................................................................................................ vii List of tables..................................................................................................................... ix List of figure ......................................................................................................................x