Engineering Biomaterial Properties for T Cell Immunotherapy by John W Hickey A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy. Baltimore, Maryland February 2019 Abstract Immune cell therapies have revolutionized our idea of a drug. Essentially they are a living drug becoming increasingly used because of their specificity (antigen targeting), durability (memory cells), and success seen in the clinic. Yet immune cell therapies, such as T cell immunotherapies, face substantial challenges for widespread adoption, including difficulty in target identification, complexity, cost, and inability to maintain and control cell function ex vivo. To solve issues facing T cell immunotherapies I engineered several novel biomaterials. I engineered magnetic particles to enrich and detect antigen-specific T cells in high-throughput which extends our capability to detect hundreds of antigen- specific T cells at once. This enables a greater understanding of the adaptive immune responses and also facilitates tailoring a precision medicine approach to antigen-specific T cell therapies. I also engineered extracellular matrix hydrogels for ex vivo and for in vivo stimulation, which preserves and improves cellular function and reduces the cost and labor, decreasing barriers to patients in the future. Finally, the engineering process for optimal properties of these biomaterials also revealed key biology of T cells such as nanoscale receptor organization and mechanical and environmental influences of T cell activation. ii Thesis Committee Jonathan P. Schneck, M.D. Ph.D. (primary adviser, reader) Professor, Department of Pathology Johns Hopkins University School of Medicine Hai-Quan Mao, Ph.D. (reader) Professor, Department of Materials Science and Engineering Johns Hopkins University Jordan J. Green, Ph.D. Professor, Department of Biomedical Engineering Johns Hopkins University School of Medicine Andrea Cox, M.D. Ph.D. Professor, Department of Medicine Johns Hopkins University School of Medicine iii Acknowledgements I am incredibly grateful to have had the opportunity to do a PhD. My success is the result of hundreds of people and institutions whom have supported me in my journey and education. This acknowledgement section will thus be horribly incomplete, but I will do my best to thank and recognize all who have supported me specifically during my time at Johns Hopkins University. First, the Johns Hopkins Biomedical Engineering Department has been behind me 100% of the time and supportive of me every step of the way. One of the reasons that I decided to come to Johns Hopkins University was because I recognized that the Department actually cares about their students’ wellbeing and their students’ success. I have to say that a lot of this is because of Hong Lan who is the most excellent BME PhD Program manager that I know. I do not know how she accomplishes all she does for each one of us (more than 200 of us I think) and still make each one of us feel special. Thank you Hong for all of your help over the past 5.5 years. One of the things the Department helped me out with was the ability to rotate with different advisers. This was another critical factor in deciding to come to Johns Hopkins because I had little idea to the research I wanted to spend the next several years of my life dedicating myself to. Here I need to acknowledge that what was supporting my rotations was an NIH T32 training grant and I am very grateful to the NIH for these programs and the money that is spent in developing students to become researchers. Beyond this support I was also given an INBT (Institute for Nanobiotechnology) cancer research training grant to work together with Dr. Hai-Quan Mao and Dr. Jonathan Schneck being co-advised, which though unusual allowed me to have advice, mentoring, flexibility, and iv resources from both laboratories during my time at Johns Hopkins University. Then with their help, I was able to write a successful NSF graduate fellowship which then funded the last three years of my PhD. I now strongly support the generous support of the U.S. government to young scientists because this fellowship allowed me to be more innovative and independent in the projects I pursued during my PhD rather than just working on established projects. These awards have snowballed and resulted in an ARCS foundation scholarship. This scholarship was generously given by private donors and was for traveling and presenting at conferences, going to mini-courses, and professional development. This single award helped me to a) establish and publish my research in academic, commercial, and clinical settings, b) understand what I wanted to do in the future, and c) help me network for a postdoctoral fellowship. I am very grateful for generous individuals that give and for the ARCS foundation which coordinates these efforts. Finally, I received a Siebel Scholar award, which has allowed our family to not worry about finances so much as we have been finishing up the PhD and searching for a postdoctoral fellowship position. In the same vein I should say that one of the reasons that I have been able to receive all of these awards is because of Johns Hopkins University. The reputation carries a lot of weight with donors, but also there is an incredible support staff that seeks out these opportunities and creates even more for the students who attend. Indeed one such opportunity JHU has produced has been my involvement with the group Medical and Educational Perspectives. This is a non-profit group which focuses on helping students commercialize the products or research they complete both with medical applications in the developing world and in the developed world. The Provost’s office at JHU sponsored v a grant that funded this group and allowed me to take a class in medical device commercialization for developing countries, and then travel with a team of biomedical engineers to India to work on a new material for affordable prosthetic legs. This was a once-in-a-lifetime experience and I am so grateful that I could go and for what I learned. Maybe even more so, I am grateful for the friends that I developed through this course and trip: Carmen Kut and Akhila Denduluri—both leaders of the MEP organization. I then joined the team leadership and continued on from there in our escapades to improve student entrepreneurship education at JHU, public health campaigns, and high-school outreach. Along the way we added others to the team—Meg Chow, Alina Predescu—all are incredibly talented, academically acclaimed, but most of all good friends and I thoroughly enjoyed working with and learning from during my time at JHU. Needless to say, those from MEP were not the only people that I admired or was mentored by. In fact because Hopkins offers so many different activities and opportunities, I had many. One of my passions is teaching. The Center for Educational Resources at JHU had just started a program called the Preparing Future Faculty program. Kelly Clark and Mike Reese really have spearheaded these efforts. I joined at the end of my first year because of my interest in teaching and completed the program within a year. Through the process I was amazed at the time and energy that went into such a program, which is something not directly recognized as being any one person’s responsibility at the school. Nevertheless, all events were excellent and helped to shape the way I teach and approach teaching as more of an experiment and a science project. Kelly was exceptionally good at creating new opportunities and letting me know about them as well. She put together the first Teaching as Research cohort which I joined. It vi was the first time I did a research project and she spent a lot of time with me and others to help us understand how to develop a project and present one as well. She also put together the first ever Teaching Shark Tank which I also entered and won. This then started a cascade of events where she was very involved in helping me to create the app Tcrunch for improved student teacher communication and is still helping me. She always has impressed me as someone fully competent and very intelligent but mostly cares about the students at JHU. In line with teaching mentors, I was also very fortunate to have a teaching assistantship under Dr. Eileen Haase. I like to think of her as the heart of the JHU BME teaching program that pumps life into the whole department because of all the courses she has developed and manages for the entire curriculum. After observing her teaching in the course I TA’d with her, she observed also my love of teaching as I had created and taught two undergraduate Immunoengineering courses, one for the developing world and the other for the developed world. She offered to me to develop an online Immunoengineering Master’s level course. This, being a 3-credit course created from scratch, in an online environment that I had never encountered, was daunting, yet with her encouragement I pursued this alongside Elana Ben-Akiva—another BME PhD graduate student. Dr. Haase was extremely patient with both of us as it took us nearly two times as long to develop the content than we had promised and also worked closely giving us personalize feedback and advice for how to develop the course and how to arrange and present the content. I have and will look up to Dr. Haase as a teacher for inspiration in my own teaching in the future. vii Beyond extracurricular activities that JHU offers, JHU provides an extremely fertile soil for research.