TOWARDS PERSONALIZED MEDICINE IN PSYCHIATRY: FOCUS ON SUICIDE Daniel F. Levey Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Program of Medical Neuroscience, Indiana University April 2017 ii Accepted by the Graduate Faculty, Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Andrew J. Saykin, Psy. D. - Chair ___________________________ Alan F. Breier, M.D. Doctoral Committee Gerry S. Oxford, Ph.D. December 13, 2016 Anantha Shekhar, M.D., Ph.D. Alexander B. Niculescu III, M.D., Ph.D. iii Dedication This work is dedicated to all those who suffer, whether their pain is physical or psychological. iv Acknowledgements The work I have done over the last several years would not have been possible without the contributions of many people. I first need to thank my terrific mentor and PI, Dr. Alexander Niculescu. He has continuously given me advice and opportunities over the years even as he has suffered through my many mistakes, and I greatly appreciate his patience. The incredible passion he brings to his work every single day has been inspirational. It has been an at times painful but often exhilarating 5 years. I need to thank Helen Le-Niculescu for being a wonderful colleague and mentor. I learned a lot about organization and presentation working alongside her, and her tireless work ethic was an excellent example for a new graduate student. I had the pleasure of working with a number of great people over the years. Mikias Ayalew showed me the ropes of the lab and began my understanding of the power of algorithms. Despite being a New England Patriots fan he’s a pretty decent guy. Peter Phalen helped to teach me the ways of R coding and provided some clinical perspective (while also occasionally distracting me with talk of politics and philosophy.) In no particular order, Evan Winiger, Rebecca Learman, Naga Venipenta, Farnoosh Khan, Vivek Venugopal, Helen Dainton, one of the greatest parts of my time in the Niculescu lab has been seeing you move on to take the next steps in v your lives. I’m glad to have known you, and thank you for allowing me to live vicariously through your successes. I want to thank my parents and sister for their love and support over the years. I cannot adequately express in words my love and appreciation for you all. So instead I will thank my father for his marathon lectures, which helped prepare me for the rigors of graduate school. I must thank my lifelong friend Brian Marler. He provided a hand in a time of great need and really helped me turn my life around. I am forever grateful. And he joins me as one of several hardcore IU football fans on the planet earth, so he’s good for that as well. Lastly, I’d like to thank my beautiful and patient wife and my amazing son for being the reason I wake up every morning. vi Daniel F. Levey Towards Personalized Medicine in Psychiatry: Focus on Suicide Psychiatric disorders cost an estimated $273 billion annually. This cost comes largely in the form of lost income and the chronic disability that often strikes people when they are young and can last decades. While the monetary costs are quantifiable, the suffering of each individual patient is no less vital. As many as 1 in 5 persons diagnosed with mental illness will commit suicide, a contributing factor in suicide being the second leading cause of death of people age 15-34. There is a critical need to find better ways to identify and help those who are at risk. Understanding mental illness and improving treatment has been difficult due to the heterogeneous and complex etiology of these illnesses. A significant challenge for the field is integrating findings from diverse laboratories all over the world contributing to the ever expanding literature and translating them into actionable treatment. Our lab employs a convergent functional genomics approach which incorporates multiple independent lines of evidence provided by genetic and functional genomic data published in the primary literature as a Bayesian strategy to prioritize experimental findings. Heritability and genetics clearly play an important role in psychiatric disorders. We looked at schizophrenia and alcoholism in separate case-control analyses in order to identify and prioritize genes related to these disorders. We were able to reproduce these findings in additional independent cohorts using vii polygenic risk scores. We found overlap in these disorders, and identified possible underlying biological processes. Genetics play an important role in identifying clinical risk, particularly at the population level. At the level of the individual, gene expression may provide more proximal association to disease state, assimilating environmental, genetic, as well as epigenetic influence. We undertook N of 1 analyses in a longitudinally followed cohort of psychiatric participants, identifying genes which change in expression tracking an individual’s change in suicidal ideation. These genes were able to predict suicidal behavior in independent cohorts. When combined with simple clinical instruments these predictions were improved. This work shows how multi- level integration of genetic, gene expression, and clinical data could be used to enable precision medicine in psychiatry. Andrew J. Saykin, Psy. D. - Chair viii Table of Contents Introduction: Precision Medicine ...................................................................... 1 Convergent Functional Genomics .................................................................. 7 Universal Materials and Methods ................................................................... 8 GWAS Studies ........................................................................................... 8 Gene Expression Studies ........................................................................... 8 Convergent Functional Genomics ............................................................. 12 Workflow ................................................................................................... 15 Discovery ............................................................................................... 15 Prioritization ........................................................................................... 15 Validation ............................................................................................... 16 Prediction ............................................................................................... 16 Understanding ........................................................................................ 16 Chapter 1: Schizophrenia .............................................................................. 17 Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction ...................................................... 21 Introduction ........................................................................................... 21 Materials and Methods ............................................................................ 24 Figures ................................................................................................... 28 Results ................................................................................................... 28 Discussion .............................................................................................. 98 Conclusions and future directions ........................................................... 109 ix Chapter 2: Alcoholism ................................................................................ 113 Genetic Risk Prediction and Neurobiological Understanding of Alcoholism .... 117 Introduction ......................................................................................... 117 Materials and Methods .......................................................................... 120 Figures ................................................................................................. 129 Results ................................................................................................. 129 Discussion ............................................................................................ 150 Conclusion ............................................................................................ 168 Chapter 3: Focus on Suicide ....................................................................... 170 Epidemiology ........................................................................................ 171 Clinical Risk Assessment Scales .............................................................. 172 Treatment ............................................................................................ 173 Etiology/genetics .................................................................................. 179 Paths to Pathology ................................................................................ 180 The Biology of Suicide ........................................................................... 181 SKA2 .................................................................................................... 184 SLC4A4 ................................................................................................ 185 SAT1 and polyamines (SMOX) ............................................................... 185 Serotonin ............................................................................................