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Download Thesis This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Genetics of Gene Expression and its relationship with Adiposity Glastonbury, Craig Anthony Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 04. Oct. 2021 The Genetics of Gene Expression and its relationship with Adiposity Craig A. Glastonbury King's College London A thesis submitted for the degree of Doctor of Philosophy 2016 This thesis is dedicated to my parents, Mark & Jacqueline. To my sister Natalie, nephew Mason, and my partner Rodrigo. Your daily support allows me to do what I love. Thank you. Acknowledgements Whilst this thesis is the product of my own work, there have been many collaborations, discussions, coffee chats and rants that have really shaped how I think about science and that have influenced my work substantially over the last three years. Many people at TwinsUK have been incredibly supportive in all aspects of my studies. I would first like to thank Ana Vi~nuela.From the start of my PhD to when you left to join Emmanouil Dermitzakis in Geneva, you were incredibly supportive, insightful and fun to talk to. As a stand-in supervisor whilst Kerrin was on maternity leave, you really guided me, and not just with a constant supply of M&M's! There are many current colleagues and friends I would like to thank here, that have made my three years extremely enjoyable and stimulating. Alex Couto Alves, you are a fantastic person to work with, and have filled the role as a mentor to me. You have influenced my ability to think crit- ically and our countless discussions over coffee have been a real source of joy in my academic life. I hope to see you one day leading your own group, as you're a fantastic scientist with your heart in the right place. Antonino Zito and Abhishek Nag, you are two close friends and colleagues of mine who are extremely talented academics and have often helped in many aspects of both my PhD and life outside academia. Abhishek, you are a sporting force to be reckoned with! Never have I felt so exhausted than after playing squash with you. Antonino, you're a strong minded and independent scientist. I know you will succeed in your future and that we will stay close friends. I would of course also like to thank my supervisor Kerrin Small. Kerrin, you are a kind, caring mentor and an excellent scientist. You have made my PhD a very enjoyable and stim- ulating experience and you have always been incredibly supportive and insightful. As your first PhD student, I am grateful for working with you and I am sure we will continue to work well into the future whilst I am at Oxford. I would also like to thank Tim Spector. Tim, you constantly surprise me with your ability to manage so much so seamlessly. I've never seen you flustered or too busy to stop and chat. Thank you for running such a successful and enjoyable place to work. I would like to thank my Partner Rodrigo Pracana. Both of us pursu- ing PhDs has been stressful with many of our weekends lost to genetics. However, it hasn't tested us at all, and after five years in your company, you remain the closest and most loved person in my life. My best friends, Carla Curtis-Tansley, Slavina Georgieva and Isha Puri. All of you have been incredibly supportive and understanding. You're the kindest friends anyone could wish for and I know we will continue to be friends into the distant future. For three years, every Monday, I would meet twins to conduct clinical visits and perform a wide range of tests. Whilst this was tiring and at times tested me, I have never met such generous people. So in part, this thesis is dedicated to all volunteers, as none of my work and many other pieces of research would be possible, if not for the Twins. 4 0.1 Publications A list of publications to which I have contributed to during my PhD: Chapter3 : Menni, C, Glastonbury, C, K Nikolaou, K Small, K Mahney, T Spector, and A.M Valdes. \Metabolomic profiling to dissect the role of visceral fat in cardio metabolic health". In: Obesity Bailey, et al.*. \Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open angle glaucoma". In: Nature Genetics. Small, K, L Quaye, A Hough, M Todorcevic, A Mahajan, M Horikoshi, A Buil, A Vinuela, Glastonbury, C, J Brown A Bell, R Cox, Gloyn A, Karpe F, and Mc- Carthy M. \Characterisation of the KLF14 trans-regulatory network". In: Submitted (Nature). J.S. El-Sayed Moustafa, J. Fernandez, M. Civelek, C. Glastonbury, M. Todorce- vic, A. Mahajan, M. Horikoshi, I.Yet, M.Simon, G. Thorleifsson, U. Thorsteinsdottir, J. Bell, A. Gloyn, R. Cox, A. Lusis, F. Karpe, M. McCarthy K. Small. "Mechanistic and functional properties of the KLF14 trans-eQTL network associated to risk of type 2 diabetes" In: Preparation Kaul, S, H Xu, E Maruko, Glastonbury, C, K Small, G Dallinga-Thie, M Civelek, M Thomas, I Goldberg, and M Sorci-Thomas. \Procollagen C-endopeptidase enhancer protein 2 (PCPE2) Deficiency Profoundly Affects Adipose Distribution in Mice and Humans Linking HDL Metabolism to Adipocyte Biology". In: Preparation. Chapter4 : Glastonbury, C, A. Vinuela, A. Buil, R. Durbin, E. Dermitzakis, T. Spector, and K. Small. \Adiposity-dependent regulatory effects on multi-tissue transcriptomes". In: AJHG. Other: Tsai, PC*, Glastonbury, C*, A Vineula, E Dermitzakis, T Spector, and K. Small. \Tobacco smoke modulates gene expression and DNA methylation via genetic variation in multiple human tissues". In: Preparation 6 0.2 Attributions This page outlines the specific attributions per (research) chapter. Analysis performed by collaborators was used to perform additional and novel research presented in this thesis. Anything not listed on this page was performed by myself. 0.2.1 Chapter 3 - Pervasive eect of cardio-metabolic traits on peripheral tissue gene expression regulation exon level eQTLs, genotype QC and heritability calculations performed and previ- ously described in Buil et al.(2015). 0.2.2 Chapter 4 - BMI-dependent regulatory effects on multi- tissue transcriptomes exon level quantification’s and genotype QC performed and published described in Buil et al.(2015). 0.2.3 Chapter 5 - Population level variability in adipose tis- sue cell-type composition and its link to obesity Genotype QC performed and previously described in Buil et al.(2015). 7 Abstract The major focus of this thesis will concern the consequences and down- stream impacts of obesity and adiposity-related traits on the human body by utilising RNA-sequencing measurements from three primary tissues (Subcutaneous adipose tissue, Whole blood & Skin) and one cell line, LCLs (Lymphoblastoid cell lines). I will discuss how we can use gene expression and population genetic vari- ation to understand the heterogeneous nature of obesity outcome in the population and to uncover the complex relationship between the effects of obesity on peripheral tissue biology, the environment and the conse- quences of obesity on gene regulation. First, I will examine the extent of gene expression association measured in peripheral tissues to multiple cardio-metabolic, hormonal and adiposity related measurements. I will characterise the heritability of gene expression in these four sources and discuss the tissue specificity of both trait associations and genetic effects on gene expression. Second, I will describe how BMI can act as a po- tent modifier of gene expression in adipose tissue by modelling BMI as an exposure/environment to detect and for the first time replicate BMI- dependent eQTLs (G × BMI) that are specific to adipose tissue. Lastly, I will explore the cell type heterogeneity of adipose tissue, a pertinent problem for many investigators performing gene expression based stud- ies in bulk complex tissues. I will show how many BMI gene expression associations are driven by macrophage heterogeniety amongst samples, that cell type variability is heritable and describe examples of cis-eQTLs driven by macrophage proportion in adipose tissue. Contents 0.1 Publications................................5 0.2 Attributions................................7 0.2.1 Chapter 3 - Pervasive eect of cardio-metabolic traits on periph- eral tissue gene expression regulation..............7 0.2.2 Chapter 4 - BMI-dependent regulatory effects on multi-tissue transcriptomes..........................7 0.2.3 Chapter 5 - Population level variability in adipose tissue cell- type composition and its link to obesity............7 1 Introduction1 1.0.1 Overview.............................1 1.1 Obesity biology and associated co-morbidities.............1 1.1.1 Prevalence and impact......................1 1.1.2 Heritability of obesity and related traits............2 1.1.3 Genetic etiology of Obesity...................3 1.1.4 Systemic effects of obesity...................
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