_____________________________________________________________ CHRONIC KIDNEY DISEASE IN HIV POPULATIONS: PREVALENCE, RISK FACTORS AND ROLE OF TRANSFORMING GROWTH FACTOR BETA (TGF-β1) POLYMORPHISMS BY STUDENT: UDEME EKPENYONG EKRIKPO (Student No: EKRUDE001) SUBMITTED TO THE UNIVERSITY OF CAPE TOWN IN FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE DOCTOR OF PHILOSOPHY (NEPHROLOGY) FACULTY OF HEALTH SCIENCES UNIVERSITY OF CAPE TOWN DATE: 29th July 2019 SUPERVISOR: PROF. IKECHI OKPECHI CO-SUPERVISORS:University PROF. ANDRE PASCAL of KENGNE Cape Town PROF. AMINU BELLO PROF. COLLET DANDARA PROF. AMBROISE WONKAM 1 | P a g e The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town DECLARATION I, UDEME EKPENYONG EKRIKPO, hereby declare that the work on which this dissertation/thesis is based is my original work (except where acknowledgements indicate otherwise) and that neither the whole work nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. I empower the university to reproduce for the purpose of research either the whole or any portion of the contents in any manner whatsoever. Signature: Date: 29th July 2019. 2 | P a g e DECLARATION: INCLUSION OF PUBLICATIONS I confirm that I have been granted permission by the University of Cape Town’s Doctoral Degrees Board to include the following publications in my PhD thesis, and where co-authorships are involved, my co-authors have agreed that I may include the publications. 1. Chronic kidney disease in the global adult HIV-infected population: A systematic review and meta- analysis. PLoS One. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195443 2. Prevalence and correlates of chronic kidney disease (CKD) among ART-naïve HIV patients in the Niger- Delta region of Nigeria. Medicine (Baltimore). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916672/ 3. Prevalence and correlates of traditional risk factors for cardiovascular disease in a Nigerian ART-naïve HIV population: a cross-sectional study. BMJ Open. https://bmjopen.bmj.com/content/8/7/e019664.long 4. Urinary Transforming Growth Factor-Beta 1 (uTGF-β1) and prevalent chronic kidney disease risk in HIV- positive patients in West Africa (Accepted for publication with Kidney International Reports). 5. Association of Genetic Polymorphisms of TGF-β1, HMOX1 and APOL1 with CKD in Patients with HIV- related nephropathies in Extreme Southern Nigeria [submitted to American Journal of Kidney Disease (AJKD)]. SIGNATURE: DATE: 29th July 2019 STUDENT NAME: UDEME EKPENYONG EKRIKPO STUDENT NO: EKRUDE001 3 | P a g e DEDICATION This work is dedicated to the people who made the greatest sacrifice for this work to come to fruition – my wife (Edidiong Udeme Ekrikpo) and children (Inyeneabasi, Inimfonabasi and Ifiokabasi). You will grow to fulfill your God-given call on earth. I also dedicate this work to all the HIV patients in Nigeria with Chronic kidney disease who daily go through the anxieties of living with HIV and CKD in a developing country. 4 | P a g e ACKNOWLEDGEMENT This work would not have seen the light of day if financial support did not come from the individuals named below: Mrs. Arit Ibanga, Elder & Mrs. Obot Udoette, Elder & Mrs. Benjamin Udobia, Barrister Mfon Daniel, Elder Wisdom Ekpo, Barr. & Dr (Mrs.) Onofiok Luke, Mr. & Mrs. Akpan Ntekpere, Dr & Mrs. Abraham, Barr. & Dr. (Mrs.) Abasiodiong Ekpenyong, Dr Ime Essien and Prof Emmanuel Ekanem, Rev. (Dr) & Mrs. Uma Ukpai, Mrs. Erika Akpan (Nee Mboho), Elder (Mrs) Unwana Ossom and Prof & Mrs. Etim Essien. I also acknowledge the Postgraduate Academic Mobility for African Physician Scientist (PAMAPS) for paying my school fees and stipend for upkeep for the first two years of the program. My Supervisors – Prof Ikechi Okpechi (who was very patient with me while teaching me the art of manuscript writing); Prof. Andre-pascal Kengne (who made my statistics skills so much better and taught me the principle of consistency in medical research); Dr. Aminu Bello (whose command of “research English” has made me a better researcher); Professors Collette Dandara and Ambroise Wonkam (who demystified genetic research for me and hence for generations of young researcher in my part of Sub-Saharan Africa). My heart is filled with gratitude. I would not have grown in research without you. I also thank Prof. Tatfeng Mirabeau for allowing me access to his laboratory and his wealth of experience. To the staff of the HIV unit of UUTH, Uyo, I thank you for all the support you gave me during data collection. I am indebted to you. My special appreciation goes to Mr. Akan Etuk for helping me with sample storage through the period. I am also indebted to Drs. Akpabio Akpabio, Edesiri Ighorodje, Uduak Udofia, Aquaowo Udosen for helping coordinate sample collection in the Clinics. I thank Mr. Eseme King, Mrs. Cecilia Ndiuwem, Mr. Aniebiet Obot for their support in the laboratory component of this work. 5 | P a g e TABLE OF CONTENTS Declaration 2 Declaration: Inclusion of Publications 3 Dedication 4 Acknowledgement 5 Table of Contents 6 List of figures 10 List of tables 12 List of acronyms 14 Addenda 16 Abstract 17 CHAPTER 1: INTRODUCTION 18 CHAPTER 2: OVERVIEW OF METHODS 34 CHAPTER 3: Chronic kidney disease in the global adult HIV-infected population: A 45 systematic review and meta-analysis Abstract 46 Introduction 47 Methods 47 Identification of studies 49 Assessment of methodological quality of included articles 49 6 | P a g e Study selection and data extraction 49 Statistical analyses 49 Results 50 Discussion 56 References 62 CHAPTER 4: Prevalence and correlates of chronic kidney disease (CKD) among ART- 89 naïve HIV patients in the Niger-Delta region of Nigeria Abstract 90 Introduction 90 Methods 91 Result 91 Discussion 92 Limitation 95 Conclusion 95 Acknowledgements 95 References 95 CHPATER 5: Prevalence and correlates of traditional risk factors for cardiovascular 97 disease in a Nigerian ART-naïve HIV population: a cross-sectional study Abstract 98 Strengths and limitations of study 98 7 | P a g e Introduction 98 Methods 99 Results 99 Discussion 102 Conclusion 109 References 109 CHAPTER 6: Urinary Transforming Growth Factor-Beta 1 (uTGF-β1) and prevalent 111 chronic kidney disease risk in HIV-positive patients in West Africa Abstract 113 Introduction 114 Methods 115 Results 118 Discussion 120 Conclusion 124 References 129 CHAPTER 7: Association of Genetic Polymorphisms of TGF-β1, HMOX1 and APOL1 132 with CKD in Patients with HIV-related nephropathies in Extreme Southern Nigeria Abstract 134 Introduction 135 Methods 136 8 | P a g e Results 138 Discussion 140 Conclusion 143 References 152 CHAPTER 8: SYNTHESIS-CONCLUSION AND RECOMMENDATION 154 Recommendations and future work 162 REFERENCES 164 9 | P a g e LIST OF FIGURES CHAPTER 1 Figure 1: Canonical pathway for TGF-beta 1 induced renal fibrosis 28 Figure 2: Pleotropic effect of TGF-beta 29 CHAPTER 2 Figure 3: Outlay of PhD activities 34 CHAPTER 3 Figure 1: Flow diagram for selection of studies 48 Figure 2: Forest plot showing the overall CKD prevalence in the HIV-infected 54 population using the MDRD, CKD-EPI and Cockcroft-Gault equations Figure 3: Funnel plot for included studies across different serum creatinine based 55 GFR equations Figure 4: Summary of pooled prevalence of CKD in HIV populations across WHO 56 regions Figure 5: Summary of pooled prevalence of CKD in HIV populations of the African 58 sub-region Supplementary figure 1: Forest plot showing the pooled prevalence of CKD in HIV 85 populations for studies with at least two eGFR estimates using MDRD, CKD-EPI and CG equations Supplementary figure 2: Funnel plots for studies with two or more eGFR values 86 10 | P a g e Supplementary figure 3: Forest plot showing the pooled prevalence for studies with 87 two or more MDRD-based eGFR estimates across the WHO regions CHAPTER 4 Figure 1: Map of Nigeria showing Akwa Ibom State 91 Figure 2: Relationship between CKD prevalence and median CD4 count (2002-2016) 93 CHAPTER 5 Figure 1: Trends of traditional cardiovascular disease risk factors prevalence (A) over 101 the study period (B) across age categories Figure 2: Changes in cardiovascular disease (CVD) risk factor prevalence across CD4 104 categories Figure 3: Relationship of other cardiovascular disease risk factors with hypertension 106 among HIV patients CHAPTER 6 Figure 1: Median urinary TGF-beta-1 levels across CKD stages for HIV-CKD patients 131 11 | P a g e LIST OF TABLES CHAPTER 3 Table 1: Summary of extracted data from all included studies 51 Table 2: Summary statistics from meta-analyses of prevalence studies on CKD in 57 people with HIV using random effects model and arcsine transformations Supplementary table 1: PRISMA 2009 checklist 70 Supplementary table 2: Search strategy for PubMed, Web of science, EBSCO host and 72 AJOL Supplementary table 3: Scoring criteria for quality of studies 74 Supplementary table 4: Assessment of methodological quality of included articles 75 Supplementary table 5: Summary statistics from meta-analyses of prevalence studies 79 on CKD in people with HIV random effects model and arcsine transformations (subgroup analyses of gender, ARV status, CD4 count levels, age