THE UNIVERSITY OF CHICAGO MAPPING THE GENETIC DETERMINANTS OF IMMUNE DISEASE SUSCEPTIBILITY A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF HUMAN GENETICS BY SILVIA NJERI KARIUKI CHICAGO, ILLINOIS JUNE 2016 TABLE OF CONTENTS List of figures……………………………………………………………………………………………………….... iv List of tables…………………………………………………………………………………………………………... v List of supplementary figures……………………………………………………………………………….. vi List of supplementary tables…………………………………………………………………………………. vii Acknowledgements……………………………………………………………………………………………….. ix Abstract…………………………………………………………………………………………………………………. x Chapter 1: Introduction………………………………………………………………………………………… 1 Chapter 2: Genetic analysis of the pathogenic molecular sub-phenotype interferon- alpha identifies multiple novel loci involved in systemic lupus erythematosus………………………………………………………………………………… 13 2.1 Abstract………………………………………………………………………………….….. 13 2.2 Introduction…………………………………………………………………………….… 14 2.3 Results……………………………………………………………………………………..…. 16 2.4 Discussion…………………………………………………………………………………… 27 2.5 Methods……………………………………………………………………………………… 30 2.6 Appendix: Supplementary Materials…………………………………………. 39 Chapter 3: Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes…………… 52 3.1 Abstract………………………………………………………………………………….……. 52 3.2 Introduction…………………………………………………………………………….….. 53 3.3 Methods……………………………………………………………………………………..… 55 ii 3.4 Results………………………………………………………………………………….……… 60 3.5 Discussion…………………………………………………………………………………… 79 3.6 Appendix: Supplementary Materials…………………………………………... 85 Supplementary File 3.1 available online Chapter 4: Mapping variation in cellular and transcriptional response to 1,25- dihydroxyvitamin D3 in peripheral blood mononuclear cells………………… 107 4.1 Abstract………………………………………………………………………………….……. 107 4.2 Introduction…………………………………………………………………………….….. 108 4.3 Methods……………………………………………………………………………………..… 110 4.4 Results………………………………………………………………………………….……… 116 4.5 Discussion…………………………………………………………………………………… 129 4.6 Appendix: Supplementary Materials………………………………………….. 135 Chapter 5: Conclusions…………………………………………………………………………………………… 147 References………………………………………………………………………………………………………………. 152 iii LIST OF FIGURES Figure 2.1 Top signals of association with increased serum IFN- LE cases 18 α activity in S Figure 2.2 in the discovery phase……………………………………………………………………. cells…………………………………………………………………………………………..…… 25 Tissue specific analysis of gene networks in different immune Figure 3.1 Transcriptional response patterns shared across the different treatments Cormotif……………………………………………………………………………………….. 70 and ancestries identified by implementing a joint Bayesian analysis using Figure 3.2 Direction of response in the different correlation motifs………………… 71 Figure 3.3 Sharin ……………… 73 Figure 3.4 Inter-ethnicg of enriched differential biological response pathways patterns across…………………………………….. Cormotifs 75 Figure 4.1 GWAS of max)…………….. 119 Figure 4.2 inhibition of cellular proliferation by 1,25D (I inding sites and transcriptional response………………………………………………………………… 125 Associations between SNPs in vitamin D receptor (VDR) b iv LIST OF TABLES Table 2.1 List of top replicated SNPs associated with IFN- - Americans..............................................................................................................…… 20 α in European Table 2.2 List of top SNPs associated with serum IFN- - Americans………………………………………………………………………………….... 21 α in African Table 2.3 - GWAS data……..……………………………………………………………………………. 23 Top 10 canonical pathways from IFN α associated SNPs in initial discovery Table 2.4 ………………………………………………. 26 Network density and network strength analysis for tissue specific gene Table 3.1 Proportionnetworks in of different genes in immune each Cormotif cells pattern containing vitamin D receptor ……………………………………………………………………… 78 Table 4.1 cis(VDR)-eQTLs binding for transcriptional sites response to 1,25D.…………………………… 123 Table 4.2 Association between top Imax GWAS SNPs and transcriptional response……………………………………………………………………………………… 128 v LIST OF SUPPLEMENTARY FIGURES Experimental Design…………..………………………………… 85 Supplementary Figure 3.1 indicating the sources of transcriptome-wide Supplementary Figure 3.2 variationPrincipal …………………………………………….components analysis (PCA) of …………………the expression data86 -corrected expression data indicating the sources of transcriptome-wide Supplementary Figure 3.3 variationPrincipal componentsafter correction analysis for technical (PCA) of covariates covariates……………….……………..……………………………… 87 Inter-ethnic variation……………..……………………………… 88 Supplementary Figure 3.4 Examining the effect of serum 25D levels on transcriptional response………………………………………………………………… 89 Supplementary Figure 3.5 Treatment-specific response patterns in the oxidative ……………………………………… 91 Supplementary Figure 3.6 phosphorylation pathway-regulated genes in the “1,25D-all” Cormotif pattern………………………………………………………………….. 93 Supplementary Figure 3.7 Network of down Genes with significant inter-ethnic differential expression…………………………………………………………….. 94 Supplementary Figure 3.8 Experimental Design..……………………………………………. 135 Supplementary Figure 4.1 Correlation between serum 25D levels and global ………………………………………………………………… 136 Supplementary Figure 4.2 Alleleancestry fre ……………… 137 Supplementary Figure 4.3 quency distribution of top………………… SNPs... ……… 138 Supplementary Figure 4.4 MappingRegulatory lo gmarks2 fold changenear rs6451692. response cis-eQTLs…………… 139 Supplementary Figure 4.5 vi LIST OF SUPPLEMENTARY TABLES List of top 10 SNPs associated with IFN- ………………………………………………........ 39 Supplementary Table 2.1 α in the GWAS discovery cohort replication cohort………………………………………………….. 40 Supplementary Table 2.2 List of top 323 SNPs from discovery GWAS genotyped in the Clinical and serologic characteristics of the replication cohort..………………………………………………………………….. 47 Supplementary Table 2.3 in the replication cohort.………………………………………… 48 Supplementary Table 2.4 Autoantibody associations observed in European SLE patients observed in African American SLE patients in the replication cohort…………………………….. 50 Supplementary Table 2.5 Autoantibody associations ………………….……………………………………………… 51 Supplementary Table 2.6 Top 5 enriched networks by Ingenuity Pathway SampleAnalysis characteristics…………….……………………………… 96 Supplementary Table 3.1 -stabilized log2- transformed expression data…………………………………… 97 Supplementary Table 3.2 Principal components analysis of variance -stabilized log2- transformed expressi Supplementary Table 3.3 covariatesPrincipal components…………………………………………………………… analysis of variance …. 98 on data adjusted for s Supplementary Table 3.4 LPS,Biological identified pathways using enrichedlinear mixed at a- FDReffects < 0.05 model among..…….. gene 99 significantly DE in response to single treatment with 1,25D or the different Cormotif patterns.………………………………... 101 Supplementary Table 3.5 Biological pathways enriched at a FDR < 0.05 among genes in Diseases enriched among down-regulated genes in the “1,25D-all” C ……………. 104 Supplementary Table 3.6 Enrichment oformotif VDR ChIP pattern- at a FDR < 0.05 s responsive to 1,25D treatment………………………………………………… 106 Supplementary Table 3.7 seq peaks among gene The top SNPs identified in the GWAS of Imax.…………. 140 Supplementary Table 4.1 vii Association between top Imax-associated SNPs in chromosome 5, and transcription response Supplementary Table 4.2 …..……………………………………………………………… 141 of nearby genes (within 100kb) exp ………………………… 142 Supplementary Table 4.3 Gene set enrichment analysis of significantly differentially Responressedse cis (DE)-eQTLs genes found at FDR in open< 0.01 chromatin regions - Supplementary Table 4.4 seq……….………………………………………………………………… 144 detected by FAIRE Genes whose transcription responses are associated with inhibition of cellular prolif Supplementary Table 4.5 0.2...………………………………………………………………………… 145 eration by 1,25D at a FDR < Genes associated with inhibition of cellula 1,25D …………………………………………………………… 146 Supplementary Table 4.6 r proliferation by (Imax) viii ACKNOWLEDGEMENTS and mentorshipI would first like to thank my advisor, Anna Di Rienzo, for her enormous support of my thesis work. Her devotion to my development as a graduate student in her lab, and as a scientist in general, is truly humbling, and I am grateful for her mentorship and encouragement tohesis continue committee, pursuing Carole my scientificOber, Marcelo interests. Nobrega I would and also John Novembre,like to thank for the their members fruitful of discussions my t and valuable guidance onstant encouragement thr throughout my thesis . I project, as well as their c embers of the Di Rienzooughout lab for my their years valuable at grad contributions school would also like to thank the m discussions that enabled further understandingto my projects onof theVitamin data. D,The and friendships for their helpful I have gained in this lab, as well as in the department of Human Genetics, be treasured. have truly enriched my graduate school experience, and will always I would also like to acknowledge and thank Dr. Tim Niewold, to whom I am grateful invaluable,for spiking myand interest gave me in the the solid field foundation of human genetics. for pursuing My experiences this PhD program in his labin Human were truly Genetics. I am also grateful to members of the Niewold Lab who helped me with data . collection