Gene%c regulaon of gene expression variaon Barbara E. Stranger Sec%on of Gene%c Medicine Ins%tute for Genomics and Systems Biology Center for Data Intensive Science ENCODE Users group mee%ng, Stanford University 6/8/2016 Outline • The Immunological Variaon (ImmVar) Project – Baseline eQTLs in adap%ve and innate immunity • Context specificity • Role in disease – Ac%vaon eQTLs Outline • The Immunological Variaon (ImmVar) Project – Baseline eQTLs in adap%ve and innate immunity • Context specificity • Role in disease – Ac%vaon eQTLs The Immunological Variaon Project (ImmVar) Goal: Understand how gene%c variability translates into gene expression variability in adap%ve and innate immunity and contributes to higher order phenotypes ImmVar Study Design Boston-based healthy donors (n=415) European American (EU, n=215) Phenogenetic Project African American (AA, n=115) (Phillip De Jager) East Asian (EA, n=85) Naïve CD4+ CD14+16- T-cell activation Dendritic cell T-cells monocytes activation Transcriptome profiling (Affy Exon 1.0 ST) eQTL mapping + cis- and trans- Genome-wide genotyping & imputation cis-eQTL analysis (baseline) 1Mb 1Mb 1Mb window SNPs Model: residual gene expression profile (control for age, sex, PCgt, PCge) + Genotyped and imputed SNPs Significance assessed by 10,000 permutaons per gene: Nominal p < 0.01 tail of the minimal permutaon p-value 1) Analysis performed separately for each cell-type and populaon 2) Mul%-ethnic Meta-analysis for each cell type T. Raj et al 2014 Science Detected eGenes Baseline eQTLs in CD4+ T and CD14+16- 30% of tested genes have cis-eQTL associaons Up to 17% of genes with a cis-eQTL, have >= 2 independent signals Outline • The Immunological Variaon (ImmVar) Project – Baseline eQTLs in adap%ve and innate immunity • Context specificity • Role in disease – Ac%vaon eQTLs allelic direc%on different genes eQTL presence/ different SNPs same gene, single SNP, effect size variability absence flip log2 expr log2 expr -log10 p -log10 p -log10 p 0 0 condion 1 1 1 2 2 log2 expr log2 expr 0 0 1 1 condion2 2 2 4-6% of Populaon specificity of cis-eQTLs are populaon-specific cis-eQTLs? Monocytes T-cells For shared-popula=on eQTLs: Fold change across popula=ons highly correlated; Pearson’s r: 0.85 -0.95 Lile populaon-specificity of presence/absence or fold-change modulaon BUT those differences might be highly relevant for populaon-diverged phenotypes Bayesian model average and a hierarchical model BFBMA; Flutre et al. 2013 Populaon specific cis-regulatory effects TARSL2: threonyl-tRNA synthetase-like 2 ~40% cell-type specific cis-eQTLs are cell-type specificeQTLs? For eQTLs shared across cell types: Fold change across cell types less highly correlated; r: 0.49-0.64 Evidence for cell – type specificity in presence/absence AND fold change Cell-type specificity of cis-eQTLs in a rheumatoid arthri%s risk FADS genes: 11q12-q13 fay acid desaturase locus involved in atopic disease CD52 cis-eQTL shows direc%onal regulatory effects across cell types CD52 lymphocyte cell-surface glycoprotein, func%on in an%-adhesion, role in lymphoma. It is the protein targeted by alemtuzumab, a monoclonal an%body used for the treatment of chronic lymphocy%c leukemia Sex-differen%ated eQTLs • Autosomal gene%c variaon contributes to sexual dimorphism (Ober et al. 2008; Heid et al. 2010) • Sex-specific eQTLs have been detected in mice (Yang et al. 2006) and humans (Dimas et al. 2012, Kent et al. 2012, Yao et al. 2014, Kukurba et al. 2015) X% of cis-eQTLs exhibit sex-bias Male Female 9.5 9.5 CLL risk locus. chronic lymphocyc 9.0 9.0 leukemia: monocytes 8.5 Male risk is 2X 8.5 female risk (Slager et al. 2012) 8.0 8.0 Expression of BAK1 p= 1.3e-6 p= 0.025 CC CT TT CC CT TT rs210142 genotype BAK1: BCL2-Antagonist/Killer 1; role in apoptosis, interacts with the tumor suppressor P53 aer exposure to cell stress Outline • The Immunological Variaon (ImmVar) Project – Baseline eQTLs in adap%ve and innate immunity • Context specificity • Role in disease – Ac%vaon eQTLs GWAS-associated SNPs are more likely to be eQTLs Nicolae et al. 2010 PLoS Gene:cs GWAS: Where is the causal disease variant and what does it do? Gene A Gene B Gene C Gene A Gene B Gene C Gene A Gene B Gene C Nica and Dermitzakis Hum Mol Genet 2008 Common disease variants are cis-eQTLs in ImmVar data Traits # SNPs Monocytes T-cells Shared GWAS Curated (LD-pruned) 1,068 94 53 29 Cancers 121 7 3 1 Neurodegenerative diseases 55 19 0 1 Neuropsychiatric 27 3 4 3 Metabolic diseases 161 13 2 7 Height 180 12 5 1 Autoimmune disease associated SNPs Regulatory Trait Concordance, RTC score > 0.9 (Nica et al 2010): T-cells 106 genes, monocytes 123 genes Polarization in the regulatory effects of neurodegenerative and inflammatory disease variants Traits Cell-specificity Monocytes Shared T Cells (random vs observed) All cis eQTLs GWAS Monocytes T-cells Alzheimer's disease p < 0.05 Parkinson's disease HDL Cholesterol Type 2 diabetes Systemic Lupus Erythematosus Body Mass Index Breast cancer Ankylosing Spondylitis Psoriasis Height Ulcerative Colitis Celiac disease Primary Biliary Cirrhosis Ovarian cancer Lung cancer Colorectal cancer Restless Leg Syndrome Crohn's disease Systemic sclerosis Bipolar Schizophrenia Testicular germ cell cancer Prostate cancer Type 1 diabetes p < 0.05 Multiple Sclerosis Rheumatoid Arthritis 0.00 0.25 0.50 0.75 1.00 Proportion of cell specifcity Monocyte-specific cis-eQTL for CD33 associated with Alzheimer’s Disease Plotted SNPs ● ●● 2 100 ● r rs3826656 ● ● ● ●● ● 10 1 ● ● ● ● ● ●● ● ● 0.8 ●● ●●●● ● ●● ● ●● ● ● ●● 0.6 ●●●● ● ●●●● ●● 80 ●●●●●● ● ● ● Recombination rate (cM/Mb) Recombination rate ●● ●● ● ● ●● ●● ●●●●● 0.4 ● ● ● ●● ●●● 8 ● ●●●●●●● ●●● ● ● ●●●●● ●● ●● ● ●●●● ● ● ● ● ● 0.2 ● 0 ●● ●● ●●● ●● ● ●●● ●●● ● ● ●●●●●● ●● ● ●●● ● ●●●● ●●●● ● ● ● ● ● ● 60 ● ● ● ● ●● 6 ● ● ●● Monocytes value) ● ● − ● ●● ● ● ● (p ● ● −1 ● ●● ● 10 ● ● g ●● ● ● o ● l ● ● 40 ● 4 ●● ● − ● ●● ● ●● ● ● ● ●●●●●● CD33 Expression ● ●● ● ● ●● ●●●●● ● ● ● ● ● ●●●●● ● ● ● ● ●●● ●●●●● ● ● ● ● ●● −2 ● ● ● ● ●● ● ●● ● ● ● ● ● 20 2 ● ● ●●● ●●● ●● ●●● ●●●● ●●● ● ● ● ●● ●● ●● ●●● ●●● ● ●●●●●●●● ● ● ●●● ● ●● ●●● ●●●●●●●●●● ●● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ●● ●●●● ● ●● ● ●●●● ●●● ●● ● ● ● ● ●●● ●●●● ●●● ●●●● ● ●● ●● ●●● ●●●●●●●● ●●● ●●●●●●●●●●●●●● ●● ●● ●● ● ● ●●●● ● ● ●●●●●●● ●●●●●●●● ●●●●●●●●●●● ●●●● ●●●●● ●●●●●●●●● ●●●●●●●●●●●●●●●●●● ●●● ●●● ●●● ●●●●●● ●●●●●●●●●●●●●●● ●●●● ●●●●●●●●●●●●●●●● ● ●●●●●●●●●●●● ●●●●●●●●●●●●●● ●●● ●●●●●●●●●●●●●● ●●● ●●●●●●●● ●● ●●●●●●●●● ●●● ●●●●●● ●●●●●●●●●●●●● ●●●●● ●●●●●●●●●●●●●●●●●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●● ●●●●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 0 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 0 AA AG GG Plotted SNPs rs3826656 CLEC11A2 KLK2 KLK6 KLK13 CD33 VSIG10L SIGLEC8 ZNF175 HAS1 10 r rs3826656 100 GPR32 KLK3 KLK5 KLK12 SIGLEC7 IGLON5 CEACAM18 SIGLEC5 0.8 ● ACPT KLKP1 KLK7 KLK14 SIGLECL1 NKG7 SIGLEC12 SIGLEC14 0.6 ● ● 8 80 ● Recombination rate (cM/Mb) Recombination rate 1 ● C19orf480.4 KLK4 KLK8 CTU1 ETFB SIGLEC6 MIR99B ● ● ● ● 0.2 ●● SNORD88B KLK9 SIGLEC9 CLDND2 FLJ30403 ● ● ● ● ● ● ●● ●● ● ●● ● ● 51.4 51.6 51.8 52 52.2 ●● ●● ● ●●● ● ● ●● 6 SNORD88A KLK10 SIGLEC17P LIM2 MIRLET7E 60 ●● ●● ●● ●● ●●● ● ● Position on chr19 (Mb) ● ●● ● value) ●●● ● ● ●●●● ● ● − ●● ● ● ● SNORD88C KLK11 LOC147646 MIR125A ●● ● ● ●● ● ●● ●●● ● ● ● ● (p ●● ● ● ● 0 ● ●● ●●● ● 10 ● ● ● ●● ●● ● ● ● ● g ●●●● ● ●● ●● o ●● ● T-cells l 4 40 ●● ●● ● ● ●● − ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ● ● ● ●● ● ● ●● ●● ● ● ● ●● ● ● ● 2 ● ● ● ●●● ● ●● ● ● ● 20 ● ● ● ● ●● ●● ● ● ●● ● ●● ● ● ●●●● ● ●●● ● ●● ● ● ●●● ●● ●●● ● ● ●● ●● ●●● ● ● ● ●● ●●● ●● −1 ●● ●● ● ● ● ●●● ●●● ● ● ● ●● ●●●●● ● ● ● ●● ● ●● CD33 Expression ●●● ●●●●●● ● ● ●●● ●●●● ●●● ● ●● ● ● ●●●●●●●●●●● ●●●● ●●● ●●●●●●●●●●●●● ●●● ●●●● ●● ● ●●● ●●●● ●●●●●●●● ●●●●● ●● ●● ●●●● ●●●●● ●●●●●●●●●●●●●●●● ●●●●●●●● ● ●●●●●● ●●●●●●●●●●●●●● ●●●●● ●●●●●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●●● ●●● ●●●● ●●●●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 0 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● 0 ● ● CLEC11A KLK2 KLK6 KLK13 CD33 VSIG10L SIGLEC8 ZNF175 HAS1 AA AG GG GPR32 KLK3 KLK5 KLK12 SIGLEC7 IGLON5 CEACAM18 SIGLEC5 rs3826656 ACPT KLKP1 KLK7 KLK14 SIGLECL1 NKG7 SIGLEC12 SIGLEC14 C19orf48 KLK4 KLK8 CTU1 ETFB SIGLEC6 MIR99B SNORD88B