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Imputed Gene Associations Identify Replicable Trans-Acting Genes Enriched in Transcription Pathways and Complex Traits

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Imputed Gene Associations Identify Replicable Trans-Acting Genes Enriched in Transcription Pathways and Complex Traits bioRxiv preprint doi: https://doi.org/10.1101/471748; this version posted November 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits Heather E. Wheeler1,2,3, , Sally Ploch1, Alvaro N. Barbeira4, Rodrigo Bonazzola4, Alireza Fotuhi Siahpirani5, Ashis Saha6, Alexis Battle6,7, Sushmita Roy8, and Hae Kyung Im4, 1Department of Biology, Loyola University Chicago, Chicago, IL 2Department of Computer Science, Loyola University Chicago, Chicago, IL 3Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 4Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 5Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 6Department of Computer Science, Johns Hopkins University, Baltimore, MD 7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 8Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI Regulation of gene expression is an important mechanism SNPs associated with gene expression in cis, typically mean- through which genetic variation can affect complex traits. A ing SNPs within 1 Mb of the target gene. Because effect sizes substantial portion of gene expression variation can be ex- are large enough, around 100 samples in the early eQTL stud- plained by both local (cis) and distal (trans) genetic variation. ies could detect replicable associations in the reduced multi- Much progress has been made in uncovering cis-acting expres- ple testing space of cis-eQTLs (1–3). sion quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take ad- trans-eQTLs have been more difficult to replicate because vantage of our ability to predict the cis component of gene ex- their effect sizes are usually smaller and the multiple testing pression coupled with gene mapping methods such as PrediX- burden for testing all SNPs versus all genes can be too large can to identify high confidence candidate trans-acting genes and to overcome. A few studies have had some success; one, with their targets. That is, we correlate the cis component of gene a discovery cohort of 5311 individuals and a replication co- expression with observed expression of genes in different chro- hort of 2775 individuals, identified and replicated 103 trans- mosomes. Leveraging the shared cis-acting regulation across eQTLs in whole blood (4). Unlike cis-eQTLs, trans-eQTLs tissues, we combine the evidence of association across all avail- are more likely to be tissue-specific, rather than shared across able GTEx tissues and find 2356 trans-acting/target gene pairs tissues (5). However, even when trans-eQTLs are discovered, with high mappability scores. Reassuringly, trans-acting genes the mechanism by which the SNP acts is not immediately are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor clear. binding sites. Interestingly, trans-acting genes are more signifi- Here, we apply PrediXcan (6) and MultiXcan to map trans- cantly associated with height than target or background genes, acting genes, rather than mapping trans-eQTLs (SNPs). Our consistent with percolating trans effects. Our scripts and sum- method provides directionality, that is, whether the trans- mary statistics are publicly available for future studies of trans- acting gene activates or represses its target gene. We use acting gene regulation. genome-transcriptome data sets from the Framingham Heart Study (FHS) (7), Depression Genes and Networks (DGN) co- gene expression | trans-eQTLs | genetic prediction | complex trait genetics hort (8), and the Genotype-Tissue expression (GTEx) Project (5). We show that our approach, called trans-PrediXcan, can Correspondence: [email protected], [email protected] identify replicable trans-acting regulator/target gene pairs. To leverage sharing of cis-eQTLs across tissues and improve our power to detect more trans-acting effects, we combine predicted expression across tissues in our trans-MulTiXcan model and show that it increases significant trans-acting gene Introduction pairs >10-fold. Transcription is modulated by both proximal genetic varia- Pathway analysis reveals the trans-acting genes are enriched tion (cis-acting), which likely affects DNA regulatory ele- in transcription and nucleic acid binding pathways and tar- ments near the target gene, and distal genetic variation (trans- get genes are enriched in known transcription factor bind- acting), which likely affects regulation of a transcription fac- ing sites, indicating that our method identifies genes of ex- tor (or coactivator) that goes on to regulate a target gene, of- pected function. We show that trans-acting genes are more ten located on a different chromosome from the transcrip- strongly associated with height than target or background tion factor gene. Expression quantitative trait loci (eQTL) genes, demonstrating that trans-acting genes likely play a key mapping has been successful at identifying and replicating role in the biology of complex traits. Wheeler et al. | bioRχiv | November 15, 2018 | 1–10 bioRxiv preprint doi: https://doi.org/10.1101/471748; this version posted November 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Methods Mappability quality control. Genes with mappability scores less than 0.8 and gene pairs with a positive cross- Genome and transcriptome data. mappability k-mer count were excluded from our analysis (17). Gene mappability is computed as the weighted aver- Framingham Heart Study (FHS). We obtained genotype and age of its exon-mappability and untranslated region (UTR)- exon expression array data (7, 9) through application to db- mappability, weights being proportional to the total length of GaP accession phs000007.v29.p1. Genotype imputation and exonic regions and UTRs, respectively. Mappability of a k- gene level quantification were performed by our group previ- mer is computed as 1/(number of positions k-mer maps in the ously (10), leaving 4838 European ancestry individuals with genome). For exonic regions, k = 75 and for UTRs, k = 36. both genotypes and observed gene expression levels for anal- Cross-mappability between two genes, A and B, is defined ysis. We used the Affymetrix power tools (APT) suite to as the number of gene A k-mers (75-mers from exons and perform the preprocessing and normalization steps. First 36-mers from UTRs) whose alignment start within exonic or the robust multi-array analysis (RMA) protocol was applied untranslated regions of gene B (17). which consists of three steps: background correction, quan- In addition, to further guard against false positives, we re- tile normalization, and summarization (11). The summarized trieved RefSeq Gene Summary descriptions from the UCSC expression values were then annotated more fully using the hgFixed database on 2018-10-04 and removed genes from annotation databases contained in the huex10stprobeset.db our analyses with a summary that contained one or more of (exon-level annotations) and huex10sttranscriptcluster.db the following strings: "paralog", "pseudogene", "retro". (gene-level annotations) R packages available from Biocon- ductor. The genotype data were then split by chromo- some and pre-phased with SHAPEIT (12) using the 1000 trans-PrediXcan. In order to map trans-acting regulators of Genomes phase 3 panel and converted to vcf format. These gene expression, we implemented trans-PrediXcan, which files were then submitted to the Michigan Imputation Server consists of two steps. First, we predict gene expression levels (https://imputationserver.sph.umich.edu/start.html) (13, 14) from genotype dosages using models trained in independent for imputation with the Haplotype Reference Consortium cohorts and tissues, as in PrediXcan (6). This step gives us an version 1 panel (15). Approximately 2.5M non-ambiguous estimate of genetic component of gene expression, GReX\ , strand SNPs with MAF > 0.05, imputation R2 > 0.8 and, to for each gene. In the second step, for each GReX\ esti- match GTEx gene expression prediction models, inclusion in mate, we calculate the correlation between GReX\ and the HapMap Phase II were retained for subsequent analyses. observed expression level of each gene located on a differ- ent chromosome. As in Matrix eQTL (18), variables were Depression Genes and Networks (DGN). We obtained geno- standardized to allow fast computation of the correlation and type and whole blood RNA-Seq data through application to test statistic. In the discovery phase, we predicted gene ex- the NIMH Repository and Genomics Resource, Study 88 pression in the FHS cohort using each of 44 tissue mod- (8). For all analyses, we used the HCP (hidden covariates els from the GTEx Project. Significance was assessed via with prior) normalized gene-level expression data used for the Benjamini-Hochberg false discovery rate (FDR) method the trans-eQTL analysis in Battle et al. (8) and downloaded (19), with FDR < 0.05 in each individual
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