A meta-analysis of gene expression quantitative trait loci in brain

Abstract

Current catalogs of brain expression quantitative trait loci (eQTL) are incomplete and the findings do not replicate well across studies. All existing cortical eQTL studies are small and emphasize the need for a meta-analysis. We performed a meta-analysis of 424 brain samples across five studies to identify regulatory variants influencing gene expression in human cortex. We identified 3584 genes in autosomes and chromosome X with false discovery rate q<0.05 whose expression was significantly associated with DNA sequence variation. Consistent with previous eQTL studies, local regulatory variants tended to occur symmetrically around transcription start sites and the effect was more evident in studies with large sample sizes. In contrast to random SNPs, we observed that significant eQTLs were more likely to be near 5'-untranslated regions and intersect with regulatory features. Permutation-based enrichment analysis revealed that SNPs associated with schizophrenia and bipolar disorder were enriched among brain eQTLs. Genes with significant eQTL evidence were also strongly associated with diseases from OMIM (Online Mendelian Inheritance in Man) and the NHGRI (National Human Genome Research Institute) genome-wide association study catalog. Surprisingly, we found that a large proportion (28%) of ~1000 autosomal genes encoding proteins needed for mitochondrial structure or function were eQTLs (enrichment P-value=1.3 × 10⁻⁹), suggesting a potential role for common genetic variation influencing the robustness of energy supply in brain and a possible role in the etiology of some psychiatric disorders. These systematically generated eQTL information should be a valuable resource in determining the functional mechanisms of brain gene expression and the underlying biology of associations with psychiatric disorders.

Introduction

Psychiatric disorders like schizophrenia, bipolar disorder, major depressive disorder, autism and substance use disorders account for a significant proportion of disability world-wide¹ and cause enormous personal and societal burdens.² The lifetime prevalence estimates range from 0.1% (autism spectrum disorder) to 24% (nicotine dependence).³ These disorders have a significant genetic component, with estimates of heritability ranging from 37% (major depressive disorder) to 81% (schizophrenia).³

Recent genome-wide association studies (GWAS) investigating the genetic architecture of psychiatric disorders have identified many common variants that meet consensus criteria for significance and replication.^{4, 5, 6} Understanding the biological mechanisms by which these common variants contribute to complex traits is challenging. The main reason is that the majority (>90%) of disease-associated variants from many GWAS lie in noncoding regions,⁷ making evaluation of their function difficult. However, accumulating evidence suggests that these noncoding common variants are involved in transcriptional regulatory mechanisms such as promoter and enhancer elements⁸ and enriched within expression quantitative trait loci (eQTL).^{8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20} In addition, about 77% of SNPs implicated in GWAS were within or in high linkage disequilibrium (LD) with DNase I hypersensitivity sites, a marker for open chromatin subject to transcriptional regulation.^7,21,22

eQTL studies measure genetic variation and gene expression in the same individuals, and thus link DNA variation to mRNA variation.⁸ These studies have received particular attention due to their inherent relevance to the control of gene expression and because they provide a way to generate hypotheses about the functional meaning of GWAS findings via relatively simple data base queries.^11,23,24

There are relatively few eQTL studies of human brain tissue^{25, 26, 27, 28} or brain disease.^23,29 Current catalogs of brain eQTLs are incomplete and the findings do not replicate well across studies—all existing brain eQTL studies are small and highlight the need for a meta-analysis.³⁰ Thus, we performed an eQTL ‘meta-analysis' of gene expression and GWAS data for 424 normal brain samples from five studies—Gibbs et al.,²⁷ Colantuoni et al.,³¹ Myers et al.,²⁶ Stanley Medical Research Institute (SMRI),^32,33 and the NIH Genotype-Tissue Expression (GTEx) project.³⁴ We identified more than 3000 genes whose expression was significantly associated with DNA sequence variation. Many of these genes have been implicated in psychiatric disorders. Surprisingly, we found that a large proportion (28%) of ~1000 autosomal genes encoding proteins needed for mitochondrial structure or function were eQTLs. This suggests a potential role for common genetic variation influencing the robustness of energy supply in brain and a possible role in the etiology of some psychiatric disorders.

Materials and methods

Gene expression data

The quality control procedures for each study are described in the Supplementary Methods. Briefly, we included brain cortical samples from neuropathologically normal subjects of European ancestry and aged ⩾20 years at death. We downloaded raw intensity files from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) and conducted extensive quality control procedures. As in our prior work, we processed gene expression data as consistently as possible across all studies.^30,35 First, we mapped the probe sequences for all expression arrays to the genome (UCSC hg19) using Bowtie³⁶ and removed probes that did not map, mapped to multiple locations or intersected a polymorphic SNP (HapMap3 (ref. 37) and 1000 Genomes Project data³⁸) because such probes can result in inaccurate expression.³⁹ Second, we excluded outlier samples on the basis of inter-sample correlations³⁰ or if phenotypic sex did not match mean expression of probesets on chrX and chrY. Third, we also used hierarchical clustering (R function hclust) and principal component analysis (PCA) to evaluate overall performance of all arrays. Samples were clustered using the R function hclust with the average link function. The distance function used in clustering was defined as 1-|corr(s1, s2)|, where s1 and s2 refer to the expression profiles of two samples. PCA was conducted using the approach of Price et al.⁴⁰ To combine data from different microarrays, probes (Illumina data) or probesets (Affymetrix data) were linked to the corresponding Entrez gene identifiers from annotation files. We used mean expression if there were multiple probes/probesets for an Entrez gene identifier.

Genotype data

For each study, we excluded samples that were related (π>>0.04), moderate relatedness with many subjects (indicating contamination or poor quality), low call rate (<0.9), inconsistent phenotype-genotype sex and ancestry outliers detected by principal component analysis. We removed SNPs with low call rate (<0.9), low minor allele frequency (MAF <0.01), deviation from Hardy–Weinberg equilibrium (P_HWE <1 × 10⁻⁸), and allele frequencies inconsistent with the 1000 Genomes Project reference panel (MAF difference <0.07). We imputed genotype dosages using the 1000 Genomes Project reference panel using MaCH-admix.⁴¹ MaCH-admix does not require phasing before imputation, which is suitable for small studies. ChrX was imputed in males using the option in MaCH-admix and females were imputed in the same way as autosomes. We retained SNPs with imputation R²⩾0.3 and MAF greater than max (0.05, 5/2N).

Evaluation of covariates

Detailed information about covariate evaluation is in the Supplementary Methods. Briefly, we selected covariates for gene expression in two steps. First, we assessed all covariates by computing the type III sum of squares (SAS, v9.2) that compares a full model containing all covariates to a reduced model excluding the covariate under consideration. The impact of a covariate was quantified by determining the number of genes with a false discovery rate (FDR)⁴² <0.05. We included an ‘impactful' covariate when ⩾1% of genes met this criterion. Second, we regressed out the selected covariates and performed PCA on the residuals. The final covariate list included impactful covariates from the first step and the significant principal components from the second step. For the genotype data from each study, we excluded outliers that fall apart from HapMap3 CEU subjects. Supplementary Figure S1 depicts genotype PC1 versus genotype PC2 of samples in each study together with HapMap3 samples. To determine the genomic PCs that need to be included for adjustment of population stratification, we employed several methods. First, we examined a scree-plot (Supplementary Figure S2) per study, which shows the proportions of total variance in genotype data explained by various PCs. Second, we tested genome-wide association between each PC as a dependent variable and SNPs as independent variables and calculated the genomic inflation factor⁴³ from each association test. Supplementary Figure S3 shows the contribution of each PC to genomic inflation factor. In all studies, PC1 is clearly the major contributor to λ_GC. There are far lesser contributions from PC2-5. Third, we evaluated whether inclusion of PC1 is enough or several more PCs may be needed to control for population substratification. For the latter approach, we included PC1-PC5 in eQTL analysis for each study and meta-analyzed eQTLs explained below. The meta-analysis results from the two approaches were very similar. A scatter plot of t-test statistics from the two approaches showed that the magnitude and direction were almost identical (Supplementary Figure S4, Pearson's correlation=0.98). The clustering pattern of significant local SNP–gene eQTLs near transcription start sites remained the same (Supplementary Figure S11). Number of significant eQTLs at varying FDR thresholds reduced marginally as expected (Supplementary Table S3). We present all tables and figures in the manuscript on the basis of eQTL analysis with genomic PC1.

eQTL analysis

We used MatrixEQTL⁴⁴ to conduct the gene expression linear regression GWAS for each study while controlling for study-specific covariates. We evaluated all ‘local' eQTLs (SNP–gene distance <1  Mb). We did not evaluate ‘distant' eQTLs given the large number of statistical comparisons and consequent low power.³⁰ The local eQTLs for each study were then meta-analyzed using a fixed effects model.⁴⁵ ChrX eQTL analysis was done separately for males and females in each study and then combined using fixed effects meta- analysis, and male and female results combined using Fisher's test.⁴⁶ FDR was used to control for multiple comparisons. FDR was computed separately for chr1-22 and chrX as the P-values were based on different models (t-statistics for autosomes and χ² for chrX). We used sign tests to compare the signs of t-statistics between the five studies. Under the null hypothesis, half of the signs will be the same between two studies. The significance of the observed proportion was evaluated using the binomial distribution.

Enrichment analyses

Common variants identified from GWAS may influence susceptibility to diseases via regulation of gene expression.^8,9 We evaluated this broad hypothesis using enrichment analyses.

First, we assessed whether SNPs associated with psychiatric disorders were enriched among genetic variants that were part of a cortical eQTL (that is, SNP–gene pair) using permutation tests.¹⁰ Specifically, we evaluated the overlap between eQTLs in human cortex with five psychiatric disorders studied by the Psychiatric Genomics Consortium (PGC): attention-deficit hyperactivity disorder, autism, bipolar disorder, major depressive disorder and schizophrenia (SCZ).⁵ We obtained results files from the PGC website (https://pgc.unc.edu/Sharing.php#SharingOpp) from a GWAS meta-analysis of these disorders in independent cases and controls.⁴⁷ There were 1 065 656 GWAS SNPs common to the five PGC results files and our brain eQTL SNPs. We excluded the extended major histocompatibility locus (eMHC, chr6:25–34 Mb) given its high gene density, LD and functionally clustered genes. We compared LD-pruned sets of GWAS SNPs generated via PLINK (—indep-pairwise 100 25 0.8).⁴⁸ For each disorder, we generated 10 000 randomized SNP sets, each the same size as the original list of associated GWAS SNPs at a given P-value threshold matched on MAF distribution of the original list and sampled without replacement from the null set. For each set, we determined the number of significant eQTL SNPs at FDR threshold of 0.05. These permutations yielded an empirical enrichment P-value, calculated as the proportion of 10 000 randomized sets in which the number of eQTL SNPs exceeds the originally observed number of eQTL SNPs at the FDR threshold. We repeated this analysis for a recent larger SCZ GWAS.⁴⁹

Second, we evaluated whether genes that were part of a SNP–gene eQTL in brain were enriched for functional roles in biological pathways or similar cellular functions. We evaluated the following gene sets previously associated with SCZ: expert-curated lists of synaptic genes,⁵⁰ genes encoding postsynaptic density proteins,⁵¹ genes encoding the NMDA (N-methyl-D-aspartate) receptor⁵² and activity-regulated cytoskeleton-associated protein complex,⁵² genes whose mRNAs interact with FMRP,⁵³ genes encoding components of voltage-gated calcium channels (all CACN* RefSeq genes)⁴⁹ and genes whose proteins interact with a calcium channel subunit.⁵⁴ We also evaluated OMIM disease genes,⁵⁵ genes with an eQTL in peripheral blood from the largest human eQTL study,³⁰ and the human orthologs of genes with local eQTLs in mouse brain.⁵⁶ We tested for enrichment using a right-sided Fisher's exact test compared with all 17 537 autosomal genes tested in our meta-analysis and for 9855 brain-expressed genes (defined as mean expression greater than the 25% quantile in three of the five studies in this meta-analysis).

Bioinformatic evaluation

We evaluated whether brain eQTLs were enriched for variants implicated in complex diseases using the NHGRI GWAS catalog (http://www.genome.gov/26525384, downloaded September 2013).⁵⁷ We selected GWAS SNP associations with reported P-values <1 × 10⁻⁹ and keeping the SNP-trait association with the smallest P-value. Many local eQTLs span an extended region containing multiple eQTL SNPs with significant correlation. These are not independent associations but result from high LD between associated eQTL SNPs. We summarized these regions using ‘clumping' (that is, the index eQTL SNP with the strongest association plus the genomic range defined by other eQTL SNPs in high LD with the index SNP) for each significant gene.⁴⁹ We focused on genes with q<0.05 and performed clumping using PLINK to retain eQTL SNPs with r²<0.6 within 500-kb windows (—clump-P1 0.05—clump-P2 0.05—clump-r² 0.6—clump-kb 500). To guard against a falsely inflated intersection rate with the GWAS catalog SNPs, we used q-values rather than P-values as input for clumping and identified GWAS catalog SNPs with reported P-values <1 × 10⁻⁹ that were intersecting the clumped regions.

Results

Meta-analysis of eQTL

We first conducted eQTL analyses for each of the five cortical studies. After quality control, sample sizes ranged from 24 to 189 and the numbers of transcripts ranged from 10 038 to 15 857 per study (17 537 genes evaluated at least one study). Supplementary Figures S5–S9 show plots of gene location versus eQTL location. We defined a local eQTL as an SNP–gene eQTL±1 Mb of the transcription start or end sites for a gene and distant otherwise. As expected, local eQTLs tended to have stronger effects than distant eQTLs. Studies with small sample sizes showed much weaker local eQTLs.

We next conducted a meta-analysis of 424 brain samples across five studies to identify regulatory variants influencing gene expression in human cortex (Table 1). As previous eQTL studies^14,30,35,58 reported that distant eQTLs are usually weaker than local eQTLs, replicate poorly and require considerably larger sample sizes for reliable detection, we restricted our meta-analysis to the detection of local eQTLs. To evaluate the consistency of effects between studies, we performed sign tests between all pairs of studies (Supplementary Table S1). Sign tests were done in two ways: selecting SNP–gene pairs from the first study with P<1 × 10⁻⁵ and evaluating the signs for the same SNP–gene pairs in the second study, and by reversing the procedure. Sign tests for the results of the three studies with N>50 were always highly significant (concordance rates=69–80%, P=1.5 × 10⁻⁷ or smaller). More stringent P-value cutoffs gave similar results. The sign tests indicate the general comparability of the five data sets and also show the dramatic effect of increased sample size.

Table 1. Sample summary.

Study	Subjects	Cortical region	Genes	SNPs	RNA array	DNA array
Colantuoni et al.31	56	Frontal	14 308	7 887 134	IL Human 49 K Oligo array	IL 650 K
Gibbs et al.27	124	Frontal	12 010	7 874 224	IL HumanRef-8	IL 550 K
GTEx	24	Frontal	13 524	7 780 852	RNA-seq (IL HiSeq 2000)	IL Omni 5 M
Myers et al.26	189	Frontal, temporal	15 857	6 391 052	IL HumanRef-8	AF 500 K
SMRI	31	Frontal	10 038	6 779 110	AF HG-U133a	AF 5.0

Abbreviations: AF, Affymetrix; GTEx, Genotype-Tissue Expression project; IL, Illumina; SMRI, Stanley Medical Research Institute; SNP, single-nucleotide polymorphism.

Number of European-ancestry subjects aged ⩾20 after quality control.

The number of eQTLs at varying FDR thresholds is summarized in Supplementary Table S2. We used a standard FDR threshold <0.05 throughout the paper. At this threshold, there were 176 794 significant autosomal SNP–gene pairs arising from 159 151 SNPs and 3520 genes. This includes more SNP–gene pairs than that found in individual studies (Table 2). As expected, we detected more eQTLs from studies with larger sample sizes. Figure 1a shows distribution of q-values for the most significant association for each gene in autosomes and chromosome X. Figure 1b depicts a Manhattan plot for the primary results, showing the q-value of the most significant SNP for each of 17 546 autosomal genes and 650 genes tested on chrX. The most significant association was in CRYBB2 (rs997872, q=1.75 × 10⁻³⁸). CRYBB2 encodes βB2-crystallin, which is a structural protein in the ocular lens,⁵⁹ but recent studies demonstrated that this gene is expressed in several regions of the mammalian brain⁶⁰ and βB2-crystallin has a role in hippocampal function and behavioral phenotypes.⁵⁹ The second most significant signal was for CHURC1 (churchill domain containing protein 1; rs10131002, q=1.18 × 10⁻³⁰). A prior study⁶¹ identified CHURC1 as a potential candidate gene for autism. Another top association signal was for NSUN2 (rs567289, q=1.94 × 10⁻²³) which encodes a tRNA methyltransferase and causes an autosomal form of mental retardation (OMIM 611091).^62,63

Table 2. Summary of meta-analysis results in autosomes (q<0.05).

Study	SNP–gene eQTL pairs	Unique SNPs	Unique genes	Genes overlapping with meta-analysis
Colantuoni et al.31	10 792	10 767	364	250 (7%)
Gibbs et al.27	110 541	103 099	2101	1279 (36%)
GTEx	0	0	0	0 (0%)
Myers et al.26	67 534	63 768	1308	864 (25%)
SMRI	1018	1018	42	22 (1%)
Meta-analysis	176 794	159 151	3520	3520 (100%)

Abbreviations: GTEx, Genotype-Tissue Expression project; SMRI, Stanley Medical Research Institute; SNP, single-nucleotide polymorphism.

Overlapping genes compare an individual study to the 3520 genes with q<0.05 in the meta-analysis.

Figure 1.

Distribution of q-values and Manhattan plot. (a) Distribution of q-values for the most significant association for each gene in autosomes and chromosome X. Red dotted line denotes q-value of 0.05. (b) Manhattan plot of −log10(q) for the most significant association for each of 17 546 autosomal genes and 650 genes in chromosome X. Genes with −log10(q) >20 are highlighted. Red dotted line denotes q=0.05.

The X chromosome is enriched for genes important in brain development, mental retardation and intellectual disability.^{64, 65, 66, 67, 68} Of 650 chrX genes, there were 1486 significant SNP–gene pairs arising from 1321 SNPs and 64 genes (Figure 1b). Comparison of significant eQTL genes with OMIM revealed that several genes previously implicated in mental retardation showed association signals from sex-combined analysis: OPHN1 (OMIM 300127, q=0.004 with rs618306 ), ARHGEF6 (OMIM 300267, q=0.005 with rs150810369), ACSL4 (OMIM 300157, q=0.01 with X:108198176), SRPX2 (OMIM 300642, q=0.03 with rs35728723), IGBP1 (OMIM 300139, q=0.03 with rs12846068), IL1RAPL1 (OMIM 300206, q=0.04 with rs7471803).

We next asked whether there are genomic regions with unusually higher or lower numbers of eQTLs. We evaluated the relationship between the numbers of genes and eQTLs within each 1 Mb interval of the genome. The MHC region (chr6:31–33 Mb) showed more significant genes than expected (41 of 93 genes were significant eQTLs). On the other hand, none of the 32 genes in chr1:152–153 Mb was an eQTL. This region contains a cluster of late cornified envelope genes, which are specifically expressed in skin.

Characteristics of local SNPs

We examined functional consequences of significant SNPs with q<0.05 (143 679 unique SNPs) using the Ensembl Variant Effect Predictor (VEP) tool.⁶⁹ VEP reports a set of consequence terms defined by the Sequence Ontology (http://www.sequenceontology.org). Detailed information can be found at http://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences. We used options (--most_severe, --per_gene) to output only the most severe consequence per gene. If a gene has multiple transcripts, an SNP was assigned to the transcript with the most severe predicted consequence. If more than one transcript has the same predicted consequence, VEP tool selected the transcript at random. Most significant SNPs were intronic (65.9%) followed by intergenic (14.6%), or upstream (7.1%) or downstream (5.8%) of protein coding sequence. Notably, only a small number of SNPs were exonic (2.0%). As shown in Figure 2a, SNPs in the 5'-untranslated region had the highest overlap with regulatory features (69.4%), and intergenic SNPs had the lowest overlap (10.6%). The overall proportion of variants in a regulatory feature was 13.6%. Next, we asked whether similar functional consequences could be observed from nonsignificant SNPs. We randomly selected the same number (143 679) of MAF-matched SNPs from SNP–gene pairs with q>0.5 and repeated the procedure (Figure 2b). Similar to the significant eQTL SNPs, most of the nonsignificant SNPs were intronic (50.1%), followed by intergenic (39.3%), upstream (4.4%), downstream (3.8%) and exonic regions (0.6%). Notably, the percentage of SNPs in intergenic regions increased by 25%. SNPs in the 5'-untranslated region again had the highest rate (63.8%) of overlap with regulatory features and SNPs in intergenic regions had the lowest rate (6.7%) of overlapping with regulatory features. The overall proportion of variants that fall in a regulatory feature was lower (9.2%) than the set of significant SNPs.

Figure 2.

Predicted functional consequences of local eQTL SNPs. (a) Functional consequences of significant eQTLs (q<0.05, 143 679 unique SNPs) using Ensembl Variant Effect Predictor tool. Each SNP was assigned to the most severe predicted consequence. The ratio on each bar represents number of SNPs with regulatory features divided by number of SNPs in each functional category. (b) Functional consequences of randomly selected, MAF-matched, insignificant eQTLs (q>0.5, 143 679 unique SNPs). eQTL, expression quantitative trait loci; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.

We evaluated whether there were significant differences between the classifications of significant and randomly selected nonsignificant eQTL SNPs. The overall distributions were significantly different between the two sets of SNPs (χ² P<1 × 10⁻⁴). Each functional consequence relative to intergenic also revealed significant difference between the two sets of SNPs (Supplementary Table S4). Odds ratios ranged from 3.5 to 9.2 and all P-values were <1 × 10⁻⁴. SNPs in 5'-untranslated region showed the largest difference and were 9.2 times more likely to be significant eQTLs.

Prior studies observed clustering of significant local SNP–gene eQTLs near transcription start sites.^{11,26,30,70,71} We replicated this pattern (Supplementary Figure S10) which was more evident in the studies with larger samples.

Brain eQTLs and psychiatric disorders

We evaluated enrichment of brain eQTLs in regard to SNPs associated with five psychiatric disorders studied by the PGC and a recent larger SCZ GWAS (Table 3). As shown in prior studies,⁴⁷ SNPs associated with SCZ and bipolar disorder showed highly significant enrichments for eQTLs. This enrichment in brain eQTLs remained significant regardless of different statistical cutoffs used to generate the SNPs of interest. SNPs associated with attention-deficit hyperactivity disorder, autism and major depressive disorder showed much less enrichment in eQTLs, possibly owing to smaller sample sizes and fewer significant SNPs in the GWAS results.

Table 3. eQTL enrichment analysis of LD-pruned SNPs from PGC GWAS meta-analyses.

GWAS threshold	PGC autism	PGC ADHD	PGC bipolar	PGC MDD	PGC SCZ	Sweden SCZ
P<0.0001	6 (6e−4)	0 (1.0)	9 (2e−4)	0 (1.0)	9 (0.0047)	86 (<1e−4)
P<0.01	91 (0.11)	61 (0.89)	153 (<1e−4)	78 (0.40)	165 (<1e−4)	816 (<1e−4)
P<0.1	719 (0.141)	630 (0.88)	580 (<1e−4)	756 (0.0075)	982 (<1e−4)	3639 (<1e−4)

Abbreviations: ADHD, attention-deficit hyperactivity disorder; eQTL, expression quantitative trait loci; GWAS, genome-wide association study; LD, linkage disequilibrium; MDD, major depressive disorder; PGC, Psychiatric Genomics Consortium; SCZ, schizophrenia; SNP, single-nucleotide polymorphism.

eQTL SNPs with q<0.05 were used for enrichment tests. Each cell gives the number of overlapping SNPs between eQTL SNPs and SNPs at the given threshold for a GWAS data set. The parentheses are empirical P-values obtained after 10 000 permutations with ‘<1e−4' meaning that none of 10 000 simulations yielded an eQTL count greater than the observed count. Due to high LD, the extended MHC region (chr6: 25–34 Mb) was removed. The first five data sets were imputed to HapMap3, and the rightmost column to 1000 Genomes and so the numbers of overlapping SNPs are greater.

To complement the permutation-based enrichment tests, we also applied the Bayesian framework implemented in SHERLOCK⁷² to the Sweden SCZ GWAS results.⁴⁹ Briefly, SHERLOCK aligns the genetic architecture of SCZ against eQTL results to evaluate overlap and to summarize the evidence that a given SNP supports a functional role for the gene. A gene showing a high positive Bayes factor supports the evidence that it is more likely to be associated with SCZ via transcriptional regulation. Supplementary Table S5 lists the top predicted genes and their supporting SNPs of SCZ that meet logarithm Bayes factor >4.0 (that is, the posterior probability of the gene being associated with SCZ is >e⁴ or >55 times more likely). Among 27 predicted genes with logarithm Bayes factor >4.0 (Supplementary Table S5), many are associated with SCZ as expected and also in regions known to be associated with bipolar disorder (ITIH4, GLT8D1, GNL3, NEK4), five major psychiatric disorders (FTSJ2, PCGEM1, C10orf32) and Parkinson's disease (C10orf32). Some of these genes were in high LD regions (for example, chr10:104.5–105.2 Mb and chr3:52.2–53.2 Mb, Supplementary Figures S12 and S13).

Gene set enrichment

Genomic studies of SCZ have implicated biological pathways using multiple types of genomic data (common variation, rare CNVs and rare exonic variation).^{49,50,52,73,74} We asked whether genes in significant SNP–gene eQTLs in human cortex were enriched for pathways previously implicated in SCZ. Table 4 summarizes the results of enrichment tests using the gene sets selected from the literature. In either all genes or brain-expressed genes, we did not observe enrichment of eQTL genes among any gene sets hypothesized to be associated with SCZ.

Table 4. Enrichment test of eQTL genes (q<0.05) in gene sets.

Gene set	Genes	Overlap	OR1 (P)	OR2 (P)
Implicated in schizophrenia
FMRP interactor53	780	125	0.75 (0.99)	0.72 (0.99)
Synaptic functional gene group50	947	170	0.86 (0.96)	0.82 (0.98)
Synaptic signaling pathways50	121	29	1.26 (0.17)	1.28 (0.18)
Calcium channel subunit interactor54	189	28	0.69 (0.98)	0.68 (0.97)
Calcium subunit49	24	4	0.80 (0.74)	0.62 (0.83)
Postsynaptic genes51	687	113	0.78 (0.99)	0.68 (0.99)
NMDA receptor52	58	9	0.73 (0.85)	0.65 (0.91)
ARC52	24	2	0.36 (0.97)	0.31 (0.98)
Other gene sets
Nuclear-encoded mitochondrial genes75	914	257	1.60 (1.3 × 10−9)	1.39 (1.0 × 10−4)
Oxidative phosphorylation genes76	88	24	1.50 (0.06)	1.41 (0.11)
Nuclear regulators of mitochondria genes76	14	2	0.66 (0.80)	0.31 (0.95)
OMIM55	2914	609	1.06 (0.12)	1.15 (0.009)
‘godot' eQTL study in blood (q<0.001)30	6662	1578	1.43 (9.4 × 10−21)	1.36 (6.9 × 10−11)
Significant strain effect in mouse brain diallel56	9534	1986	1.11 (0.003)	0.90 (0.98)

Abbreviations: ARC, activity-regulated cytoskeleton; eQTL, expression quantitative trait loci; NMDA, N-methyl-D-aspartate; OMIM, Online Mendelian Inheritance in Man.

For enrichment tests, we used 3520 eQTL genes in autosomes with false discovery rate (FDR) q<0.05. OR1 is odds ratio using all tested autosomal genes (17 537), and OR2 is odds ratio using brain-expressed, autosomal genes (9855). P-values are from right-sided Fisher's exact tests.

We conducted a series of enrichment analyses with the list of genes with significant eQTL evidence (Table 4). First, using functional annotation clustering in DAVID,⁷⁷ genes with eQTL evidence were very significantly enriched (Fisher's exact test P-value=3.24 × 10⁻⁹) for GO gene sets related to multiple mitochondrial gene sets (Supplementary Table S6). To adjust for common biases due to gene size, LD within and between genes, and pathway sizes, we generated a set of independent, nominally associated genomic intervals using clumping implemented in PLINK and then tested it for enrichment in GO gene sets using InRich.⁷⁸ Analysis was restricted to 4074 GO categories containing genes between 5 and 3000 to account for pathway sizes. We used permutation to get empirical P-values per pathway and to correct for multiple-testing. Multiple GO pathways related to mitochondrial structure and function were ranked as top pathways (Supplementary Table S7). This result is consistent with the DAVID results, indicating that mitochondrial pathways are robust findings regardless of different gene-set enrichment methods. We tested for enrichment in mitochondrial pathways by further analyses using nuclear-encoded mitochondrial genes from MitoCarta (http://www.broadinstitute.org/pubs/MitoCarta),⁷⁵ autosomal oxidative phosphorylation genes,⁷⁶ and nuclear-encoded transcriptional regulators of mitochondrial genes.^76,79 Of 914 nuclear-encoded mitochondrial genes, 257 genes (28%) overlapped with genes showing significant eQTL evidence. We observed strong enrichment of significant eQTL genes in autosomal mitochondrial genes (odds ratio=1.60, P=1.3 × 10⁻⁹ using all genes; odds ratio=1.39, P=1.0 × 10⁻⁴ using brain-expressed genes). However, no enrichment was observed for nuclear regulators of mitochondrial genes (P=0.80 using all genes, P=0.95 using brain-expressed genes) and oxidative phosphorylation genes (P=0.06 using all genes, P=0.11 using brain-expressed genes).

Second, genes expressed in multiple tissues tend to have local regulatory elements.⁸⁰ To evaluate the hypothesis, we compared eQTL genes in peripheral blood³⁰ with genes having local eQTLs in our meta-analysis. We found strong overlap between eQTLs in these two tissues. Of 6662 genes with significant local eQTL evidence in peripheral blood (q<0.001), 1578 genes (24%) overlapped with genes with local eQTL evidence in brain (odds ratio=1.43, P=9.4 × 10⁻²¹ using all genes). Restricting to 5261 genes expressed in both tissues, 70.7% of 1193 eQTL genes in brain were eQTL genes in blood (Supplementary Figure S14).

Third, gene regulation might be conserved across species. We compared our brain eQTL genes with their mouse orthologs with local eQTL evidence in a carefully conducted brain RNA-seq study. The enrichment of human brain eQTLs in genes from mouse brain samples was significant (odds ratio=1.11, P=0.003).⁵⁶

Brain eQTLs, GWAS and OMIM

To assess the biological relevance of brain eQTLs for annotation of variants implicated in human diseases, we compared unique SNPs in autosomes and chrX (after filtering at q<0.05 and keeping the SNP with the smallest q-value if there were multiple SNP–gene pairs) to the NHGRI GWAS catalog.⁵⁷ We restricted our search to GWAS SNPs with P<1 × 10⁻⁹, yielding 2946 SNPs for 471 traits from 869 papers. Of the 2946 SNPs implicated by GWAS, 528 (17.9%) were part of a local eQTL (178 directly associated with 94 traits and 350 SNPs indirectly via a proxy SNP with r²>0.2). The 10 most frequent traits were height (12 SNPs), inflammatory bowel disease (11), Crohn's disease (9), plasma phospholipid levels (6), total cholesterol (5), chronic kidney disease (4), coronary heart disease (4), HDL cholesterol (4), metabolite levels (4) and red blood cell traits (4). We evaluated brain eQTLs that overlap with the SNPs associated with central nervous system-related phenotypes (Table 5), and identified overlap with bipolar disorder, Parkinson's disease and nicotine dependence.

Table 5. eQTL SNP clumping regions and brain diseases from the NHGRI GWAS catalog.

Region	eQTL SNPs	Index eQTL SNP	eQTL SNP q	Gene	Disease	PMID	GWAS SNP	GWAS P	Other genes
chr2:97351561–97476219	84	rs62152787	0.002058	CNNM4	BIP	22182935	rs2271893	2E−10	hsa-mir-3127, MIR3127, LMAN2L, FER1L5, CNNM4
chr3:52214610–52529899	106	rs9863753	1.9E−6	STAB1	BIP	22182935	rs7618915	3E−10	hsa-mir-135a-1, hsa-let7g, WDR82, TWF2, TNNC1, TLR9, STAB1, SEMA3G, PPM1M, PHF7, NISCH, MIRLET7G, MIR135A1, GLYCTK, DNAH1, BAP1, ALAS1
chr3:52537969–52898427	42	rs11712872	2.92E−12	ITIH3	AUT, ADHD, BIP, MDD, SCZ	23453885	rs2535629	3E−12	TMEM110-MUSTN1, TMEM110, STAB1, SPCS1, SNORD69, SNORD19B, SNORD19, PBRM1, NT5DC2, NEK4, MUSTN1, ITIH3, ITIH4, ITIH1, HBII-210, HBII108B, HBII108, GNL3, GLT8D1, C3orf78
chr6:28162780–28239681	12	rs1531681	0.008303	NKAPL	SCZ	22037552	rs1635	7E−12	chr6.tRNA62- SerGCT, ZNF193, ZNF187, ZKSCAN4, NKAPL, LOC222699
chr15:78808235–78926018	121	rs12902493	0.000168	AGPHD1	ND	18385739	rs1051730	6E−20	PSMA4, CHRNB4, CHRNA5, CHRNA3, AGPHD1
chr17:43543075–43848638	2	17_43543075	4.64E−9	PLEKHM1	PD	21292315	rs2942168	1E−28	hsa-mir-4315-1, PLEKHM1, MIR4315-1, MIR4315-2, MGC57346, LRRC37A4, LOC644172, CRHR1, C17orf69
chr17:43848412–43931907	277	rs116853553	1.03E−8	CRHR1	PD	21738487	rs12185268	3E−14	LOC100128977, IMP5, CRHR1
chr17:44762589–44865603	74	rs199448	8.23E−9	NSF	PD	19915575	rs199533	1E−14	WNT3, NSF

Abbreviations: ADHD, attention-deficit hyperactivity disorder; AUT, autism; BIP, bipolar disorder; eQTL, expression quantitative trait loci; GWAS, genome-wide association study; MDD, major depressive disorder; ND, nicotine dependence; NHGRI, National Human Genome Research Institute; PD, Parkinson's disease; SCZ, schizophrenia; SNP, single-nucleotide polymorphism.

The ‘Gene' column refers to the gene in which an index eQTL SNP was located. ‘Other genes' column shows other named genes in the genomic interval. This table includes GWAS SNP associations with reported P-values <1 × 10⁻⁹ from the NHGRI GWAS catalog and keeping the GWAS SNP-trait association with the smallest P-value. The extended MHC region (chr6:25–34 Mb) was excluded.

We compared our eQTL genes to OMIM⁵⁵ which catalogs genes often containing rare variation with strong effects. We observed significant enrichment of genes with significant brain eQTL evidence in OMIM disease genes (odds ratio=1.15, P=0.009). Mitochondrial complex I deficiency and Leigh syndrome were the second most frequent diseases in our data (FOXRED1, NDUFA2, NDUFA10, NDUFAF1, NDUFAF2, NDUFAF4 and NDUFS2).

Protein–protein interaction

We used DAPPLE⁸¹ to evaluate whether genes with strong evidence of local eQTLs connected via protein–protein interactions. Genes with evidence of local eQTLs showed somewhat higher network connectivity (direct P=0.04 and indirect P=0.01). However, many of these genes were in small networks rather than a single network, suggesting that there is no a dominant functional network related to all these genes (Supplementary Figure S15).

Discussion

We performed a meta-analysis of local regulatory variation of 424 postmortem brain samples from five human brain eQTL studies. Our analysis of local eQTLs in this relatively large sample size allowed us to identify more eQTLs than those from individual studies.

Consistent with prior findings, we observed that local regulatory variants tend to occur symmetrically around transcription start sites, and effect was more evident in studies with large sample sizes. Significant eQTLs tended to be near 5'-untranslated regions and intersect with regulatory features. In accordance with previous eQTL studies showing that eQTLs are more likely to overlap with SNPs implicated in GWAS,¹⁰ we observed that SNPs associated with SCZ and bipolar disorder were enriched among brain eQTLs. Many brain eQTLs are also associated with central nervous system-related diseases (Table 5).

We compared our results with previous findings from the literature. Myers et al.²⁶ and Liu et al.²⁸ reported significant associations between RPS26 and rs11171739 in prefrontal cortex. Cheung et al.⁸² reported a significant association between RPS26 and rs2271194 (in high LD with rs11171739) in lymphoblastoid cells. We observed strong associations for both RPS26–rs11171739 (q=7.7 × 10⁻¹¹) and RPS26–rs2271194 (q=1.3 × 10⁻¹⁰). Another eQTL study of human liver identified a significant RPS26 and rs2292239 relationship and suggested RPS26 as a candidate susceptibility gene for type 1 diabetes.⁸³ We observed a strong correlation for the RPS26–rs2292239 pair (q=5 × 10⁻⁵) as well.

There are expression variants that are specific to tissues, cells, anatomical regions and diseases.^14,34 However, the substantial overlap (24%) between eQTLs from the largest eQTL study in peripheral blood³⁰ and eQTLs in brain implies that there are many local regulatory variants showing more ubiquitous effects independent of tissue types. Indeed, sample size is a key factor in replicating findings within and between tissues³⁰ may be the most important factor of successful eQTL mapping. Another study that examined eQTLs in blood, adipose tissue and liver reported that about 30% of local eQTLs overlap in those three tissues, suggesting that there are shared expression control mechanisms between tissues.⁸³

We identified a significant number of brain eQTLs that influence the expression of nuclear-encoded genes involved in mitochondrial function and strong evidence of functional clusters related to mitochondrial function (for example, nuclear-encoded mitochondrial genes, P=1.3 × 10⁻⁹). Moreover, mitochondrial complex I deficiency genes involved in local eQTL were a frequent overlap. This raises an intriguing possibility, that common genetic variation influences the expression of sets of autosomal genes that influence the number and/or function of mitochondria. Nuclear-encoded autosomal genes (~1000 based on MitoCarta⁷⁵) and mitochondrial-encoded genes (13 genes in human⁸⁴) are involved in ATP synthesis, cellular energy metabolism and oxidative phosphorylation, as well as regulation of cellular calcium levels, steroid synthesis, production of free radicals and regulation of apoptosis.⁸⁵ The central nervous system has a very high metabolic rate because neurons require large amounts of ATP for maintenance of ionic gradients across the cell membranes and for neurotransmission. Neuronal function and survival depend critically on mitochondrial function and oxygen supply.⁸⁶ Thus, it is conceivable that minor deviations from normal mitochondria functioning can have devastating consequences on the integrity of cells and influence a variety of diseases, including aging,⁸⁷ cancer,⁸⁸ metabolic traits,⁸⁹ neurodegenerative diseases⁸⁵ and psychiatric disorders.^90,91

Although most patients with psychiatric disorders do not have classical mitochondrial diseases caused by mutations of nuclear or mitochondrial DNA, multiple lines of evidences support that impairment in any processes related to normal mitochondria function may be critical in neurobiology of psychiatric disorders.^85,91 A study of large, rare CNVs in SCZ observed significant enrichment in gene products localized to mitochondria.⁹² Impaired neuronal differentiation in hair follicle-derived induced pluripotent stem cells from SCZ cases is associated with mitochondrial dysfunction.⁹³ A recent meta-analysis of autism spectrum disorders suggests an association with mitochondrial dysfunction.⁹⁴ Mutations and deletions in mitochondrial DNA have been reported to be associated with mood disorders and bipolar disorder.^95,96 Postmortem brain samples of bipolar disorder cases showed a pronounced decrease in the expression of nuclear genes regulating oxidative phosphorylation.⁹⁷ Taken together, gene pathways or networks involving mitochondria function may have an etiological role for some psychiatric disorders.

There are several limitations of this study. First, more data are required. Our sample size was less than that required for confident local eQTL identification.³⁰ Second, this investigation included only normal adult brain samples. Inclusion of data from cases with psychiatric disorders or from earlier developmental stages would likely be informative. Third, although consistent quality control steps were applied, different DNA and RNA platforms across studies may have impacted our findings. To evaluate the impact of between-study heterogeneity, we performed a random-effect meta-analysis using ‘REML' method in metaphor R package (Supplementary File, http://cran.r-project.org/web/packages/metafor/index.html). We observed that the P-values from random-effect model tend to be larger than fixed-effect model. This is not surprising since fixed-effect models are known to produce tighter confidence intervals and more significant P-values than random-effect models in the presence of between-study heterogeneity.^{98, 99, 100} The genomic control inflation factors for the fixed-effect and random-effect analyses were 1.08 and 0.87, respectively. Top signals from random-effect model and fixed-effect model were quite different. Many significant SNP–gene pairs from fixed-effect model became nonsignificant via random-effect model.¹⁰¹ Small sample sizes, different expression platforms and unknown differences across our studies could possibly introduce such a large variation in effect sizes and thus inflated between-study heterogeneity. We need to be more cautious about interpretation of the fixed-effect results. On the other hand, there can be a large uncertainty in meta-analysis about the presence and the extent of between-study heterogeneity with limited number of studies. It was pointed out that strong inferences about heterogeneity or lack thereof should be avoided.⁹⁸ Finally, analysis of postmortem human brain tissues face many challenges as we cannot fully control for all potential confounders that might have impacted the integrity of brain expression assessment (for example, antemortem history, medication use, licit or illicit substance use disorders, cause of death or postmortem delay).

Despite these limitations, the eQTLs and pathways identified in this investigation warrant further exploration as potential candidates involved in pathogenesis of psychiatric disorders. Annotating SNPs identified from GWAS of psychiatric disorders with brain eQTL information will be a valuable resource to characterize the functions of causal variants and generate testable hypotheses for the mechanism underlying GWAS findings.

Dr Sullivan was on the SAB of Expression Analysis (Durham, NC, USA). The remaining authors declare no conflict of interest.