Discovery and reproducibility of sparse components enriched for disease heritability.

(A) Heat map of known covariates and correlation with individual scores from each of the 500 components (left) and 56 sparse components (right) in FF data. (B) Heat map of condition specificity scores for the sparse components in FF data. Each row is a stimulation (naïve, LPS, or IFN) and each column is a sparse component. (C) Component replication between component 282 (CG) and component 337 (FF LPS24) for the most highly scored genes. The gene scores from the two components (in CG and FF) are highly correlated. (D) Proportion of heritability for 18 selected complex traits that can be attributed to each sparse component from the FF data. Shown here are enrichment statistics (with standard error) comparing the proportion of SNP heritability within the components divided by the proportion of total SNPs represented at FDR-corrected P < 0.05. (E) Gene Ontology (GO) enrichment for genes in component 61 and 22. AD: Alzheimer’s disease; PD: Parkinson’s disease; AUT: Autism; MS: Multiple Sclerosis; SCZ: Schizophrenia; T2D: Type 2 Diabetes; LUP: Lupus; PBC; Primary Biliary Cirrhosis; RA: Rheumatoid Arthritis; IBD: Inflammatory Bowel Disease; CRN: Crohn’s Disease; CEL: Celiac Disease; UC: Ulcerative Colitis; HDL: High-density lipoprotein Cholesterol; LDL: Low-density lipoprotein Cholesterol; BMI: Body Mass Index; CAD: Coronary Artery Disease; HGT: Height.</p

<i>MAPT</i> exons 2 and 10 show unique changes in splicing with development.

Volcano plot of p-value and fold change comparing antenatal and postnatal cases by Student’s t-test using Bonferroni correction for multiple comparisons. Triangles indicate gene level data, circles exon level. Vertical line indicates 1.5-fold change, horizontal line threshold of significance.</p

qPCR on human fetal and adult cortex demonstrating shift towards 1N and 4R tau during development.

<p>Taqman primers for <b>A</b>, 0N, <b>B</b>, 1N, <b>C</b>, 2N and, <b>D</b>, 4R tau were used with normalization to GAPDH and total tau. P-values using Mann-Whitney test.</p

Structure of the <i>MAPT</i> gene and protein.

Alternative splicing of MAPT produces six canonical isoforms. grey = constitutive exons, white = not expressed in human central nervous system.</p

Overview of the study design and method.

(A) The gene expression datasets used in this study. Stimulated monocyte gene expression profiles from Fairfax et al. [12] in four conditions: response to lipopolysaccharide at 24 hours (LPS24) and at 2 hours (LPS2), interferon-γ (IFN-γ), and naive (left panel). Peripheral blood monocytes (MP) and macrophages (MC) from the Cardiogenics Consortium (right panel). (B) Overview of the SDA approach. An illustration of decomposition of gene expression datasets to yield component vectors for relative contribution of each individual, gene and condition. The individual scores matrices are then used as phenotypes with SNP genotypes in order to identify genetic variation correlated with the components (top). The stimulation or cell-activity scores matrix is used to identify the contribution of each condition for the components (middle). The gene scores matrix is used to identify the contribution of each gene within the components (bottom).</p

0N3R is the predominant tau proteoform in human fetal cortex.

<p><b>A</b>, Immunoblots with fetal and adult brain homogenates were probed with antisera to total tau (HT7). <b>B</b>, Treatment of the fetal brain homogenates with phosphatase resolves the banding pattern to a single species with similar electrophoretic mobility to the 0N3R tau in the protein ladder. Molecular weights are indicated in kDa after each isoform.</p

<i>Trans</i>-eQTLs colocalized in disease or trait-associated GWAS loci.

(A) Significant trans-eQTLs in FF data (FDR trans-eSNP on Y-axis and trans-eQTL components on X-axis. The red colored boxes reflect the effect size for the trans-eQTLs while the horizontal colored header reflects the condition activity scores. Trans-eQTLs that are in Alzheimer’s or Parkinson’s disease-associated loci (right panel). Alzheimer’s disease includes GWAS susceptibility loci from Alzheimer’s related traits including the age of onset, age-related cognitive decline, and APOE ε4 carriers. (B) Colocalization of trans-eQTLs at Parkinson’s disease susceptibility locus CTSB (left panel) and Alzheimer’s disease-associated loci MS4A4A (middle panel) and CLU (right panel). The x-axis in each panel shows the physical position on the chromosome (Mb). The y-axis shows the -log10(P) association p-values for Parkinson’s disease [23–24] (left panel) and Alzheimer’s disease GWAS [20–22] (middle and right panels). Listed on top are ‘coloc’ posterior probability for hypothesis 3 (PP.H3) and 4 (PP.H4). PP.H3: Association with eQTL and GWAS, two independent causal SNPs. PP.H4: Association with eQTL and GWAS, one shared SNP. (C) Transcription factors whose binding sites occurrence is enriched in the target set of genes within each sparse component compared to the expected occurrence estimated from a background set.</p

Immature regions show lower expression of <i>MAPT</i> and exon 10.

<p><b><i>A</i>,</b> Regional and temporal variation in <i>MAPT</i> expression, <b><i>B</i>,</b> exon 2 splicing, <b><i>C</i></b>, exon 3 splicing and <b><i>D</i>,</b> exon 10 splicing. *Region with p<0.05 by generalized linear model including age, region, sex and RIN score as covariates, Bonferroni’s correction for multiple comparisons. ⁺Reference region. <i>CGE</i> caudal ganglionic eminence, <i>DIE</i> diencephalon, <i>DTH</i> dorsal thalamus, <i>FC</i> frontal cerebral wall, <i>LGE</i> lateral ganglionic eminence, <i>MGE</i> medial ganglionic eminence, <i>OC</i> occipital cerebral wall, <i>PC</i> parietal cerebral wall, <i>TC</i> temporal cerebral wall, <i>URL</i> upper rhombic lip, <i>VF</i> ventral forebrain, <i>A1C</i> primary auditory cortex, <i>AMY</i> amygdala, <i>CBC</i> cerebellar cortex, <i>DFC</i> dorsolateral prefrontal cortex, <i>HIP</i> hippocampus, <i>ITC</i> inferior temporal cortex, <i>M1C</i> primary motor cortex, <i>MD</i> mediodorsal nucleus of the thalamus, <i>MFC</i> medial prefrontal cortex, <i>OFC</i> orbital prefrontal cortex, <i>S1C</i> primary sensory cortex, <i>STC</i> superior temporal cortex, <i>STR</i> striatum, <i>V1C</i> primary visual cortex, <i>VFC</i> ventrolateral prefrontal cortex, regions are defined in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195771#pone.0195771.ref027" target="_blank">27</a>].</p

Macrophage-specific <i>trans</i>-eQTL colocalized in Parkinson’s disease associated CTSB locus.

(A) The genotype for Parkinson’s disease susceptibility allele rs1296028 is significantly associated with the individual scores of CG component 46. The rs1296028 affects the expression of 16 genes in component 46 in macrophage (CG) (left panel). Tissue specificity scores suggest CG component 46 is active in macrophage (Right). P-value: ***: trans-eGenes with PIP > 0.5 and 2.5% distributional cut-off (green dotted line) are shown. Trans-eQTL associations that replicated (FDR CTSB). The beta coefficients from Mendelian randomization analysis are shown for the significant trans-eGenes. (D) Experimental validation using THP-1 derived macrophages. CTSB was knocked-down using siRNA during 48 h and the levels of the top-scoring genes in the component were measured by qPCR. Data was normalized against scramble siRNA (SCR). P-value: *: <0.05 | ***: <0.001.</p

<i>Trans</i>-eQTL colocalized in Alzheimer’s disease associated <i>MS4A</i> locus.

(A) The genotypes for Alzheimer’s disease susceptibility allele rs983392 are significantly associated with the individual scores of component 26. rs983392 is trans-eQTL to FF component 26 with 54 genes (left panel). The component 26 is active only at baseline (right panel). (B) Circular plot demonstrating the chromosomal position of trans-eSNP (rs983392) and the 54 trans target genes. The minor and AD-protective allele rs983392-G is associated with decreased (blue lines) and increased (red lines) expression of trans-eGenes. The colored dots are trans-eQTL that replicates in ImmVar baseline monocytes (red and yellow color dots denote trans-eQTL association at FDR trans-eGenes with PIP > 0.5 and 2.5% distributional cut-off are shown. (C) Alzheimer’s disease SNP rs983392 mediates trans-effects to two trans-eGenes through cis-mediator MS4A4A. (D) Experimental validation using THP-1 derived macrophages. MS4A4A was knock-down using siRNA for 48 h, IFNg 20 ng/ml was added during the last 24 h. The levels of the top-scoring genes in the component were measured by qPCR. Data was normalized against scramble siRNA (SCR). P-value: *: <0.05 | **: <0.01 | ***:<0.001 vs SCR. ##: <0.01 vs siMS4A4A. (N = 5 independent experiments).</p