Figures and data
Overview of the multi-omics protocol for analyzing frontal cortex of schizophrenia subjects and controls.
(A) Overview of the experimental design starting from postmortem human frontal cortex samples to generate cell type-specific H3K27ac, H3K4me3 and RNA profiles.
(B) Heatmap of the expression of neuronal and glial cell markers across all NeuN+ and NeuN- frontal cortex samples from 29 control subjects and 29 schizophrenia subjects.
Comparison of epigenomic and transcriptomic landscapes in the frontal cortex of schizophrenia subjects and controls.
(A) Differential enhancer/promoter peaks and DEGs obtained by comparing schizophrenia (n = 29) and controls (n = 29). The differential peaks or DEGs were identified using FDR < 0.05.
(B) Exemplar genomic track view of H3K27ac, H3K4me3 and RNA signals for matched AF-schizophrenia/control and AT-schizophrenia/control pairs in NeuN+ and NeuN- cells. 50Mb region displayed: chr1:68,000,000-118,000,000 (GRCh38).
(C) Volcano plots showing genes associated with differential enhancer and promoter peaks and DEGs. Candidate genes for schizophrenia or genes involved in significant GO terms are labeled. The horizontal lines indicate FDR of 0.05.
(D) Venn diagrams on the relationship among genes associated with differential enhancer or promoter peaks and DEGs.
Genome-wide multidimensional clusters in the frontal cortex of schizophrenia subjects and controls.
(A) Integrative analysis using EpiSig. 814 EpiSig clusters across 348 genome-wide sequencing datasets were grouped into 6 sections. The heatmap shows the signal in each EpiSig cluster (row: EpiSig cluster; column: marker).
(B) For each EpiSig cluster, from left to right, the heatmaps are: the region percentage in each chromosome; the genomic annotation; the CpG annotation; the percentage of enhancer; the difference signal between schizophrenia and controls in NeuN+ and NeuN- nuclei.
Transcriptional regulatory processes in the frontal cortex of schizophrenia subjects and controls.
(A) Heatmap of z-score PPR for top 10 significantly differentially expressed TFs (FDR < 0.05) ranked by absolute change in PPR for NeuN+ (upper panel) and NeuN- (lower panel) schizophrenia vs control nuclei samples.
(B) Overrepresented pathway analysis (FDR < 0.05) for 203 downstream regulatees common to the top 4 schizophrenia vs control NeuN+-specific TFs (ZNF333, SOX2, ZEB1 and RBPJ).
(C) Overrepresented pathway analysis (FDR < 0.05) for 225 downstream regulatees common to the top 4 schizophrenia vs control NeuN--specific TFs (FOS, BCL6, IRF1 and KLF15).
Epigenomic alterations affected by antipsychotic treatment.
(A) Scatter plot of average pairwise change in PPR (PPRschizophrenia – PPRcontrol) for AF vs AT NeuN+ cohorts. Orange regions show cohort (AF – AT) < 0.5 (i.e., alterations recovered by antipsychotic treatment), whereas beige regions show cohort (AT – AF) > 0.5 (i.e., alterations consequence of antipsychotic treatment). TFs FDR < 0.05 highlighted in red.
(B) Scatter plot of average pairwise change in PPR (PPRschizophrenia – PPRcontrol) for AF vs AT NeuN- cohorts. Dark blue regions show cohort (AF – AT) < 0.5 (i.e., alterations recovered by antipsychotic treatment), whereas cyan regions show cohort (AT – AF) > 0.5 (i.e., alterations consequence of antipsychotic treatment). TFs FDR < 0.05 highlighted in red.
(C) Number of DEG regulatees by TFs, and number of DEGs in NeuN+ nuclei from AF-schizophrenia/control pairs.
(D) Number of DEG regulatees by TFs, and number of DEGs in NeuN- nuclei from AF-schizophrenia/control pairs.
(E) Number of DEG regulatees by TFs, and number of DEGs in NeuN+ nuclei from AT-schizophrenia/control pairs.
(F) Number of DEG regulatees by TFs, and number of DEGs in NeuN- nuclei from AT-schizophrenia/control pairs.
(G) Functional enrichment analysis of union of genes from AF-schizophrenia/control pairs in NeuN+ nuclei.
(H) Functional enrichment analysis of union of genes from AF-schizophrenia/control pairs in NeuN- nuclei.
(I) Pairwise expression difference (schizophrenia – control) of an exemplar AF-schizophrenia/control cohort DEG (TUBB2A) across all 29 schizophrenia-control pairs in NeuN+ nuclei.
(J) H3K27ac tracks for PDK1 (member of the 84 gene set in E) in NeuN+ nuclei. Box highlighting the FOXO1 DNA-binding motif in promoter at position chr2: 172,555,706 – 172,555,718 (GRCh38). Two exemplar AT-schizophrenia/control cohort pairs showing differential H3K27ac peak intensity around motif locus and an example AF-schizophrenia/control cohort patient pair with no difference.
Effect of antipsychotic treatment on differential enhancers/promoters and DEGs in NeuN+ and NeuN- nuclei from the frontal cortex of schizophrenia subjects and controls.
(A) Differential enhancer/promoter peaks and DEGs obtained by comparing AF-schizophrenics and individually matched controls.
(B) Differential enhancer/promoter peaks and DEGs obtained by comparing AT-schizophrenics and individually matched controls.
Epigenomic effect of age on treated schizophrenia subjects.
(A) Violin plots for Pearson’s R correlation coefficients of age vs expression for 742, 622 and 242 genes from control, AF-schizophrenia, and AT-schizophrenia NeuN+ nuclei, respectively.
(B) Violin plots for Pearson’s R correlation coefficients of age vs expression for 1031, 389 and 351 genes from control, AF-schizophrenia, and AT-schizophrenia NeuN- nuclei, respectively.
(C) Number of pairwise TF PPR and pairwise gene expression differences correlated with age in NeuN+ nuclei from AF-schizophrenia/control pairs.
(D) Number of pairwise TF PPR and pairwise gene expression differences correlated with age in NeuN+ nuclei from AT-schizophrenia/control pairs.
(E) Heatmap for the 14 age positively-correlated (schizophrenia – control increase with age) and 12 age negatively-correlated (schizophrenia – control decrease with age) genes of the significant GO term “Regulation of kinase activity” from the AT-schizophrenia/control NeuN+ cohort.
(F) Example gene, WNK1 pairwise expression difference (schizophrenia – control) vs age (Pearson’s R = 0.73; p-value = 0.003).
(G) Example gene, SFRP2 pairwise expression difference (schizophrenia – control) vs age (Pearson’s R = -0.70; p-value = 0.005).
(H) Example TF, EGR2 pairwise PPR difference (schizophrenia – control) vs age (Pearson’s R = 0.69; p-value = 0.0003
(I) Number of pairwise TF PPR and pairwise gene expression differences correlated with age in NeuN- nuclei from AF-schizophrenia/control pairs.
(J) Number of pairwise TF PPR and pairwise gene expression differences correlated with age in NeuN- nuclei from AT-schizophrenia/control pairs.
(K) Heatmap for the 5 age positively-correlated (schizophrenia – control increase with age) genes of the significant GO term “Beta-catenin independent WNT signaling” from the AT-schizophrenia/control NeuN- cohort.
