Joint-Tissue Integrative Analysis Identified Hundreds of Schizophrenia Risk Genes

Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways

Identifying genes whose expression is associated with schizophrenia (SCZ) risk by transcriptome-wide association studies (TWAS) facilitates downstream experimental studies. Here, we integrated multiple published datasets of TWAS, gene coexpression, and differential gene expression analysis to prioritize SCZ candidate genes for functional study. Convergent evidence prioritized Propionyl-CoA Carboxylase Subunit Beta (PCCB), a nuclear-encoded mitochondrial gene, as an SCZ risk gene. However, the PCCB's contribution to SCZ risk has not been investigated before. Using dual luciferase reporter assay, we identified that SCZ-associated SNPs rs6791142 and rs35874192, two eQTL SNPs for PCCB, showed differential allelic effects on transcriptional activities. PCCB knockdown in human forebrain organoids (hFOs) followed by RNA sequencing analysis revealed dysregulation of genes enriched with multiple neuronal functions including gamma-aminobutyric acid (GABA)-ergic synapse. The metabolomic and mitochondrial function analyses confirmed the decreased GABA levels resulted from inhibited tricarboxylic acid cycle in PCCB knockdown hFOs. Multielectrode array recording analysis showed that PCCB knockdown in hFOs resulted into SCZ-related phenotypes including hyper-neuroactivities and decreased synchronization of neural network. In summary, this study utilized hFOs-based multi-omics analyses and revealed that PCCB downregulation may contribute to SCZ risk through regulating GABAergic pathways, highlighting the mitochondrial function in SCZ.

Human forebrain organoids-based multi-omics analyses reveal PCCB's regulation on GABAergic system contributing to schizophrenia

Identifying genes whose expression is associated with schizophrenia (SCZ) risk by transcriptome-wide association studies (TWAS) facilitates downstream experimental studies. Here, we integrated multiple published datasets of TWAS (including FUSION, PrediXcan, summary-data-based Mendelian randomization (SMR), joint-tissue imputation approach with Mendelian randomization (MR-JTI)), gene coexpression, and differential gene expression analysis to prioritize SCZ candidate genes for functional study. Convergent evidence prioritized Propionyl-CoA Carboxylase Subunit Beta ( PCCB ), a nuclear-encoded mitochondrial gene, as an SCZ risk gene. However, the PCCB ’s contribution to SCZ risk has not been investigated before. Using dual luciferase reporter assay, we identified that SCZ-associated SNP rs35874192, an eQTL SNP for PCCB , showed differential allelic effects on transcriptional activities. PCCB knockdown in human forebrain organoids (hFOs) followed by RNA-seq revealed dysregulation of genes enriched with multiple neuronal functions including gamma-aminobutyric acid (GABA)-ergic synapse, as well as genes dysregulated in postmortem brains of SCZ patients or in cerebral organoids derived from SCZ patients. The metabolomic and mitochondrial function analyses confirmed the deceased GABA levels resulted from reduced tricarboxylic acid cycle in PCCB knockdown hFOs. Multielectrode array recording analysis showed that PCCB knockdown in hFOs resulted into SCZ-related phenotypes including hyper-neuroactivities and decreased synchronization of neural network. In summary, this study utilized hFOs-based multi-omics data and revealed that PCCB downregulation may contribute to SCZ risk through regulating GABAergic system, highlighting the mitochondrial function in SCZ.

Molecular Quantitative Trait Locus Mapping in Human Complex Diseases

Mapping quantitative trait loci (QTLs) for molecular traits from chromatin to metabolites (i.e., xQTLs) provides insight into the locations and effect modes of genetic variants that influence these molecular phenotypes and the propagation of functional consequences of each variant. xQTL studies indirectly interrogate the functional landscape of the molecular basis of complex diseases, including the impact of non-coding regulatory variants, the tissue specificity of regulatory elements, and their contribution to disease by integrating with genome-wide association studies (GWAS). We summarize a variety of molecular xQTL studies in human tissues and cells. In addition, using the Alzheimer's Disease Sequencing Project (ADSP) as an example, we describe the ADSP xQTL project, a collaborative effort across the ADSP Functional Genomics Consortium (ADSP-FGC). The project's ultimate goal is a reference map of Alzheimer's-related QTLs using existing datasets from multiple omics layers to help us study the consequences of genetic variants identified in the ADSP. xQTL studies enable the identification of the causal genes and pathways in GWAS loci, which will likely aid in the discovery of novel biomarkers and therapeutic targets for complex diseases. © 2022 Wiley Periodicals LLC.

Facial emotion identification impairments in Chinese persons living with schizophrenia: A meta-analysis

BACKGROUND

Facial emotion identification (FEI) deficits are associated with impaired social functioning in persons living with schizophrenia (PLwS), but the research on emotion-specific FEI deficits remains inconclusive. Furthermore, existing studies on FEI deficits are limited by their small sample sizes. We performed a meta-analysis of studies comparing the FEI abilities between Chinese PLwS and healthy controls in terms of the six basic facial emotions (happiness, sadness, fear, disgust, anger, and surprise), as well as contempt, calmness, and neutral facial expressions.

METHODS

Major Chinese- and English-language databases were searched to retrieve case-control studies that compared the FEI task performance between Chinese PLwS and healthy controls (HCs) and reported the emotion-specific correct identification scores for PLwS and HCs. The Joanna Briggs Institute Critical Appraisal Checklist for Case-control Studies ("JBI checklist," hereafter) was used to assess the risk of bias (RoB) of the included studies. Statistical analysis was performed using the "meta" package of R 4.1.2.

RESULTS

Twenty-three studies with a total of 28 case-control cohorts and 1,894 PLwS and 1,267 HCs were included. The RoB scores of the included studies ranged from two to seven. PLwS had statistically significantly lower FEI scores than HCs and the corresponding emotion-specific pooled standard mean differences (95% confidence intervals) were -0.69 (-0.88, -0.50) for happiness, -0.88 (-1.12, -0.63) for sadness, -1.44 (-1.83, -1.06) for fear, -1.18 (-1.60, -0.76) for disgust, -0.91 (-1.24, -0.57) for anger, -1.09 (-1.39, -0.78) for surprise, -0.26 (-0.51, -0.01) for contempt, -0.31 (-0.52, -0.09) for calmness, and -0.42 (-0.65, -0.18) for neutral. In the analyses of sources of heterogeneity, drug-naïve status, clinical setting, positive and negative psychotic symptoms, and RoB were significant moderators of the magnitudes of FEI deficits.

CONCLUSIONS

Chinese PLwS have significant FEI impairments in terms of recognizing the six basic facial emotions, contempt, calmness, and neutral emotions, and the magnitude of impairment varies depending on the type of emotion, clinical characteristics, and the level of RoB of the study. It is necessary to consider the characteristics of FEI deficits and the clinical moderators in the FEI deficits to develop remediation strategies targeting FEI deficits in schizophrenia.