Integrative analysis of transcriptome-wide association study and mRNA expression profile identified risk genes for bipolar disorder

Objective

Bipolar disorder (BD) is a debilitating neuropsychiatric disorder, which is associated with genetic variation through “vast but mixed” Genome-Wide Association Studies (GWAS). Transcriptome-Wide Association Study (TWAS) is more effective in explaining genetic factors that influence complex diseases and can help identifying risk genes more reliably. So, this study aims to identify potential BD risk genes in pedigrees with TWAS.

Methods

We conducted a TWAS analysis with expression quantitative trait loci (eQTL) analysis on extended BD pedigrees, and the BD genome-wide association study (GWAS) summary data acquired from the Psychiatric Genomics Consortium (PGC). Furthermore, the BD-associated genes identified by TWAS were validated by mRNA expression profiles from the Gene Expression Omnibus (GEO) Datasets (GSE23848 and GSE46416). Functional enrichment and annotation analysis were implemented by RStudio (version 4.2.0).

Results

TWAS identified 362 genes with P value < 0.05, and 18 genes remain significant after Bonferroni correction, such as SEMA3G (P_TWAS=1.07 × 10^-11), ALOX5AP (P_TWAS=3.12 × 10^-8), and PLEC (P_TWAS=1.27 × 10^-7). Further 6 overlapped genes were detected in integrative analysis, such as UQCRB (P_TWAS=0.0020, P_mRNA=0.0000), TMPRSS9 (P_TWAS=0.0405, P_mRNA=0.0032), and SNX10 (P_TWAS=0.0104, P_mRNA=0.0015). Using genes identified by TWAS, Gene Ontology (GO) enrichment analysis identified 40 significant GO terms, such as mitochondrial ATP synthesis coupled electron transport, mitochondrial respiratory, aerobic electron transport chain, oxidative phosphorylation, mitochondrial membrane proteins, and ubiquinone activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis identified significant 15 pathways for BD, such as Oxidative phosphorylation, endocannabinoids signaling, neurodegeneration, and reactive oxide species.

Conclusions

We found a set of BD-associated genes and pathways, validating the important role of neurodevelopmental abnormalities, inflammatory responses, and mitochondrial dysfunction in the pathology of BD, offering novel information for comprehending the genetic basis of BD.