A pilot study on the impact of dopamine, serotonin, and brain-derived neurotrophic factor genotype on long-term functional outcomes after subarachnoid hemorrhage

Identification of upregulated NF-κB inhibitor alpha and IRAK3 targeting lncRNA following intracranial aneurysm rupture-induced subarachnoid hemorrhage

Background

This study was performed to identify genes and lncRNAs involved in the pathogenesis of subarachnoid hemorrhage (SAH) from ruptured intracranial aneurysm (RIA).

Methods

Microarray GSE36791 was downloaded from Gene Expression Omnibus (GEO) database followed by the identification of significantly different expressed RNAs (DERs, including lncRNA and mRNA) between patients with SAH and healthy individuals. Then, the functional analyses of DEmRNAs were conducted and weighted gene co-expression network analysis (WGCNA) was also performed to extract the modules associated with SAH. Following, the lncRNA-mRNA co-expression network was constructed and the gene set enrichment analysis (GSEA) was performed to screen key RNA biomarkers involved in the pathogenesis of SAH from RIA. We also verified the results in a bigger dataset GSE7337.

Results

Totally, 561 DERs, including 25 DElncRNAs and 536 DEmRNAs, were identified. Functional analysis revealed that the DEmRNAs were mainly associated with immune response-associated GO-BP terms and KEGG pathways. Moreover, there were 6 modules significantly positive-correlated with SAH. The lncRNA-mRNA co-expression network contained 2 lncRNAs (LINC00265 and LINC00937) and 169 mRNAs. The GSEA analysis showed that these two lncRNAs were associated with three pathways (cytokine-cytokine receptor interaction, neurotrophin signaling pathway, and apoptosis). Additionally, IRAK3 and NFKBIA involved in the neurotrophin signaling pathway and apoptosis while IL1R2, IL18RAP and IL18R1 was associated with cytokine-cytokine receptor interaction pathway. The expression levels of these genes have the same trend in GSE36791 and GSE7337.

Conclusion

LINC00265 and LINC00937 may be implicated with the pathogenesis of SAH from RIA. They were involved in three important regulatory pathways. 5 mRNAs played important roles in the three pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12883-021-02156-1.

Enhancing Research Through the Use of the Genotype-Tissue Expression (GTEx) Database

Despite a growing interest in multi-omic research, individual investigators may struggle to collect large-scale omic data, particularly from human subjects. Publicly available datasets can help to address this problem, including those sponsored by the NIH Common Fund, such as the Genotype-Tissue Expression (GTEx) database. This database contains genotype and expression data obtained from 54 non-diseased tissues in human subjects. But these data are often underutilized, because users may find the browsing tools to be counterintuitive or have difficulty navigating the procedures to request controlled data access. Furthermore, there is limited knowledge of these resources among nurse scientists interested in incorporating such information into their programs of research. This article outlines the procedures for using the GTEx database. Next, we provide one exemplar of using this resource to enhance existing research by investigating expression of dopamine receptor type 2 (DRD2) across brain tissues in human subjects.