J Korean Neurosurg Soc.  2022 Jan;65(1):4-12. 10.3340/jkns.2021.0035.

Identification of Differentially-Methylated Genes and Pathways in Patients with Delayed Cerebral Ischemia Following Subarachnoid Hemorrhage

• Kim BJ
• Youn DH
• Chang IB
• Kang K
• Jeon JP

• KMID: 2523908
• DOI: http://doi.org/10.3340/jkns.2021.0035

Abstract

Objective
: We reported the differentially methylated genes in patients with subarachnoid hemorrhage (SAH) using bioinformatics analyses to explore the biological characteristics of the development of delayed cerebral ischemia (DCI).
Methods
: DNA methylation profiles obtained from 40 SAH patients from an epigenome-wide association study were analyzed. Functional enrichment analysis, protein-protein interaction (PPI) network, and module analyses were carried out.
Results
: A total of 13 patients (32.5%) experienced DCI during the follow-up. In total, we categorized the genes into the two groups of hypermethylation (n=910) and hypomethylation (n=870). The hypermethylated genes referred to biological processes of organic cyclic compound biosynthesis, nucleobase-containing compound biosynthesis, heterocycle biosynthesis, aromatic compound biosynthesis and cellular nitrogen compound biosynthesis. The hypomethylated genes referred to biological processes of carbohydrate metabolism, the regulation of cell size, and the detection of a stimulus, and molecular functions of amylase activity, and hydrolase activity. Based on PPI network and module analysis, three hypermethylation modules were mainly associated with antigen-processing, Golgi-to-ER retrograde transport, and G alpha (i) signaling events, and two hypomethylation modules were associated with post-translational protein phosphorylation and the regulation of natural killer cell chemotaxis. VHL, KIF3A, KIFAP3, RACGAP1, and OPRM1 were identified as hub genes for hypermethylation, and ALB and IL5 as hub genes for hypomethylation.
Conclusion
: This study provided novel insights into DCI pathogenesis following SAH. Differently methylated hub genes can be useful biomarkers for the accurate DCI diagnosis.

Keyword

Subarachnoid hemorrhage; Intracranial aneurysm; DNA methylation; Computational biology; Epigenetics; Delayed cerebral ischemia

Figure

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  Fig. 1. Functional enrichment analyses of hypermethylated (A) and hypomethylated genes (B) between subarachnoid hemorrhage patients with and without delayed cerebral ischemia. The blue-colored boxes indicate statistical significance.

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  Fig. 2. Module cluster analyses of hypermethylated genes and related gene enrichment analysis between delayed cerebral ischemia (DCI) and non-DCI patients following subarachnoid hemorrhage.

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  Fig. 3. Module cluster analyses of hypomethylated genes and related gene enrichment analysis between delayed cerebral ischemia (DCI) and non-DCI patients following subarachnoid hemorrhage.

Reference

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