Epigenome-wide DNA methylation profiling in aneurysmal subarachnoid hemorrhage and delayed ischemic neurologic deficit: a prospective observational study.

Background: The molecular mechanisms underlying aneurysmal subarachnoid hemorrhage (aSAH) and delayed ischemic neurologic deficit (DIND) remain poorly understood. We hereby present the study investigating epigenome-wide profile of DNA methylation in adults with aSAH and DIND.

Methods: A prospective observational epigenome-wide association study (EWAS) was conducted with DNA extracted from the peripheral whole blood of subjects with aSAH. DNA methylation profiling was conducted using Infinium MethylationEPIC v2.0 BeadChip microarray with a total number of 814,206 probes. Healthy matched controls were obtained from the publicly available dataset (GSE246337, n = 500) with 1:1 matching. DIND was determined by a combination of clinical symptoms and radiographic vasospasm. Differentially methylated probes (DMPs) were identified using linear regression model with Benjamini-Hochberg correction. This study was registered with ClinicalTrials.gov (NCT06881329).

Results: 122 participants were included: 61 prospectively recruited with aSAH and 61 external age-, sex-, race-and ethnicity-matched controls. Among aSAH patients, 32 developed DIND (52%). Overall, with linear regression we identified 2,642 DMPs associated with aSAH after multiple testing correction, and the lack of significant DIND-associated methylation changes. Specifically, as the top hit, we detected significant hypomethylation of cg15004555 (Δβ = - 0.254) in aSAH patients, annotated to exon 2 of AIM2, a gene whose expression is critical for AIM2-driven inflammasome activation. The functional enrichment analysis revealed that genes associated with the identified methylation changes were enriched in ontology terms related to specific biological processes such as immune response, pain modulation, phosphorus metabolism, as well as cellular components including cis-Golgi network or beta-catenin complex.

Conclusions: Our prospective observational EWAS identified significant DNA methylation changes in the blood cells and demonstrated a functional link to specific biological processes in aSAH. Further validation studies are necessary to confirm our findings.