Epigenome-wide DNA Methylation Profiling in Aneurysmal Subarachnoid Hemorrhage and Delayed Ischemic Neurologic Deficit

The goal of this observational study is to investigate DNA methylation changes in adults with bleeding from brain aneurysm, which is called aneurysmal subarachnoid hemorrhage (aSAH), and their association with delayed ischemic neurologic deficit (DIND). The main questions it aims to answer are:

Are there specific DNA methylation changes in peripheral blood that differentiate patients with aSAH from healthy individuals? Can DNA methylation changes in peripheral blood predict the development of DIND following aSAH? Researchers will compare blood DNA methylation profiles of aSAH patients to healthy controls and also do subgroup analysis of patients with DIND versus those without DIND to see if there are distinct methylation patterns associated with aSAH and DIND.

Participants with aSAH will:

• Have a blood sample collected shortly after admission to hospital.
• Undergo epigenome-wide DNA methylation profiling using the Infinium MethylationEPIC v2.0 BeadChip microarray.
• Be monitored for the development of DIND, defined by clinical symptoms and radiographic vasospasm.

This study aims to identify potential epigenetic biomarkers for aSAH susceptibility and DIND risk, which could improve early diagnosis and risk stratification in affected patients.

Study Overview

• Status: Active, not recruiting
• Conditions: Subarachnoid Hemorrhage, Aneurysmal; Delayed Cerebral Ischemia; Intracranial Aneurysm; Cerebral Vasospasm After Subarachnoid Hemorrhage

Detailed Description

This is a prospective observational case-control epigenome-wide association study (EWAS) designed to investigate DNA methylation changes in peripheral blood of patients with aneurysmal subarachnoid hemorrhage (aSAH) and their potential association with delayed ischemic neurologic deficit (DIND). The study aims to identify epigenetic biomarkers that may contribute to the pathophysiology of aSAH and DIND, as well as to assess whether these methylation patterns can serve as predictive markers for disease progression.

Study Design and Procedures

Population:

• Patients diagnosed with aSAH will be prospectively recruited from a tertiary neurosurgical center.
• The prospectively recruited patients will be anonymized and classified into DIND and non-DIND groups based on clinical and radiological criteria.
• Healthy control subjects will be matched for age, sex, race, and ethnicity using a publicly available dataset (GSE246337).

Data Collection and Processing:

• Peripheral whole blood samples (10 mL) will be collected within days 1-4 post-hemorrhage before the onset of vasospasm.
• DNA will be extracted using the salting-out method, followed by bisulfite conversion for methylation profiling.
• Genome-wide DNA methylation analysis will be performed using the Infinium MethylationEPIC v2.0 BeadChip microarray, covering ~850K CpG sites.
• Genotyping will be performed using Illumina Global Screening Array (GSA-24) v3.0 consisting of over 654 000 unique loci. PLINK v1.9 software will be used for the variant filtering and statistical analyses. We consider in this analysis only bi-allelic SNPs on autosomes. If this analysis yields significant associations between SNPs and DIND, methylation quantitative trait loci will be analyzed for examination of long-range interactions between relevant SNPs and differentially methylated CpG sites. These SNP-methylation interactions could provide unique and novel data on the vasospasm mechanism.

• Data processing will be performed using SeSAME R package with rigorous quality control measures, including:

  • Removal of probes spanning SNPs with a minor allele frequency >1%.
  • Filtering out probes with low bead count or detection p-values.
  • Exclusion of sex chromosome-associated probes and incorrectly mapped probes.

Diagnosis of DIND:

• DIND will be clinically defined as a new focal neurological deficit or Glasgow Coma Scale (GCS) decline of ≥2 points, lasting >1 hour and not attributable to other causes such as hydrocephalus, hyponatremia or rebleeding.
• Radiological confirmation of vasospasm will be based on cerebral angiography, CT angiography (CTA), or transcranial Doppler (TCD) findings.

Statistical Analysis Plan

Differentially Methylated Probes (DMPs):

• Identification of DMPs will be conducted using linear regression models, with Benjamini-Hochberg correction for multiple comparisons.
• Only CpG sites with an absolute Δβ-value >5% and an adjusted p-value <0.05 will be considered significant.
• Epigenetic clocks (Horvath clock, Hannum clock, SkinBlood clock, PhenoAge clock, GrimAge clock) will estimate biological age based on DNA methylation patterns at specific CpG sites

Machine Learning Analysis:

• LASSO regression will be applied for feature selection to identify methylation patterns most predictive of aSAH vs. healthy controls and DIND vs. non-DIND.
• Performance of the predictive models will be assessed using the R² metric.

Functional Enrichment Analysis:

• Gene Set Enrichment Analysis (GSEA) using "GENE2FUNC" function of Functional Mapping and Annotation of Genome-Wide Association Studies platform (FUMA GWAS) and Genomic Regions Enrichment of Annotations Tool (GREAT) will be used to identify biological pathways associated with significant methylation changes.
• Pathway analysis will focus on immune response, neuroinflammation, endothelial dysfunction, and phosphorous metabolism, as these processes have been implicated in aSAH pathophysiology.

Quality Assurance and Data Validation

Internal Data Validation:

• Automated data checks will be used to identify inconsistencies in methylation profiles.
• Comparative analysis against reference datasets will ensure that methylation patterns align with known biological mechanisms.

Source Data Verification:

• Methylation profiles will be cross-checked with publicly available databases to ensure consistency with previous epigenome-wide association studies.
• Patient demographic and clinical data will be verified against electronic medical records to ensure accuracy.

Handling Missing Data:

• If methylation data for specific CpG sites is missing or below detection thresholds, these sites will be excluded from analysis.
• Missing clinical data will be handled using multiple imputation methods to minimize bias.

Sample Size Justification

Cohort Composition:

• 61 aSAH patients (32 with DIND, 29 without DIND).
• 61 matched healthy controls from GSE246337.

The relatively small sample size was chosen based on previous EWAS studies in aSAH Limitations and Future Directions

Tissue-Specific Limitations:

o The study uses peripheral blood DNA, which may not fully reflect methylation changes in the cerebral vasculature. Future studies should validate findings in the arterial wall of the affected vessel using low-mortality rat models or cerebrospinal fluid.

DIND Subgroup Limitations:

o Due to the relatively small sample size, findings related to DIND will require external validation in larger cohorts.

Conclusion This study aims to provide novel insights into epigenetic changes associated with aSAH and DIND. By identifying differentially methylated CpG sites, the study seeks to improve biomarker discovery for early risk stratification and potential therapeutic targets in aSAH patients.

• Study Type: Observational
• Enrollment (Actual): 61

Contacts and Locations

Study Locations

• Poland
  • West Pomerania
    • Szczecin, West Pomerania, Poland, 71-252
      • Pomeranian Medical University Hospital No. 1

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: Yes

• Sampling Method: Probability Sample

Study Population

Participants will be recruited from a tertiary neurosurgical center at Pomeranian Medical University Hospital No. 1 in Szczecin, Poland. The study population includes consecutive adult patients diagnosed with aneurysmal subarachnoid hemorrhage who meet eligibility criteria. Patients are prospectively enrolled upon admission and followed for the development of delayed ischemic neurologic deficit.

The control group consists of age-, sex-, race-, and ethnicity-matched healthy individuals selected from the publicly available GSE246337 dataset. This dataset serves as a reference population to identify epigenetic changes specific to aSAH.

Description

Inclusion Criteria:

• subarachnoid hemorrhage in computed tomography (CT) scan
• ruptured aneurysm identified with angio-CT or digital subtraction angiography (DSA)
• aneurysm successfully embolized or clipped
• obtained informed consent
• Hunt-Hess grade ≤ 3 by day 14 (initial higher grade was allowed providing that patient improved to grade 3 or higher by day 14)

Exclusion Criteria:

• < 18 years old
• unable to sign informed consent
• diagnosis of idiopathic perimesencephalic subarachnoid hemorrhage
• aneurysm identified more than 14 days after the ictus
• more than 14 days at the Intensive Care Unit
• remaining in Hunt Hess grade 5 or World Federation of Neurological Surgeons (WFNS) grade 5 from admission up to post-bleeding day 14

Study Plan

How is the study designed?

Number of groups / cohorts

3

Cohorts and Interventions

Group / Cohort
Subarachnoid hemorrhage with delayed ischemic neurologic deficit; This cohort includes patients diagnosed with aneurysmal subarachnoid hemorrhage who develop delayed ischemic neurologic deficit, defined as a new focal neurological deficit (paresis, dysphasia) or Glasgow Coma Scale decline of ≥2 points lasting >1 hour, not attributable to rebleeding, hydrocephalus, or hyponatremia. Diagnosis is confirmed with radiologic evidence of vasospasm on transcranial Doppler.
Subarachnoid hemorrhage without delayed ischemic neurologic deficit; This cohort includes patients diagnosed with aneurysmal subarachnoid hemorrhage who do not develop delayed ischemic neurologic deficit. These patients exhibit no new focal neurological deficits and no Glasgow Coma Scale decline of ≥2 points beyond the acute phase of hemorrhage. Radiologic assessments confirm the absence of significant vasospasm on transcranial Doppler.
Healthy controls without subarachnoid hemorrhage; This cohort consists of age-, sex-, race-, and ethnicity-matched healthy individuals with no history of aneurysmal subarachnoid hemorrhage (aSAH) or other neurological disorders. Participants were selected from a publicly available dataset (GSE246337). Blood DNA methylation profiles from this group serve as a baseline reference for comparison with aSAH patients

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
DNA methylation changes associated with aneurysmal subarachnoid hemorrhage and delayed ischemic neurologic deficit	Identification of differentially methylated CpG sites in peripheral blood DNA of patients with aneurysmal subarachnoid hemorrhage compared to healthy controls and to assess whether DNA methylation changes are associated with delayed ischemic neurologic deficit. The metrics and direction of DNA methylation changes will be reported as Δβ values	Within four days following the enrollment (as blood samples will be collected within days 1-4 post-hemorrhage). Methylation profiling and CpG analysis the entire batch will be conducted within one year following enrollment of the last participant

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Epigenetic clocks analysis and their association with chronological age in delayed ischemic neurologic deficit	Horvath clock, Hannum clock, SkinBlood clock, PhenoAge clock, GrimAge clock) will estimate biological age based on DNA methylation patterns at specific CpG sites. Pearson correlation of chronological age with the abovemention epigenetic clocks.	Within four days following the enrollment (as blood samples will be collected within days 1-4 post-hemorrhage). Methylation profiling and epigenetic clock analysis will be conducted within one year following enrollment of the last participant

Collaborators and Investigators

• Sponsor: Pomeranian Medical University Szczecin
• Collaborators: National Science Centre, Poland

Study record dates

Study Major Dates

• Study Start (Actual): December 20, 2021
• Primary Completion (Actual): January 12, 2025
• Study Completion (Estimated): December 31, 2025

Study Registration Dates

• First Submitted: March 10, 2025
• First Submitted That Met QC Criteria: March 10, 2025
• First Posted (Actual): March 18, 2025

Study Record Updates

• Last Update Posted (Actual): July 31, 2025
• Last Update Submitted That Met QC Criteria: July 28, 2025
• Last Verified: July 1, 2025

More Information

Terms related to this study

• Keywords: intracranial aneurysm; cerebral vasospasm; delayed cerebral ischemia; aneurysmal subarachnoid hemorrhage; delayed ischemic neurologic deficit; aneurysm rupture
• Additional Relevant MeSH Terms: Cerebrovascular Disorders; Brain Diseases; Central Nervous System Diseases; Nervous System Diseases; Vascular Diseases; Cardiovascular Diseases; Pathologic Processes; Brain Infarction; Infarction; Necrosis; Intracranial Arterial Diseases; Intracranial Hemorrhages; Stroke; Neurologic Manifestations; Cerebral Infarction; Ischemia; Aneurysm; Hemorrhage; Subarachnoid Hemorrhage; Brain Ischemia; Intracranial Aneurysm; Vasospasm, Intracranial
• Other Study ID Numbers: KB-0012/61/2021; 2021/41/N/NZ2/00844 (Other Grant/Funding Number: National Science Centre, Poland)

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: YES
• IPD Plan Description: The study's epigenome-wide DNA methylation data from peripheral blood samples of aSAH patients and healthy controls will be shared via the Gene Expression Omnibus (GEO) repository. This dataset includes processed methylation profiles and metadata necessary for secondary analysis.
• IPD Sharing Time Frame: Data is already deposited in Gene Expression Omnibus repository (GSE290201) and will be available immediately upon publication. It will remain publicly accessible indefinitely according to GEO repository policies.
• IPD Sharing Access Criteria: The methylation dataset will be available for download from Gene Expression Omnibus (GEO) repository (GSE290201). Researchers will have an access to the data following GEO's standard data use agreements, which require appropriate citation of the original study.
• IPD Sharing Supporting Information Type: STUDY_PROTOCOL

Study Data/Documents

1. Individual Participant Data Set
   Information identifier: GSE290201
   Information comments: Gene Expression Omnibus repository

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No
• product manufactured in and exported from the U.S.: No