Methylation Patterns Differ Between ICH Cases and Controls
Stacie Demel1, Savvina Prapiadou2, Mary E. Comeau3, Hannah S. Ainsworth3, Shea Wright1, Kyle B Walsh1, Miranda Marion3, Hyacinth Idu Hyacinth1, Daniel Woo4, Carl Langefeld3
1University of Cincinnati Medical Center, 2University of Patras, 3Wake Forest University, 4University of Cincinnati
To identify differential DNA methylation patterns in intracerebral hemorrhage (ICH) cases and controls
ICH is a severe stroke subtype with genetic, environmental, and behavioral risk factors.  DNA methylation (DNAm) has numerous functions, including regulating gene expression, and is influenced by environmental and behavior factors (e.g., pollution, life events and smoking). Herein we report the first methylome-wide comparison between ICH cases and matched controls. 
ICH participants (30 White, 30 Black and 30 Hispanic) and their demographically matched controls in the Ethnic/Racial Variations of Intracerebral Hemorrhage (ERICH) study underwent DNA methylation analysis utilizing the Illumina MethylationEpic v2.0 BeadChip array (> 935,000 CpG sites).  Differential DNAm (sampled 13.0 ± 7.1 days from ICH) between cases and controls across the methylome were tested, adjusting for age, sex, smoking status, race/ethnicity, and differential white blood cell count.  Pathway analysis using Enrichr Knowledge Graph (Enrichr-KG) was performed. Three gene set libraries (gene ontology (GO), KEGG, Reactome) were searched to identify top associated pathways.

In this multi-ethnic case-control analysis (median age 58, 50% female) marked differences in DNAm were observed. 274 CpG sites met false discovery rate (FDR) adjusted p< 0.05.  DNAm did not differ by race/ethnicity in the case-control analysis or between acute (< 3 days) and convalescent (> 10 days) samples. Multiple pathways including RNA processing and pexophagy were associated with DNAm ICH risk. Further, DNA regions coding SRSF4 (mRNA splicing), NBR1 (peroxisomal function) and RPS15 (translation) were differentially methylated in cases vs. controls.

Our findings support that methylation variation is associated with ICH risk. Similar methylation in acute vs. convalescent samples suggests that DNAm patterns were likely to be associated with ICH incidence rather than changes post-ICH.   Enriched pathways included autophagy and inflammation, both of which are inked to hypertension, the most common risk factor for ICH.