Deep Resequencing of the 1q22 Locus in Non-Lobar Intracerebral Hemorrhage

Objective Genome-wide association studies have identified 1q22 as a susceptibility locus for cerebral small vessel diseases, including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study, we performed targeted high-depth sequencing of 1q22 in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown.Methods A total of 95,000 base pairs spanning 1q22, including SEMA4A, SLC25A44, and PMF1/PMF1-BGLAP were sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and Rare Variant Influential Filtering Tool analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, chromatin immunoprecipitation followed by sequencing, and chromatin interaction analysis with paired-end tag databases. Multivariable Mendelian randomization assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at 1q22 could be causally related to ICH risk.Results Common and rare variant analyses prioritized variants in SEMA4A 5 '-UTR and PMF1 intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that 1q22 is spatially organized in a single chromatin loop, and that the genes therein belong to the same topologically associating domain. Chromatin immunoprecipitation followed by sequencing and chromatin interaction analysis with paired-end tag data analysis highlighted the presence of long-range interactions between the SEMA4A-promoter and PMF1-enhancer regions prioritized by association testing. Multivariable Mendelian randomization analyses demonstrated that PMF1 overexpression could be causally related to non-lobar ICH risk.

Automated summary

This study performed targeted high-depth sequencing and chromatin interaction analysis to characterize the 1q22 locus and identify potential causal mechanisms for cerebral small vessel diseases. The results showed that variants in SEMA4A and PMF1 genes were associated with non-lobar intracerebral hemorrhage risk. The analysis also revealed long-range chromatin interactions between the SEMA4A promoter and the PMF1 enhancer regions. Additionally, overexpression of the PMF1 gene was found to be causally related to non-lobar intracerebral hemorrhage risk.