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

Abstract

ObjectiveGenome‐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.MethodsA 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.ResultsCommon 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.InterpretationAltered promoter–enhancer interactions leading to PMF1 overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non‐lobar ICH risk at 1q22, offering a potential new target for prevention of ICH and cerebral small vessel disease. ANN NEUROL 2024;95:325–337