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Chromatin conformation links enhancers in intracranial aneurysm associated regions to potential candidate genes

ABSTRACT: Background and Purpose: We previously showed that intracranial aneurysm (IA)-associated single nucleotide polymorphisms (SNPs) are enriched in promoters and putative enhancers of the human circle of Willis (CoW), on which IAs develop, suggesting a role for such regulatory regions in IA. In this study we further investigated the role of these putative enhancers in the pathogenesis of IA by identifying the target genes of these enhancers and validating their regulatory activity. Methods: We selected putative enhancers in IA-associated regions from genome wide association studies, using our previously published CoW chromatin immunoprecipitation and sequencing data. Next, we used a chromatin conformation capture technique (4C) to identify physical interactions between these putative enhancers and the promoters of their target genes. Subsequently, we assessed the activity of the identified enhancers in vivo in zebrafish embryos and we analyzed gene expression of the target genes identified with 4C in CoW RNA-sequencing data and by in situ hybridization on CoW paraffin sections. Results: We identified fifteen enhancers that interact with the promoters of six target genes: SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6. For eight out of eleven enhancers that could be tested, we confirmed in vivo activity in the zebrafish embryos. These eight enhancers reside in four out of six IA-associated GWAS regions. All six target genes are expressed in the CoW and in situ hybrdization showed that these genes are expressed in multiple cell types in the CoW. Conclusions: In four out of six IA-associated GWAS regions we identified eight enhancers that are active in vivo and interact with six nearby genes, suggesting that these genes are regulated by the identified enhancers. These genes, SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6, are potential candidate genes involved in IA pathogenesis and should be studied using animal models in the future.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115304 | GEO | 2019/04/27

REPOSITORIES: GEO

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Project description:Patients diagnosed with pseudohypoparathyroidism type Ia (PHP Ia) suffer from hormonal resistance. This is often accompanied by abnormal postural and facial features, brachydactyly and dermal calcifications, a condition classified as Albright hereditary osteodystrophy (AHO) syndrome. Typically, this is the result of maternal inheritance of a mutation (or epigenetic defect) in the GNAS complex locus, encoding for the GTPase subunit Gsα. However, accurate diagnosis is often difficult. In blood platelets, Gsα couples to receptors for prostaglandin E1 and iloprost, and provides a master signal for platelet inhibition via adenylyl cyclase and cAMP-dependent protein kinase A (PKA). Here, we evaluated the iloprost-induced functional changes and phosphoproteome in platelets from eight patients with confirmed or suspected PHP Ia, one of the largest cohorts examined. Our aim was to asses how current proteomics techniques can help to find phosphorylation aberrations in these patients, and hence to improve future diagnosis Platelets from six out of eight patients (4 families), with confirmed GNAS mutations, displayed impairments in Gsα-dependent functional responses, i.e. VASP phosphorylation, aggregation, and microfluidic thrombus formation. Detailed analysis of platelet phosphoproteome revealed a consistent set of 2,516 protein phosphorylation sites, of which 453 were recognised as regulated by iloprost-Gsα, and 263 were upregulated. In five patients with AHO, we detected impairments in the iloprost-induced platelet phosphoproteome that were linked to a dysregulated platelet inhibition. The changes in these patients concerned: (i) both upregulated and downregulated phosphopeptides; (ii) a high Gsα and PKA dependency of the upregulated phosphopeptides; (iii) multiple phosphoproteins implicated in key platelet functions and biological pathways. Confirmation of these changes in iloprost-induced phosphoproteome was obtained using a panel of 14 targeted phosphopeptide assays. In contrast, or one patient with GNAS mutation diagnosed as non-AHO, we noticed reversed changes in the iloprost phosphoproteome. This combination of phosphoproteomic approaches can be a powerful tool to assist in future molecular diagnosis of patients with suspected PHP Ia.

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Chromatin conformation links enhancers in intracranial aneurysm associated regions to potential candidate genes

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