PHACTR1 splicing isoforms and eQTLs in atherosclerosis-relevant human cells
PHACTR1 splicing isoforms and eQTLs in atherosclerosis-relevant human cells
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DOI：
10.1186/s12881-018-0616-7
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发表时间：
2018-06-08
影响因子：
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通讯作者：
Lettre, Guillaume
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文献类型：
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作者：
Codina-Fauteux, Valerie-Anne;Beaudoin, Melissa;Lettre, Guillaume
背景资料：全基因组关联研究（GWAS）已经确定了磷酸酶和肌动蛋白调节因子1（PHACTR1）基因座的一个变体（rs9349379），该变体与冠状动脉疾病（CAD）相关。同一变异体也是人冠状动脉（hCA）中PHACTR1的表达数量性状位点（eQTL）。在这里，我们试图表征动脉粥样硬化相关的人类细胞中PHACTR1剪接模式。我们还探讨了rs9349379如何调节不同的PHACTR1剪接isoforms.Methods的表达：我们结合了cDNA末端快速扩增（RACE）与下一代长读DNA测序，发现所有PHACTR1转录在许多人体组织和细胞类型。我们通过qPCR检测了PHACTR1的转录本，以确定转录本特异性eQTLs.Results：我们确认了一个脑特异性长转录本，一个在单核细胞中表达的短转录本和四个中间转录本，这些转录本由于两个框内外显子的选择性剪接而不同。与以前的报道相反，我们证实了PHACTR1蛋白存在于血管平滑肌细胞中。在158 hCA从我们的收集和GTEx数据集，rs9349379只与中间PHACTR1 transcripts.Conclusions的表达水平：我们全面的转录组分析PHACTR1表明，该基因编码六个主要的转录本。其中五个在hCA中表达，动脉粥样硬化斑块在其中发展。在该组织中，rs9349379处的基因型与中间转录物的表达相关，但与免疫特异性短转录物无关。这一结果表明，rs9349379可能通过调节hCA中发现的内皮或血管平滑肌细胞中的中间PHACTR1转录物的表达而部分影响CAD。
Background: Genome-wide association studies (GWAS) have identified a variant (rs9349379) at the phosphatase and actin regulator 1 (PHACTR1) locus that is associated with coronary artery disease (CAD). The same variant is also an expression quantitative trait locus (eQTL) for PHACTR1 in human coronary arteries (hCA). Here, we sought to characterize PHACTR1 splicing pattern in atherosclerosis-relevant human cells. We also explored how rs9349379 modulates the expression of the different PHACTR1 splicing isoforms.Methods: We combined rapid amplification of cDNA ends (RACE) with next-generation long-read DNA sequencing to discover all PHACTR1 transcripts in many human tissues and cell types. We measured PHACTR1 transcripts by qPCR to identify transcript-specific eQTLs.Results: We confirmed a brain-specific long transcript, a short transcript expressed in monocytes and four intermediate transcripts that are different due to alternative splicing of two in-frame exons. In contrast to a previous report, we confirmed that the PHACTR1 protein is present in vascular smooth muscle cells. In 158 hCA from our collection and the GTEx dataset, rs9349379 was only associated with the expression levels of the intermediate PHACTR1 transcripts.Conclusions: Our comprehensive transcriptomic profiling of PHACTR1 indicates that this gene encodes six main transcripts. Five of them are expressed in hCA, where atherosclerotic plaques develop. In this tissue, genotypes at rs9349379 are associated with the expression of the intermediate transcripts, but not the immune-specific short transcript. This result suggests that rs9349379 may in part influence CAD by modulating the expression of intermediate PHACTR1 transcripts in endothelial or vascular smooth muscle cells found in hCA.