Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
Novo Nordisk, Oxford, United Kingdom.
Thromb Haemost. 2019 Jul;119(7):1072-1083. doi: 10.1055/s-0039-1687879. Epub 2019 Apr 29.
Elucidating the genetic basis underlying hepatic hemostatic gene expression variability may contribute to unraveling genetic factors contributing to thrombotic or bleeding disorders. We aimed to identify novel -regulatory variants involved in regulating hemostatic genes by analyzing allele-specific expression (ASE) in human liver samples.
Biopsies of human liver tissue and blood were collected from adults undergoing liver surgery at the Sahlgrenska University Hospital ( = 20). Genomic deoxyribonucleic acid (gDNA) and total ribonucleic acid (RNA) were isolated. A targeted approach was used to enrich and sequence 35 hemostatic genes for single nucleotide polymorphism (SNP) analysis (gDNAseq) and construct individualized genomes for transcript alignment. The allelic ratio of transcripts from targeted RNAseq was determined via ASE analysis. Public expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) data were used to assess novelty and importance of the ASE SNPs (and proxies, ≥ 0.8) for relevant traits/diseases.
Sixty percent of the genes studied showed allelic imbalance across 53 SNPs. Of these, 7 SNPs were previously validated in liver eQTL studies. For 32 with eQTLs in other cell/tissue types, this is the first time genotype-specific expression is demonstrated in liver, and for 14 ASE SNPs, this is the first ever reported genotype-expression association. A total of 29 ASE SNPs were previously associated with the respective plasma protein levels and 17 ASE SNPs to other relevant GWAS traits including venous thromboembolism, coronary artery disease, and stroke.
Our study provides a comprehensive ASE analysis of hemostatic genes and insights into the regulation of hemostatic genes in human liver.
阐明肝脏止血基因表达变异性的遗传基础，可能有助于揭示导致血栓形成或出血性疾病的遗传因素。我们旨在通过分析人类肝组织样本中的等位基因特异性表达（ASE），鉴定参与调节止血基因的新型调控变体。
从在萨赫勒格兰斯卡大学医院接受肝手术的成年人中采集肝组织和血液活检（ = 20）。分离基因组脱氧核糖核酸（gDNA）和总核糖核酸（RNA）。采用靶向方法富集和测序 35 个止血基因，进行单核苷酸多态性（SNP）分析（gDNAseq），并构建个体基因组进行转录物比对。通过 ASE 分析确定靶向 RNAseq 中转录物的等位基因比例。利用公共表达数量性状基因座（eQTL）和全基因组关联研究（GWAS）数据评估 ASE SNPs 的新颖性和重要性（和代理， ≥ 0.8）及其与相关性状/疾病的关系。
在所研究的基因中，有 60%的基因在 53 个 SNP 上表现出等位基因不平衡。其中，7 个 SNP 先前在肝 eQTL 研究中得到验证。对于其他细胞/组织类型具有 eQTL 的 32 个基因，这是首次在肝中证明基因型特异性表达，对于 14 个 ASE SNPs，这是首次报道基因型-表达关联。共有 29 个 ASE SNPs 先前与相应的血浆蛋白水平相关，17 个 ASE SNPs 与其他相关的 GWAS 性状相关，包括静脉血栓栓塞、冠心病和中风。
我们的研究提供了止血基因的全面 ASE 分析，并深入了解了人类肝脏中止血基因的调控。
