CC BY-NC-ND 4.0 · Thromb Haemost 2019; 119(07): 1072-1083
DOI: 10.1055/s-0039-1687879
Coagulation and Fibrinolysis
Georg Thieme Verlag KG Stuttgart · New York

Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver

1  Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
,
Lena Hansson
2  Novo Nordisk, Oxford, United Kingdom
3  Science For Life Laboratory (SciLifeLab), Stockholm, Sweden
,
Sofia Klasson
1  Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
,
Marcela Davila Lopez
4  Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden
,
Christina Jern
1  Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
,
Tara M. Stanne
1  Department of Laboratory Medicine, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
› Author Affiliations
Funding This study was supported by the Swedish Heart and Lung Foundation (20160316), the Swedish Research Council (2018-02543), the Swedish Stroke Association, the Swedish state under the agreement between the Swedish government and the county councils (the ALF-agreement, ALFGBG-42), the Swedish Foundation for Strategic Research (RIF14–0081), the Rune and Ulla Amlövs Foundation for Neurologic Research, the John and Brit Wennerström Foundation for Neurologic Research, the Marcus Borgströms Foundation for Neurologic Research, and the Nilsson-Ehle Endowments.
Further Information

Publication History

17 January 2019

11 March 2019

Publication Date:
29 April 2019 (eFirst)

  

Abstract

Objective 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 cis-regulatory variants involved in regulating hemostatic genes by analyzing allele-specific expression (ASE) in human liver samples.

Study Design Biopsies of human liver tissue and blood were collected from adults undergoing liver surgery at the Sahlgrenska University Hospital (n = 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, r 2 ≥ 0.8) for relevant traits/diseases.

Results 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.

Conclusion Our study provides a comprehensive ASE analysis of hemostatic genes and insights into the regulation of hemostatic genes in human liver.

Authors' Contributions

T.M.S. and C.J. conceived the research design of the present study. C.J. was responsible for sample contribution, M.O.L. and S.K. isolated gDNA and RNA and M.O.L. prepared sequencing libraries. M.O.L., L.H., and M.D.L. performed statistical analyses. M.O.L., L.H., S.K., and M.D.L. drafted the figures. M.O.L., C.J., and T.M.S. interpreted the data. M.O.L. and T.M.S. drafted the manuscript. L.H., M.D.L., and C.J. intellectually reviewed the manuscript. All authors contributed to the last revision process and approved the version to be published.


Supplementary Material