A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver

AbstractCharacterizing the relationship between genetic, epigenetic (e.g., deoxyribonucleic acid [DNA] methylation), and transcript variation could provide insights into mechanisms regulating hemostasis and potentially identify new drug targets. Several hemostatic factors are synthesized in the liver, yet high-resolution DNA methylation data from human liver tissue is currently lacking for these genes. Single-nucleotide polymorphisms (SNPs) can influence DNA methylation in cis which can affect gene expression. This can be analyzed through allele-specific methylation (ASM) experiments. We performed targeted genomic DNA- and bisulfite-sequencing of 35 hemostatic genes in human liver samples for SNP and DNA methylation analysis, respectively, and integrated the data for ASM determination. ASM-associated SNPs (ASM-SNPs) were tested for association to gene expression in liver using in-house generated ribonucleic acid-sequencing data. We then assessed whether ASM-SNPs associated with gene expression, plasma proteins, or other traits relevant for hemostasis using publicly available data. We identified 112 candidate ASM-SNPs. Of these, 68% were associated with expression of their respective genes in human liver or in other human tissues and 54% were associated with the respective plasma protein levels, activity, or other relevant hemostatic genome-wide association study traits such as venous thromboembolism, coronary artery disease, stroke, and warfarin dose maintenance. Our study provides the first detailed map of the DNA methylation landscape and ASM analysis of hemostatic genes in human liver tissue, and suggests that methylation regulated by genetic variants in cis may provide a mechanistic link between noncoding SNPs and variation observed in circulating hemostatic proteins, prothrombotic diseases, and drug response.

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The Influence of Tissue Procurement Procedures on RNA Integrity, Gene Expression, and Morphology in Porcine and Human Liver Tissue

Biopreservation and Biobanking ◽

10.1089/bio.2014.0076 ◽

2015 ◽

Vol 13 (3) ◽

pp. 200-206 ◽

Cited By ~ 12

Author(s):

Marcel Kap ◽

Anieta M. Sieuwerts ◽

Mikael Kubista ◽

Monique Oomen ◽

Shazia Arshad ◽

...

Keyword(s):

Gene Expression ◽

Liver Tissue ◽

Human Liver ◽

Human Liver Tissue ◽

Rna Integrity ◽

Tissue Procurement

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

Thrombosis and Haemostasis ◽

10.1055/s-0039-1687879 ◽

2019 ◽

Vol 119 (07) ◽

pp. 1072-1083 ◽

Cited By ~ 1

Author(s):

Martina Olsson Lindvall ◽

Lena Hansson ◽

Sofia Klasson ◽

Marcela Davila Lopez ◽

Christina Jern ◽

...

Keyword(s):

Human Liver ◽

Genome Wide Association Study ◽

University Hospital ◽

Snp Analysis ◽

Specific Expression ◽

Human Liver Tissue ◽

Expression Variability ◽

Allele Specific ◽

Specific Regulation ◽

Hemostatic Genes

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.

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Expression of the novel gene osteoactivin in rat and human liver tissue and isolated liver mononuclear phagocytes

Zeitschrift für Gastroenterologie ◽

10.1055/s-2004-816028 ◽

2004 ◽

Vol 42 (01) ◽

Author(s):

BH Haralanova-Ilieva ◽

T Armbrust ◽

G Ramadori

Keyword(s):

Liver Tissue ◽

Human Liver ◽

Mononuclear Phagocytes ◽

The Novel ◽

Human Liver Tissue ◽

Novel Gene ◽

Isolated Liver

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Iron, copper, zinc and selenium in human liver tissue measured by X-ray fluorescence spectrometry

Scandinavian Journal of Clinical and Laboratory Investigation ◽

10.3109/00365518309168851 ◽

1983 ◽

Vol 43 (8) ◽

pp. 691-697 ◽

Cited By ~ 26

Author(s):

N. Milman ◽

J. Laursen ◽

J. Pødenphant ◽

P. Staun-Olsen

Keyword(s):

Liver Tissue ◽

Human Liver ◽

Fluorescence Spectrometry ◽

Human Liver Tissue ◽

X Ray ◽

Iron Copper ◽

Copper Zinc

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Human Liver-Specific Nanocarrier in a Novel Mouse Xenograft Model Bearing Noncancerous Human Liver Tissue

European Surgical Research ◽

10.1159/000322491 ◽

2011 ◽

Vol 46 (2) ◽

pp. 65-72 ◽

Cited By ~ 6

Author(s):

Yoshifumi Matsuura ◽

Hiroshi Yagi ◽

Sachiko Matsuda ◽

Osamu Itano ◽

Koichi Aiura ◽

...

Keyword(s):

Liver Tissue ◽

Human Liver ◽

Xenograft Model ◽

Human Liver Tissue ◽

Mouse Xenograft ◽

Mouse Xenograft Model

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Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals

Thrombosis and Haemostasis ◽

10.1055/s-0040-1720980 ◽

2020 ◽

Author(s):

Annelie Angerfors ◽

Martina Olsson Lindvall ◽

Björn Andersson ◽

Staffan Nilsson ◽

Marcela Davila Lopez ◽

...

Keyword(s):

Dna Methylation ◽

Peripheral Blood ◽

Liver Tissue ◽

Association Studies ◽

Epidemiological Studies ◽

Methylation Pattern ◽

Cpg Dinucleotides ◽

Phenotypic Differences ◽

Targeted Bisulfite Sequencing ◽

Hemostatic Genes

AbstractDNA methylation has become increasingly recognized in the etiology of complex diseases, including thrombotic disorders. Blood is often collected in epidemiological studies for genotyping and has recently also been used to examine DNA methylation in epigenome-wide association studies. DNA methylation patterns are often tissue-specific, thus, peripheral blood may not accurately reflect the methylation pattern in the tissue of relevance. Here, we collected paired liver and blood samples concurrently from 27 individuals undergoing liver surgery. We performed targeted bisulfite sequencing for a set of 35 hemostatic genes primarily expressed in liver to analyze DNA methylation levels of >10,000 cytosine-phosphate-guanine (CpG) dinucleotides. We evaluated whether DNA methylation in blood could serve as a proxy for DNA methylation in liver at individual CpGs. Approximately 30% of CpGs were nonvariable and were predominantly hypo- (<25%) or hypermethylated (>70%) in both tissues. While blood can serve as a proxy for liver at these CpGs, the low variability renders these unlikely to explain phenotypic differences. We therefore focused on CpG sites with variable methylation levels in liver. The level of blood–liver tissue correlation varied widely across these variable CpGs; moderate correlations (0.5 ≤ r < 0.75) were detected for 6% and strong correlations (r ≥ 0.75) for a further 4%. Our findings indicate that it is essential to study the concordance of DNA methylation between blood and liver at individual CpGs. This paired blood–liver dataset is intended as a resource to aid interpretation of blood-based DNA methylation results.

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