Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole-genome sequences

Expanding the scope of pharmacogenomic research by including multiple global populations is integral to building robust evidence for its clinical translation. Deep whole-genome sequencing of diverse ethnic populations provides a unique opportunity to study rare and common pharmacogenomic markers that often vary in frequency across populations. In this study, we aim to build a diverse map of pharmacogenetic variants in South East Asian (SEA) Malay population using deep whole-genome sequences of 100 healthy SEA Malay individuals. We investigated the allelic diversity of potentially deleterious pharmacogenomic variants in SEA Malay population. Our analysis revealed 227 common and 466 rare potentially functional single nucleotide variants (SNVs) in 437 pharmacogenomic genes involved in drug metabolism, transport and target genes, including 74 novel variants. This study has created one of the most comprehensive maps of pharmacogenetic markers in any population from whole genomes and will hugely benefit pharmacogenomic investigations and drug dosage recommendations in SEA Malays.

Between candidate genes and whole genomes: time for alternative approaches in blood pressure genetics

Blood pressure has a significant genetic component, but less than 3% of the observed variance has been attributed to genetic variants identified to date. Candidate gene studies of rare, monogenic hypertensive syndromes have conclusively implicated several genes altering renal sodium balance, and studies of essential hypertension have inconsistently implicated over 50 genes in pathways affecting renal sodium balance and other functions. Genome-wide linkage scans have replicated numerous quantitative trait loci throughout the genome, and over 50 single nucleotide polymorphisms (SNPs) have been replicated in multiple genome-wide association studies. These studies provide considerable evidence that epistasis and other interactions play a role in the genetic architecture of blood pressure regulation, but candidate gene studies have limited scope to test for epistasis, and genome-wide studies have low power for both main effects and interactions. This review summarizes the genetic findings to date for blood pressure, and it proposes focused, pathway-based approaches involving epistasis, gene-environment interactions, and next-generation sequencing to further the genetic dissection of blood pressure and hypertension.

High-resolution melting (HRM) analysis for the detection of single nucleotide polymorphisms in microRNA target sites

BACKGROUND

The function of microRNAs (miRNAs) depends on the binding of miRNAs to their target sequences in the 3'UTR of messenger RNAs (mRNAs), which enhances the degradation of mRNAs and consequently, represses their expression. Single nucleotide polymorphisms (SNPs) in the miRNA target sequences may affect or impair the binding of miRNAs. Studies have shown that SNPs in miRNA target sites (miR-TS-SNPs) have a great influence on diverse biological functions, including pharmacogenomics and disease susceptibilities in human.

METHODS

High-resolution melting (HRM) analysis was applied for investigating the allele frequencies of 3 miR-TS-SNPs (PLA2G2A, IL-16, and NOD2) in acute leukemia. We also compared the genotypes of acute lymphoblastic leukemia patients at initial diagnosis and complete remission.

RESULTS

HRM analysis revealed 3 genotypes (both homozygous and heterozygous) in the 3 miR-TS-SNPs. The allele frequencies of all 3 miR-TS-SNPs were similar in normal individuals and patients with acute myelogenous leukemia. Most patients with acute lymphoblastic leukemia had the same genotypes at initial diagnosis and complete remission.

CONCLUSIONS

Large scale scanning of case-control studies for miR-TS-SNPs may contribute to the investigation of their roles and pathogenesis mechanisms in human diseases. Our study showed that HRM analysis can be an efficient tool for studies of miR-TS-SNPs.

Cytochrome P450-dependent eicosanoid production and crosstalk

PURPOSE OF REVIEW

This review highlights recent advances in eicosanoid biology, especially linked to the cytochrome P450 (CYP)/soluble epoxide hydrolase (sEH) axis in vascular biology and disease.

RECENT FINDINGS

Since the first reports that CYP-derived metabolites of arachidonic acid can elicit vascular smooth muscle hyperpolarization and relaxation, it has become clear that fatty acid epoxides and diols are important lipid signaling molecules. Targeting CYP epoxygenases in vivo is difficult as these enzymes are involved in the metabolism of many currently used clinical agents. However, targeting the sEH which metabolizes fatty acid epoxides to their corresponding diols is a highly effective way of manipulating levels of these lipid mediators in vivo. Indeed, sEH-/- mice are protected against the development of some forms of hypertension, and have altered adipocyte metabolism and insulin resistance, phenomena reproduced by selective sEH inhibitors.

SUMMARY

Given that elevated epoxide levels have been linked with decreased blood pressure and inflammation in animal models, inhibitors of the sEH are currently being developed for the treatment of human hypertension and inflammation/atherosclerosis. This review focuses on outlining recent insights gained in the beneficial as well as the potentially adverse aspects of interfering with the CYP/sEH axis.