Integrating Epigenomics into Pharmacogenomic Studies

Genetic polymorphisms influencing antihypertensive drug responses

Hypertension is a major contributor to cardiovascular disease and its associated morbidity and mortality. The low efficacy observed with some anti-hypertensive therapies has been attributed partly to inter-individual genetic variability. This paper reviews the major findings regarding these genetic variabilities that modulate responses to anti-hypertensive therapies such as angiotensin converting enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs), diuretics, calcium channel blockers (CCBs) and β-adrenoceptor blockers. The importance of studying these genetic polymorphisms stems from the goal to optimise anti-hypertensive therapy for each individual patient, aiming for the highest efficacy and lowest risk of adverse effects. It is important to recognise that environmental and epigenetic factors can contribute to the observed variations in drug responses. Owing to the multigenic and multifactorial nature of drug responses, further research is crucial for translating these findings into clinical practice and the establishment of reliable recommendations.

Knowledge, attitudes, and perceptions of the multi-ethnic population of the United Arab Emirates on genomic medicine and genetic testing

INTRODUCTION

The adoption and implementation of genomic medicine and pharmacogenomics (PGx) in healthcare systems have been very slow and limited worldwide. Major barriers to knowledge translation into clinical practice lie in the level of literacy of the public of genetics and genomics. The aim of this study was to assess the knowledge, attitudes, and perceptions of the United Arab Emirates (UAE) multi-ethnic communities toward genomic medicine and genetic testing.

METHOD

A cross-sectional study using validated questionnaires was distributed to the participants. Descriptive statistics were performed, and multivariable logistic regression models were used to identify factors associated with knowledge of genomics.

RESULTS

757 individuals completed the survey. Only 7% of the participants had a good knowledge level in genetics and genomics (95% CI 5.3-9.0%). However, 76.9% of the participants were willing to take a genetic test if their relatives had a genetic disease. In addition, the majority indicated that they would disclose their genetic test results to their spouses (61.5%) and siblings (53.4%).

CONCLUSIONS

This study sets the stage for the stakeholders to plan health promotion and educational campaigns to improve the genomic literacy of the community of the UAE as part of their efforts for implementing precision and personalized medicine in the country.

Experience with comprehensive pharmacogenomic multi-gene panel in clinical practice: a retrospective single-center study

AIM

To assess the prevalence of actionable pharmacogenetic interventions in patients who underwent pharmacogenetic testing with a multi-gene panel.

METHODS

We retrospectively reviewed single-center electronic health records. A total of 319 patients were enrolled who underwent pharmacogenomic testing with the RightMed test panel using TaqMan quantitative real-time PCR method and copy number variation analysis to determine the SNPs in the 27 target genes.

RESULTS

Actionable drug-gene pairs were found in 235 (73.7%) patients. Relevant guidelines on genotype-based prescribing were available for 133 (56.7%) patients at the time of testing. Based on the patients' genotype, 139 (43.6%) patients were using at least one drug with significant pharmacogenetic interactions.

CONCLUSION

Two out of three patients had at least one drug-gene pair in their therapy. Further studies should assess the clinical effectiveness of integrating pharmacogenomic data into patients' electronic health records.

Pharmacogenomics And Hypertension: Current Insights

Hypertension is a multifactorial disease that affects approximately one billion subjects worldwide and is a major risk factor associated with cardiovascular events, including coronary heart disease and cerebrovascular accidents. Therefore, adequate blood pressure control is important to prevent these events, reducing premature mortality and disability. However, only one third of patients have the effective control of blood pressure, despite several classes of antihypertensive drugs available. These disappointing outcomes may be at least in part explained by interpatient variability in drug response due to genetic polymorphisms. To address the effects of genetic polymorphisms on blood pressure responses to the antihypertensive drug classes, studies have applied candidate genes and genome wide approaches. More recently, a third approach that considers gene-gene interactions has also been applied in hypertension pharmacogenomics. In this article, we carried out a comprehensive review of recent findings on the pharmacogenomics of antihypertensive drugs, including diuretics, β-blockers, angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers, and calcium channel blockers. We also discuss the limitations and inconsistences that have been found in hypertension pharmacogenomics and the challenges to implement this valuable approach in clinical practice.

Pharmacogenomic Discovery Delineating the Genetic Basis of Drug Response

Personalized medicine has the promise to tailor medical care based on the patient's genetic make-up and clinical variables such as gender, race and exposure to environmental stimuli. Recent progress in pharmacogenetic and pharmacogenomic studies has suggested that drug response to therapeutic treatments is likely a complex trait influenced by a variety of genetic and non-genetic factors. Identifying molecular targets (e.g., genetic variants) delineating the genetic basis of drug response could help understand the complex nature of drug response. The last decade has witnessed significant advances in genome-wide profiling technologies for genetic/epigenetic variations and gene expression. As an unbiased, cell-based model for pharmacogenomic discovery, a tremendous resource of whole-genome molecular targets has been accumulated for the HapMap lymphoblastoid cell lines (LCLs) during the past decade. The current progress, particularly in cancer pharmacogenomics, using the LCL model was reviewed to illustrate the potential impact of systems biology approaches on pharmacogenomic discovery.

Cancer pharmacogenomics: strategies and challenges

Genetic variation influences the response of an individual to drug treatments. Understanding this variation has the potential to make therapy safer and more effective by determining selection and dosing of drugs for an individual patient. In the context of cancer, tumours may have specific disease-defining mutations, but a patient's germline genetic variation will also affect drug response (both efficacy and toxicity), and here we focus on how to study this variation. Advances in sequencing technologies, statistical genetics analysis methods and clinical trial designs have shown promise for the discovery of variants associated with drug response. We discuss the application of germline genetics analysis methods to cancer pharmacogenomics with a focus on the special considerations for study design.

Prakriti-based medicine: A step towards personalized medicine

The concept of personalized medicine has been around for as long as people have been practicing medicine. From Charaka to Hippocrates, all have practiced the personalized approach for treating a disease. In the 21^st century, personalized medicine is all about DNA. Whereas the single nucleotide polymorphism (SNP) and epigenetic factors influence drug response and form the basis of personalized medicine, the tridosha theory forms the basis of Prakriti-based medicine. It is well established by now that western allopathic medicine is excellent in handling acute medical crises, whereas Ayurveda has successfully demonstrated an ability to manage chronic disorders that Western medicine has been unable to cure. With effective integration of ‘omics’ Prakriti-based medicine can play a vital role in this changing scenario of global health wisdom as Ayurveda offers its modalities by way of ahara (diet), vihara (lifestyle), and aushadhi (medication), which are the three pillars of prakriti-based medicine making it a holistic science. Prakriti-based medicine and other traditional medicine systems have the potential to offer remedies to the challenging health issues like adverse drug reactions, drug withdrawals, and economic disparities among few. An integrative global approach could do wonders to health sciences benefiting a broad spectrum of patients.

Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation

The ability to predict how an individual patient will respond to a particular treatment is the ambitious goal of personalized medicine. The genetic make up of an individual has been shown to play a role in drug response. For pharmacogenomic studies, human lymphoblastoid cell lines (LCLs) comprise a useful model system for identifying genetic variants associated with pharmacologic phenotypes. The availability of extensive genotype data for many panels of LCLs derived from individuals of diverse ancestry allows for the study of genetic variants contributing to interethnic and interindividual variation in susceptibility to drugs. Many genome-wide association studies for drug-induced phenotypes have been performed in LCLs, often incorporating gene-expression data. LCLs are also being used in follow-up studies to clinical findings to determine how an associated variant functions to affect phenotype. This review describes the most recent pharmacogenomic findings made in LCLs, including the translation of some findings to clinical cohorts.

MicroRNA signatures associated with immortalization of EBV-transformed lymphoblastoid cell lines and their clinical traits

OBJECTIVE

MicroRNAs (miRNAs) are negative regulators of gene expression that play important roles in cell processes such as proliferation, development and differentiation. Recently, it has been reported that miRNAs are related to development of carcinogenesis. The aim of this study was to identify miRNAs associated with terminal immortalization of Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line (LCL) and associated clinical traits.

MATERIAL AND METHODS

Hence, we performed miRNA microarray approach with early- (p6) and late-passage (p161) LCLs.

RESULTS AND CONCLUSION

Microarray data showed that nine miRNAs (miR-20b*, miR-28-5p, miR-99a, miR-125b, miR-151-3p, miR-151:9.1, miR-216a, miR-223* and miR-1296) were differentially expressed in most LCLs during long-term culture. In particular, miR-125b was up-regulated in all the tested late-passage LCLs. miR-99a, miR-125b, miR-216a and miR-1296 were putative negative regulators of RASGRP3, GPR160, PRKCH and XAF1, respectively, which were found to be differentially expressed in LCLs during long-term culture in a previous study. Linear regression analysis showed that miR-200a and miR-296-3p correlated with triglyceride and HbA1C levels, respectively, suggesting that miRNA signatures of LCLs could provide information on the donor's health. In conclusion, our study suggests that expression changes of specific miRNAs may be required for terminal immortalization of LCLs. Thus, differentially expressed miRNAs would be a potential marker for completion of cell immortalization during EBV-mediated tumorigenesis.

The emerging role of microRNAs in drug responses

In recent years, pharmacogenomic research has begun to integrate genetics, gene expression and pharmacological phenotypes. MicroRNAs (miRNAs), 21- to 25-nucleotide, non-coding RNAs that are present in almost all metazoan genomes, are a class of gene regulators that downregulate gene expression at the post-transcriptional level. Experimental evidence for the role of miRNAs in regulating pharmacology-related genes and drug responses is increasing. Given the universal roles of miRNAs in various diseases, including cancer, miRNAs (eg, chemotherapy) are anticipated to have potential therapeutic effects in various diseases. The incorporation of miRNAs into pharmacogenomic research could provide improved insight into drug responses. However, more studies are necessary to evaluate the effects of these molecules in patients.

Pharmacogenetics in breast cancer: steps toward personalized medicine in breast cancer management

There is wide individual variability in the pharmacokinetics, pharmacodynamics, and tolerance to anticancer drugs within the same ethnic group and even greater variability among different ethnicities. Pharmacogenomics (PG) has the potential to provide personalized therapy based on individual genetic variability in an effort to maximize efficacy and reduce adverse effects. The benefits of PG include improved therapeutic index, improved dose regimen, and selection of optimal types of drug for an individual or set of individuals. Advanced or metastatic breast cancer is typically treated with single or multiple combinations of chemotherapy regimens including anthracyclines, taxanes, antimetabolites, alkylating agents, platinum drugs, vinca alkaloids, and others. In this review, the PG of breast cancer therapeutics, including tamoxifen, which is the most widely used therapeutic for the treatment of hormone-dependent breast cancer, is reviewed. The pharmacological activity of tamoxifen depends on its conversion by cytochrome P450 2D6 (CYP2D6) to its abundant active metabolite, endoxifen. Patients with reduced CYP2D6 activity, as a result of either their genotype or induction by the coadministration of other drugs that inhibit CYP2D6 function, produce little endoxifen and hence derive limited therapeutic benefit from tamoxifen; the same can be said about the different classes of therapeutics in breast cancer. PG studies of breast cancer therapeutics should provide patients with breast cancer with optimal and personalized therapy.

Impact of the 1000 genomes project on the next wave of pharmacogenomic discovery

The 1000 Genomes Project aims to provide detailed genetic variation data on over 1000 genomes from worldwide populations using the next-generation sequencing technologies. Some of the samples utilized for the 1000 Genomes Project are the International HapMap samples that are composed of lymphoblastoid cell lines derived from individuals of different world populations. These same samples have been used in pharmacogenomic discovery and validation. For example, a cell-based, genome-wide approach using the HapMap samples has been used to identify pharmacogenomic loci associated with chemotherapeutic-induced cytotoxicity with the goal to identify genetic markers for clinical evaluation. Although the coverage of the current HapMap data is generally high, the detailed map of human genetic variation promised by the 1000 Genomes Project will allow a more in-depth analysis of the contribution of genetic variation to drug response. Future studies utilizing this new resource may greatly enhance our understanding of the genetic basis of drug response and other complex traits (e.g., gene expression), therefore, help advance personalized medicine.

Pharmacogenomics in thrombosis

Inherited or acquired genetic abnormalities play a major role in thromboembolic complications. The goal of pharmacogenomics is to tailor medications to an individual's genetic makeup in order to improve the benefit-to-risk ratio. Significant findings have been documented showing the effect of certain genetic variations (e.g., in CYP2C9 and VKORC1) on the dose response to warfarin. Pharmacogenomic and genetic information is crucial to improving the efficacy and safety of pharmacotherapy and for the optimal management of thromboembolic disorders.

SCAN: SNP and copy number annotation

MOTIVATION

Genome-wide association studies (GWAS) generate relationships between hundreds of thousands of single nucleotide polymorphisms (SNPs) and complex phenotypes. The contribution of the traditionally overlooked copy number variations (CNVs) to complex traits is also being actively studied. To facilitate the interpretation of the data and the designing of follow-up experimental validations, we have developed a database that enables the sensible prioritization of these variants by combining several approaches, involving not only publicly available physical and functional annotations but also multilocus linkage disequilibrium (LD) annotations as well as annotations of expression quantitative trait loci (eQTLs).

RESULTS

For each SNP, the SCAN database provides: (i) summary information from eQTL mapping of HapMap SNPs to gene expression (evaluated by the Affymetrix exon array) in the full set of HapMap CEU (Caucasians from UT, USA) and YRI (Yoruba people from Ibadan, Nigeria) samples; (ii) LD information, in the case of a HapMap SNP, including what genes have variation in strong LD (pairwise or multilocus LD) with the variant and how well the SNP is covered by different high-throughput platforms; (iii) summary information available from public databases (e.g. physical and functional annotations); and (iv) summary information from other GWAS. For each gene, SCAN provides annotations on: (i) eQTLs for the gene (both local and distant SNPs) and (ii) the coverage of all variants in the HapMap at that gene on each high-throughput platform. For each genomic region, SCAN provides annotations on: (i) physical and functional annotations of all SNPs, genes and known CNVs within the region and (ii) all genes regulated by the eQTLs within the region.

AVAILABILITY

http://www.scandb.org.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Pharmacogenomics in type II diabetes mellitus management: Steps toward personalized medicine

Advances in genotype technology in the last decade have put the pharmacogenomics revolution at the forefront of future medicine in clinical practice. Discovery of novel gene variations in drug transporters, drug targets, effector proteins and metabolizing enzymes in the form of single-nucleotide polymorphisms (SNPs) continue to provide insight into the biological phenomena that govern drug efficacy and toxicity. To date, novel gene discoveries extracted from genome-wide association scans and candidate gene studies in at least four antidiabetic drug classes have helped illuminate possible causes of interindividual variability in response. Inadequate protocol guidelines for pharmacogenomics studies often leads to poorly designed studies, making it hard to formulate a definitive conclusion regarding the clinical relevance of the information at hand. These issues, along with the ethical, social, political, legislative, technological, and economic challenges associated with pharmacogenomics have only delayed its entry to mainstream clinical practice. On the other hand, these issues are being actively pursued and rapid progress is being made in each area which assures the possibility of gaining widespread acceptance in clinical practice.

Pharmacogenomics in cardiovascular disorders: Steps in approaching personalized medicine in cardiovascular medicine

Some of the most commonly prescribed medications are those for cardiovascular maladies. The beneficial effects of these medications have been well documented. However, there can be substantial variation in response to these medications among patients, which may be due to genetic variation. For this reason pharmacogenomic studies are emerging across all aspects of cardiovascular medicine. The goal of pharmacogenomics is to tailor treatment to an individual's genetic makeup in order to improve the benefit-to-risk ratio. This review examines the potential pharmacogenomic parameters which may lead to a future of personalized medicine. For example, it has been found that patients with CYP2C9 and VKORC1 gene variations have a different response to warfarin. Other studies looking at β-blockers, ACE inhibitors, ARBs, diuretics and statins have shown some results linking genetic variations to pharmacologic response. However these studies have not impacted clinical use yet, unlike warfarin findings, as the small retrospective studies need to be followed up by larger prospective studies for definitive results.

Exploring the relationship between polymorphic (TG/CA)n repeats in intron 1 regions and gene expression

The putative role of (TG/CA)n repeats in the regulation of transcription has recently been reported for several cancer- and disease-related genes, including the genes encoding the epidermal growth factor receptor (EGFR), hydroxysteroid (11-beta) dehydrogenase 2 (HSD11B2) and interferon-gamma (IFNG). These studies indicated a correlation between gene expression levels and the presence or length of (TG/CA)n repeats in their intron 1 regions. A genome-wide search for genes with similar features may provide evidence of whether these dinucleotide repeats represent a class of universal regulators of gene expression, which has recently begun to be investigated as a quantitative complex phenotype. Using a public database of simple repeats, we identified 330 genes containing potentially polymorphic long (TG/CA)n repeats (n >or= 12) in their intron 1 regions. One known physiological pathway, the calcium signalling pathway, was found to be enriched among the genes containing long repeats. In addition, certain biological processes, such as cation transport, signal transduction and ion transport, were found to be enriched in these genes. Genotyping of the long repeats showed that the majority of these dinucleotide repeats were polymorphic in the HapMap CEU (Caucasians from Utah, USA) samples of northern and western European ancestry. Evidence for a significant association between these repeats and gene expression was not observed in the genes selected based on their expression profiles in the HapMap CEU samples. Our current findings, therefore, do not support a role for these repeats as a class of universal gene expression regulators. A more comprehensive evaluation of the relationship between these repeats and gene expression, potentially in other tissues, may be necessary to illustrate their roles in gene regulation in the future.

Cell-based Models for Discovery of Pharmacogenomic Markers of Anticancer Agent Toxicity

The field of pharmacogenomics is challenging because of the multigenic nature of drug response and toxicity. The candidate gene approach has been traditionally utilized to determine the contribution of genetic variation to a particular phenotype; however, the sequencing of the human genome and the genetic resource provided by the International HapMap Project has allowed researchers to perform genome-wide studies without a priori knowledge. Recent work has demonstrated the usefulness of cell-based models for pharmacogenomic discovery using the HapMap samples, which are a panel of well-genotyped, human lymphoblastoid cell lines (LCLs) derived from 90 Utah residents with ancestry from northern and western Europe (CEU), 90 Yoruba in Ibadan, Nigeria (YRI), 45 Japanese in Tokyo, Japan (JPT) and 45 Han Chinese in Beijing, China (CHB). Using these cell-based models, investigators are able to study not only individual variation in drug response, but also population differences in drug response. Finally, besides single nucleotide polymorphisms (SNPs) and gene expression, these cell-based models can also be used to investigate other genetic (e.g. copy number variants, CNVs), epigenetic or environmental factors responsible for drug response.