Pharmacogenomics and cardiovascular drugs: need for integrated biological system with phenotypes and proteomic markers

New Biomarkers for Atherothrombosis in Antiphospholipid Syndrome: Genomics and Epigenetics Approaches

Antiphospholipid Syndrome (APS) is an autoimmune disorder, characterized by pregnancy morbidity and/or a hyper coagulable state involving the venous or the arterial vasculature and associated with antiphospholipid antibodies (aPL), including anti-cardiolipin antibodies (aCL), anti-beta2-glycoprotein I (anti-ß2GPI), and Lupus anticoagulant (LA). In recent years there have been many advances in the understanding of the molecular basis of vascular involvement in APS. APS is of multifactorial origin and develops in genetically predisposed individuals. The susceptibility is determined by major histocompatibility complex (MHC). Different HLA-DR and HLA-DQ alleles have been reported in association with APS. Moreover, MHC II alleles may determine the autoantibody profile and, as such, the clinical phenotype of this disease. Besides, polymorphisms in genes related to the vascular system are considered relevant factors predisposing to clinical manifestations. Antiphospholipid antibodies (aPL) induce genomic and epigenetic alterations that support a pro- thrombotic state. Thus, a specific gene profile has been identified in monocytes from APS patients -related to aPL titres in vivo and promoted in vitro by aPL- explaining their cardiovascular involvement. Regarding epigenetic approaches, we previously recognized two miRNAs (miR-19b/miR-20a) as potential modulators of tissue factor, the main receptor involved in thrombosis development in APS. aPLs can further promote changes in the expression of miRNA biogenesis proteins in leukocytes of APS patients, which are translated into an altered miRNA profile and, consequently, in the altered expression of their protein targets related to thrombosis and atherosclerosis. MicroRNAs are further released into the circulation, acting as intercellular communicators. Accordingly, a specific signature of circulating miRNAs has been recently identified in APS patients as potential biomarkers of clinical features. Genomics and epigenetic biomarkers might also serve as indices for disease progression, clinical pharmacology, or safety, so that they might be used to individually predict disease outcome and guide therapeutic decisions. In that way, in the setting of a clinical trial, novel and specific microRNA–mRNA regulatory networks in APS, modified by effect of Ubiquinol treatment, have been identified. In this review, current and previous studies analyzing genomic/epigenetic changes related to the clinical profile of APS patients, and their modulation by effect of specific therapies, are discussed.

Pharmacogenomics of oral antidiabetic medications: current data and pharmacoepigenomic perspective

Type 2 diabetes mellitus (T2DM) is an increasingly prevalent disease. Several classes of drugs are currently available to treat T2DM patients; however, clinical response to these drugs often exhibits significant variation among individuals. For the oral antidiabetic drug classes of sulfonylureas, nonsulfonylurea insulin secretagogs, biguanides and thiazolidinediones, pharmacogenomic evidence has accumulated demonstrating an association between specific gene polymorphisms and interindividual variability in their therapeutic and adverse reaction effects. These polymorphisms are in genes of molecules involved in metabolism, transport and therapeutic mechanisms of the aforementioned drugs. Overall, it appears that pharmacogenomics has the potential to improve the management of T2DM and help clinicians in the effective prescribing of oral antidiabetic medications. Although pharmacogenomics can explain some of the heterogeneity in dose requirements, response and incidence of adverse effects of drugs between individuals, it is now clearly understood that much of the diversity in drug effects cannot be solely explained by studying the genomic diversity. Epigenomics, the field that focuses on nongenomic modifications that influence gene expression, may expand the scope of pharmacogenomics towards optimization of drug therapy. Therefore, pharmacoepigenomics, the combined analysis of genetic variations and epigenetic modifications, holds promise for the realization of personalized medicine. Although pharmacoepigenomics has so far been evaluated mainly in cancer pharmacotherapy, studies on epigenomic modifications during T2DM development provide useful data on the potential of pharmacoepigenomics to elucidate the mechanisms underlying interindividual response to oral antidiabetic treatment. In summary, the present article focuses on available data from pharmacogenomic studies of oral antidiabetic drugs and also provides an overview of T2DM epigenomic research, which has the potential to boost the development of pharmacoepigenomics in antidiabetic treatment.

Peptidomics: identification of pathogenic and marker peptides

Recent years have seen great advances in mass spectrometry and proteomics, the science dealing with the analysis of proteins, their structure and function. A branch of proteomics dealing with naturally occurring peptides is often referred to as peptidomics. Direct analysis of peptides produced by processing or degradation of proteins might be useful for example for detecting and identifying pathogenic and/or biomarker peptides in body fluids like blood. In this paper, we introduce one of the standard protocols for comprehensive analysis of serum-derived peptides, which consists of methods for purification of serum peptides, detection of peptides, pattern recognition and clustering (bioinformatics), and identification of peptide sequences. Peptide identification should be followed by the investigation of their pathogenic roles using for example synthetic peptides and the establishment of their usefulness as bioclinical markers.

Association of ABCB1 gene polymorphisms with plasma lipid and apolipoprotein concentrations in the STANISLAS cohort

BACKGROUND

While involvement of ABCB1 is well known in drug transport, its metabolite transport role is not so well understood. Like other ABC transporters, ABCB1 might be implicated in cholesterol homeostasis and ABCB1 polymorphisms which are responsible for drug resistance might affect lipid homeostasis. Our objective was thus to investigate the implication of ABCB1 polymorphisms and haplotypes in the genetic variability of lipid constituents in healthy people.

METHODS

T-129C, G-1A, A61G, G1199A, C1236T, T-76A, G2677T/A and C3435T polymorphisms were genotyped in 371 supposed healthy individuals from the STANISLAS cohort. Each polymorphism was tested with plasma concentrations of total cholesterol, HDL and LDL cholesterol, triglycerides and apolipoproteins A1, B, C3 and E.

RESULTS

After adjustment for covariates, carriers of at least one 3435T allele had a significant higher level of apolipoprotein A1 (p = 0.005). In addition, significant correlations were observed in a sex-dependent manner. Women carrying either T-76 or 1236T allele (tendency with G-1 and 2677T/A) had lower total cholesterol (p < or = 0.01) and apolipoprotein B (T-76 exclusively, p=0.002). Haplotypes analysis was not more informative than the single polymorphisms except G2677T/A-C3435T haplotypes for apolipoprotein A1 concentration.

CONCLUSION

ABCB1 polymorphisms contribute to the genetic variability of plasma values of lipids and lipoproteins in healthy people.

The role of toxicoproteomics in assessing organ specific toxicity

Aims of this chapter on the role of toxicoproteomics in assessing organ-specific toxicity are to define the field of toxicoproteomics, describe its development among global technologies, and show potential uses in experimental toxicological research, preclinical testing and mechanistic biological research. Disciplines within proteomics deployed in preclinical research are described as Tier I analysis, involving global protein mapping and protein profiling for differential expression, and Tier II proteomic analysis, including global methods for description of function, structure, interactions and post-translational modification of proteins. Proteomic platforms used in toxicoproteomics research are briefly reviewed. Preclinical toxicoproteomic studies with model liver and kidney toxicants are critically assessed for their contributions toward understanding pathophysiology and in biomarker discovery. Toxicoproteomics research conducted in other organs and tissues are briefly discussed as well. The final section suggests several key developments involving new approaches and research focus areas for the field of toxicoproteomics as a new tool for toxicological pathology.

CYP3A53A allele is associated with reduced lowering-lipid response to atorvastatin in individuals with hypercholesterolemia

BACKGROUND

The cytochrome P450 isoenzyme 3A5 (CYP3A5) has an important role on biotransformation of xenobiotics. CYP3A5 SNPs have been associated with variations on enzyme activity that can modify the metabolism of several drugs.

METHODS

In order to evaluate the influence of CYP3A5 variants on response to lowering-cholesterol drugs, 139 individuals with hypercholesterolemia were selected. After a wash-out period of 4 weeks, individuals were treated with atorvastatin (10 mg/day/4 weeks). Genomic DNA was extracted by a salting-out procedure. CYP3A5*3C, CYP3A5*6 and CYP3A5*1D were analyzed by PCR-RFLP and DNA sequencing.

RESULTS

>Frequencies of the CYP3A5*3C and CYP3A5*1D alleles were lower in individuals of African descent (*3C: 47.8% and *1D: 55.2%) than in non-Africans (*3C: 84.9% and *1D 84.8%, p<0.01). Non-Africans carrying *3A allele (*3C and *1D combined alleles) had lower total and LDL-cholesterol response to atorvastatin than non-*3A allele carriers (p<0.05).

CONCLUSION

CYP3A5*3A allele is associated with reduced cholesterol-lowering response to atorvastatin in non-African individuals.

Collaborative depression care, screening, diagnosis and specificity of depression treatments in the primary care setting

The identification, referral and specific treatment of midlife patients in primary care who are distressed by mood, anxiety, sleep and stress-related symptoms, with or without clinically confirmed menopausal symptoms, are confounded by many structural issues in the delivery of women's healthcare. Diagnosis, care delivery, affordability of treatment, time commitment for treatment, treatment specificity for a particular patient's symptoms and patient receptiveness to diagnosis and treatment all play roles in the successful amelioration of symptoms in this patient population. The value of screening for depression in primary care, the limitations of commonly used screening instruments relative to culture and ethnicity, and which clinical care systems make best use of diagnostic screening programs will be discussed in the context of the midlife woman. The Sequenced Treatment Alternatives to Relieve Depression (STAR*D) program illustrates the relatively high rate of unremitted patients, regardless of clinical setting, who are receiving antidepressants. Nonmedication treatment approaches, referred to in the literature as 'nonsomatic treatments', for depression, anxiety and stress, include different forms of cognitive-behavioral therapy, interpersonal therapy, structured daily activities, mindfulness therapies, relaxation treatment protocols and exercise. The specificity of these treatments, their mechanisms of action, the motivation and time commitment required of patients, and the availability of trained practitioners to deliver them are reviewed. Midlife women with menopausal symptoms and depression/anxiety comorbidity represent a challenging patient population for whom an individualized treatment plan is often necessary. Treatment for depression comorbid with distressing menopausal symptoms would be facilitated by the implementation of a collaborative care program for depression in the primary care setting.

The integration of personalized and systems medicine: bioinformatics support for pharmacogenomics and drug discovery

Pharmacogenomics may have a deep impact on every drug treatment protocol to bring the right drug to the right patient. While pharmacogenomics can help achieve individualized medicine, the study of systems biology can help us understand the key issues in pharmacogenomics at different levels. These key issues include the associations between structure and function, the correlations between genotype and phenotype, and the interactions among gene, drug, and environment. Utilizing bioinformatics in pharmacogenomics that is conducted in a systemic way can help integrate information from different levels. At the molecular level, the detailed features of a gene and the relationship between genetic structure and function need to be explored. These detailed features include sequence analytic information such as sequence retrieval and structural modeling, sequence variation information, and sequence patterns that can correlate sequence structure to functional motifs. At the cellular level, the interactions and networks among those molecules should be examined. Higher degrees of understanding at the tissue and organism levels can help establish the correlations between genotype and phenotype. The application of bioinformatics methods in pharmacogenomics and systems biology should enable a more profound understanding of diseases at different levels and lead to both individualized and systems medicine. To facilitate up-to-date bio-informatics support, an integrated search engine and updated collections of tools are freely available at http://sysmed.pharmtao.com.

Pharmacogenomics and antihypertensive drugs: a path toward personalized medicine

Pharmacogenomics focuses on genes and the transcriptome and proteome. It has the potential to enhance healthcare management by improving disease diagnosis and implementing treatments adapted to each patient. Previously, pharmacogenetics of candidate genes focused on clinical research. It is now extended by using genome-wide approaches to elucidate the inherited basis of differences between individuals in their response to drugs. We summarize relevant polymorphisms of genes involved in the pharmacokinetics and pharmacodynamics of antihypertensive drugs and we give an overview of the state of pharmacogenomic research in hypertension medicine. Even if things are getting better, current pharmacogenetic studies still lack power, adequate selection of candidate genes and knowledge of their functions at the physiological level. Finally, some specific end point phenotypes (i.e., peptides or proteins related to the metabolic cycle targeted by the drug) should be integrated to propose data that are easily applicable to personalized medicine.

Determination of ABCB1 polymorphisms and haplotypes frequencies in a French population

The ATP-binding cassette (ABC) transporter ABCB1, or P-glycoprotein, is a transmembrane efflux pump well known for its implication in drug transport and chemoresistance. ABCB1 substrates include either drugs, such as antiretrovirals and immunomodulators, or physiological molecules like phospholipids. Pharmacogenetic analysis of ABCB1 polymorphisms, in addition to other xenobiotic metabolizing enzymes, might help to personalize and optimize drug therapy. Indeed, some polymorphisms of ABCB1 have been implicated in susceptibility to diseases, changes in drug pharmacokinetics, and in variation of the biological response to drug treatment. In addition, variant and haplotype distributions differ depending on ethnicity. Thus, some ethnies may be at higher risk for adverse events, inefficacy of treatment or prevalence of pathologies. This study aimed to determine frequencies of ABCB1 polymorphisms and haplotypes in a sample of French healthy individuals. DNA was isolated from blood-EDTA. Polymerase chain reaction-restriction fragment length polymorphism and TaqMan single nucleotide polymorphism genotyping assays were used to genotype 227 individuals for T-129C, G-1A, A61G, G1199A, C1236T, T-76A, G2677T/A and C3435T polymorphisms. The observed frequencies of the variant allele for these eight polymorphisms are 0.04, 0.08, 0.09, 0.06, 0.42, 0.46, 0.45 and 0.46 respectively. These polymorphisms are in linkage disequilibrium and haplotype frequencies were determined, the most frequent haplotype being the one with variants at position 1236, 2677 and 3435 and wild-type alleles at the other positions. Finally, the frequencies of these eight ABCB1 polymorphisms in our French individuals supposed to be healthy population are quite similar to those described in other Caucasian populations except for the C3435T polymorphism.

Genetics of inflammation in age-related atherosclerosis: its relevance to pharmacogenomics

In response to tissue injury elicited by trauma or infection, the inflammatory response, as a complex network of molecular and cellular interactions, sets an answer directed to facilitate a return to physiological homeostasis and tissue repair. The role of the genetic background and the subsequent predisposition toward the extent of the inflammatory response is determined by gene variability encoding endogenous mediators involved in the inflammatory pathway. Due to its clinical relevance, the genetics of inflammation in aging will be studied using an inflammatory disease like atherosclerosis as an example. Several studies have reported a significant difference in distribution, between patients and controls, of genes involved in inflammation. So, the proinflammatory alleles are underrepresented in control subjects and overrepresented in patients affected by atherosclerosis. These studies will allow building a risk profile that potentially enables the early identification of individuals susceptible to disease and the possible design or use of drug at the right dose for a desired effect, that is, a pharmacogenomic approach for this disease.

Enzymes and pharmacogenetics of cardiovascular drugs

To select the best drug for a patient, physicians can use pharmacogenomics to optimize the effective drug and to minimize adverse reactions. Many enzymes are involved in the pharmacokinetic and pharmacodynamic sources of cardiovascular drugs. Taking the antihypertensive drugs as an example, the variability in blood pressure response is very high in different individuals, some of them having an increase in blood pressure. The most important proteins involved in the patient response to a drug are cytochrome P450 (CYP) 2D6, CYP2C19, CYP3A4 and the ABCB1 transporter. These enzymes, at the origin of important side effects or drug interactions, are responsible, at a great extent, of the cardiovascular drug response variability. Genotyping of the most important CYP today is easy while no reliable tool has been developed for the ABC transporters ATPase dependent and linked to the other phase I and phase II enzymes. The second relevant group of enzymes are involved in pharmacodynamic action of cardiovascular drugs: enzymes of the renin-angiotensin system and enzymes of the lipid metabolism. Angiotensin converting enzyme (ACE) is the most studied target with a relevant insertion deletion polymorphism. Contradictory reported data could be explained by ethnic differences or patient sample size which are often too small.

Vascular endothelial growth factor pharmacogenetics: a new perspective for anti-angiogenic therapy

The pharmacogenetic approach to anti-angiogenic therapy should be considered a possible strategy for many pathological conditions with high incidence in Western countries, including solid tumors, age-related macular degeneration or endometriosis. While pharmacogenetic studies are building stronger foundations for the systematic investigations of phenotype–genotype relationships in many research and clinical fields of medicine, pharmacogenetic data regarding anti-angiogenic drugs are still lacking. Here we review preclinical and clinical genetic studies on angiogenic determinants such as vascular endothelial growth factor and vascular endothelial growth factor receptor-2. We suggest that pharmacogenetic profiling of patients who are candidates for the currently available anti-angiogenic agents targeting vascular endothelial growth factor and vascular endothelial growth factor receptor-2 may aid the selection of patients on the basis of their likelihood of responding to the drugs or suffering from toxicity.

Genetic information in the diagnosis and treatment of hypertension

Advancement in cardiovascular science should be measured by a number of new diagnostic and therapeutic options applied in clinical practice as a result of translational research. Hypertension genetics is a good example of such a successful transfer of knowledge from bench to bedside. There are genetic methods currently used as diagnostic tools in patients presenting with secondary forms of hypertension, including primary hyperaldosteronism, Cushing's syndrome, pheochromocytoma, and chronic kidney disease. Directed treatment that corrects pathophysiologic abnormalities is available for several monogenic forms of hypertension as a result of uncovering their underlying genetic mechanisms. Progress in hypertension pharmacogenetics and pharmacogenomics brings closer a perspective of personalized antihypertensive treatment and gene transfer strategies, which, although still considered as innovative approaches, may soon become options to treat, control, and, possibly, cure hypertension.

Pharmacogenetics, Pharmacogenomics and Personalized Medicine: Are We There Yet?

The genetic basis of a differential response to drugs has been understood for a limited number of agents for over 30 years. This knowledge has generated hope that the individual basis for response to a wide range of drugs would be quickly known, and individualized drug selection and dosing would be possible for many or all disorders. Understanding the variable response to drugs seems particularly pressing in the field of oncology, in which the stakes are high (failure to cure cancer usually leads to death), drugs commonly have a narrow therapeutic index, and toxicities can be severe (a significant frequency of toxic death is a feature of most acute myeloid leukemia protocols, for example). However, in common with many new technologies, the generalizability and clinical application of pharmacogenetics has proved more challenging than expected. Difficulties include, in many examples, a modest clinical effect relative to genotype, therapy-specific, not broad, applicability and the very major challenge of unraveling the complexity of gene-gene interactions. In addition, ethical and economic challenges to the application of pharmacogenetics have moved to the fore in recent years, particularly in the context of racial differences in outcome of therapy. Genomic, rather than candidate gene approaches to identification of relevant loci are increasingly being explored, and significant progress is being made. However, greater understanding of the complexities of multiple gene modifiers of outcome, and the statistical challenge of understanding such data, will be needed before individualized therapy can be applied on a routine basis.