Pharmacogenetics: Implications for drug development,patients and society

Clinical diagnosis and prescribing is a highly sophisticated art, requiring many years of training. Despite this, the response of individual patients to medicines (where efficacy and safety have been proven in large clinical studies) can still be somewhat variable. Knowledge of the likely response of an individual patient to a medicine will enable physicians to select the most effective and well-tolerated treatment for that patient. Pharmacogenetics is the use of genetic science and technology to provide new insights on the likely response to a particular medicine. (This contrasts with the more conventional use of genetics to elicit information about diseases.) Pharmacogenetic medicine response profiles could take the form of either gene-specific profiles, which will determine the gene variants that affect the mode of action and the metabolism of the medicine, or abbreviated single nucleotide polymorphism profiles, which are correlated with medicine-related phenotypes. In general, pharmacogenetic medicine response profiles will be unlikely to provide additional information about the patient's disease or predict any other diseases. The ethical, legal and social issues associated with medicine response profiles are clearly of a quite different magnitude from those associated with the gene-specific tests for disease.     

PREDICT: a method for inferring novel drug indications with application to personalized medicine

Inferring potential drug indications, for either novel or approved drugs, is a key step in drug development. Previous computational methods in this domain have focused on either drug repositioning or matching drug and disease gene expression profiles. Here, we present a novel method for the large‐scale prediction of drug indications (PREDICT) that can handle both approved drugs and novel molecules. Our method is based on the observation that similar drugs are indicated for similar diseases, and utilizes multiple drug–drug and disease–disease similarity measures for the prediction task. On cross‐validation, it obtains high specificity and sensitivity (AUC=0.9) in predicting drug indications, surpassing existing methods. We validate our predictions by their overlap with drug indications that are currently under clinical trials, and by their agreement with tissue‐specific expression information on the drug targets. We further show that disease‐specific genetic signatures can be used to accurately predict drug indications for new diseases (AUC=0.92). This lays the computational foundation for future personalized drug treatments, where gene expression signatures from individual patients would replace the disease‐specific signatures.     

Peripheral blood gene expression profiling for cardiovascular disease assessment

Whole blood gene expression profiling has the potential to be informative about dynamic changes in disease states and to provide information on underlying disease mechanisms. Having demonstrated proof of concept in animal models, a number of studies have now tried to tackle the complexity of cardiovascular disease in human hosts to develop better diagnostic and prognostic indicators. These studies show that genomic signatures are capable of classifying patients with cardiovascular diseases into finer categories based on the molecular architecture of a patient's disease and more accurately predict the likelihood of a cardiovascular event than current techniques. To highlight the spectrum of potential applications of whole blood gene expression profiling approach in cardiovascular science, we have chosen to review the findings in a number of complex cardiovascular diseases such as atherosclerosis, hypertension and myocardial infarction as well as thromboembolism, aortic aneurysm, and heart transplant.     

The evidence basis for coenzyme Q therapy in oxidative phosphorylation disease

The evidence supporting a treatment benefit for coenzyme Q₁₀ (CoQ₁₀) in primary mitochondrial disease (mitochondrial disease) whilst positive is limited. Mitochondrial disease in this context is defined as genetic disease causing an impairment in mitochondrial oxidative phosphorylation (OXPHOS). There are no treatment trials achieving the highest Level I evidence designation. Reasons for this include the relative rarity of mitochondrial disease, the heterogeneity of mitochondrial disease, the natural cofactor status and easy ‘over the counter availability’ of CoQ₁₀ all of which make funding for the necessary large blinded clinical trials unlikely. At this time the best evidence for efficacy comes from controlled trials in common cardiovascular and neurodegenerative diseases with mitochondrial and OXPHOS dysfunction the etiology of which is most likely multifactorial with environmental factors playing on a background of genetic predisposition. There remain questions about dosing, bioavailability, tissue penetration and intracellular distribution of orally administered CoQ₁₀, a compound which is endogenously produced within the mitochondria of all cells. In some mitochondrial diseases and other commoner disorders such as cardiac disease and Parkinson’s disease low mitochondrial or tissue levels of CoQ₁₀ have been demonstrated providing an obvious rationale for supplementation. This paper discusses the current state of the evidence supporting the use of CoQ₁₀ in mitochondrial disease.     

From the laboratory bench to the patient's bedside: an update on clinical trials with mesenchymal stem cells

Mesenchymal Stem Cells (MSCs) are non-hematopoietic multi-potent stem-like cells that are capable of differentiating into both mesenchymal and non-mesenchymal lineages. In fact, in addition to bone, cartilage, fat, and myoblasts, it has been demonstrated that MSCs are capable of differentiating into neurons and astrocytes in vitro and in vivo. MSCs are of interest because they are isolated from a small aspirate of bone marrow and can be easily expanded in vitro. As such, these cells are currently being tested for their potential use in cell and gene therapy for a number of human diseases. Nevertheless, there are still some open questions about origin, multipotentiality, and anatomical localization of MSCs. In this review, we discuss clinical trials based on the use of MSCs in cardiovascular diseases, such as treatment of acute myocardial infarction, endstage ischemic heart disease, or prevention of vascular restenosis through stem cell-mediated injury repair. We analyze data from clinical trials for treatment of osteogenesis imperfecta (OI), which is a genetic disease characterized by production of defective type I collagen. We describe progress for neurological disease treatment with MSC transplants. We discuss data on amyotrophic lateral sclerosis (ALS) and on lysosomal storage diseases (Hurler syndrome and metachromatic leukodystrophy). A section of review is dedicated to ongoing clinical trials, involving MSCs in treatment of steroid refractory Graft Versus Host Disease (GVHD); periodontitis, which is a chronic disease affecting periodontium and causing destruction of attachment apparatus, heart failure, and bone fractures. Finally, we will provide information about biotech companies developing MSC therapy.     

New insights from the last decade of research in psychiatric genetics: discoveries,challenges and clinical implications

Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.     

Utility and efficiency of linked marker genes for genetic counseling. II. Identification of linkage phase by offspring phenotypes

For a linked marker locus to be useful for genetic counseling, the counselee must be heterozygous for both disease and marker loci and his or her linkage phase must be known. It is shown that when the phenotypes of the counselee's previous children for the disease and marker loci are known, the linkage phase can often be inferred with a high probability, and thus it is possible to conduct genetic counseling. To evaluate the utility of linked marker genes for genetic counseling, the accuracy of prediction of the risk for a prospective child with a given marker gene to develop the genetic disease and the proportion of families in which a particular marker locus can be used for genetic counseling are studied for X-linked recessive, autosomal dominant, and autosomal recessive diseases. In the case of X-linked genetic diseases, information from children is very useful for determining the linkage phase of the counselee and predicting the genetic disease. In the case of autosomal dominant diseases, not all children are informative, but if the number of children is large, the phenotypes of children are often more informative than the information from grandparents. In the case of autosomal recessive diseases, information from grandparents is usually useless, since they show a normal phenotype for the disease locus. If we use information on the phenotypes of children, however, the linkage phase of the counselee and the risk of a prospective child can be inferred with a high probability. The proportion of informative families depends on the dominance relationship and frequencies of marker alleles, and the number of children. In general, codominant markers are more useful than are dominant markers, and a locus with high heterozygosity is more useful than is a locus with low heterozygosity.     

Genetic determinants of platelet function in thromboembolic diseases

Within the past decade our understanding of thromboembolic disorders has become even more sophisticated as recent discoveries have suggested the influence of gene variants on the development of atherosclerotic disease and arterial thrombosis. Candidate genes encode proteins involved in processes relevant to atherosclerosis, ranging from cholesterol metabolism to arterial thrombosis. Platelets are key elements in primary hemostasis, but also in arterial thrombosis. Moreover, a number of genetic polymorphisms of platelet proteins may also induce gain or loss of function, supporting a role predisposing some individuals to thrombotic events. However, after thousands of studies, much controversy remains whether individual platelet polymorphisms contribute to an increased likelihood of thromboembolic disorders. Although platelet polymorphisms are a promising addition to more established cardiovascular risk factors, identifying genetic variants as a single cause of cardiovascular disease would be an oversimplification; instead, the contribution of these polymorphisms should also be considered in the context of a multifactorial disease. Gene-gene and gene-environment studies would identify specific combinations associated with a high risk to suffer from these diseases. The platelet's genetic heterogeneity should also be considered in every aspect of clinical medicine, ranging from susceptibility to diseases, pathogenesis, and clinical outcome to diversity in responses to drug treatment (pharmacogenomics), and bleeding.     

Returning genetic research results to individuals: points-to-consider

This paper is intended to stimulate debate amongst stakeholders in the international research community on the topic of returning individual genetic research results to study participants. Pharmacogenetics and disease genetics studies are becoming increasingly prevalent, leading to a growing body of information on genetic associations for drug responsiveness and disease susceptibility with the potential to improve health care. Much of these data are presently characterized as exploratory (non-validated or hypothesis-generating). There is, however, a trend for research participants to be permitted access to their personal data if they so choose. Researchers, sponsors, patient advocacy groups, ethics committees and regulatory authorities are consequently confronting the issue of whether, and how, study participants might receive their individual results. Noted international ethico-legal guidelines and public policy positions in Europe and the United States are reviewed for background. The authors offer 'Points-to-Consider' regarding returning results in the context of drug development trials based on their knowledge and experience. Theses considerations include: the clinical relevance of data, laboratory qualifications, informed consent procedures, confidentiality of medical information and the competency of persons providing results to participants. The discussion is framed as a benefit-to-risk assessment to balance the potential positive versus negative consequences to participants, while maintaining the integrity and feasibility of conducting genetic research studies.     

Clinical implications of pharmacogenetics of cytochrome P450 drug metabolizing enzymes

For many drugs, pharmacogenetic polymorphisms are known affecting biotransformation and clinical outcome. The clinical importance of these variants depends on allele-frequency and the effect size of the clinical outcome parameters. Further, it depends on the therapeutic range of the drug which is affected, on predictability of drug response as well as on duration until onset of therapeutic efficacy. Consequences which arise from genotyping might be: adjustment of dose according to genotype, choice of therapeutic strategy or even choice of drug. In antidepressant drug treatment, most drugs are metabolized via the polymorphic cytochrome P450 enzyme CYP2D6. Huge differences in pharmacokinetic parameters have been consistently shown for many tricyclics, some SSRIs, and other antidepressant drugs whereas the effects on therapeutic efficacy and adverse events have been described controversially. In cardiovascular disease, oral anticoagulants, nonsteroidal anti-inflammatory drugs, oral hypoglycemic drugs and other drugs are affected by genetic polymorphisms of the cytochrome P450 drug metabolizing enzyme CYP2C9. Studies in patients or healthy volunteers revealed up to 10-fold differences in pharmacokinetic parameters due to genetic polymorphisms of CYP2C9. Pharmacogenetics based dose adjustments are one tool to individualize drug treatment according to genetic factors. They can be derived from pharmacokinetic data with the aim to obtain equal drug concentrations in each individual. Prospective validation of dose adjustments based on pharmacogenetics should be performed before routine application of such strategies. A controlled prospective clinical trial with one arm receiving genotype-based dose adjustments and the other arm receiving therapy as usual will elucidate the benefit of pharmacogenomics-based individualization of certain drug therapies.     

Genetic therapies for cardiovascular diseases

Recent advances in understanding the molecular and cellular basis of cardiovascular diseases, together with the availability of tools for genetic manipulation of the cardiovascular system, offer possibilities for new treatments. Gene therapies have demonstrated potential usefulness for treating complex cardiovascular diseases, such as hypertension, atherosclerosis and myocardial ischemia, in various animal models. Some of these experimental therapies are now undergoing clinical evaluation in patients with cardiovascular disease. However, the successful transition of these therapies into mainstream clinical practice awaits further improvements to vector platforms and delivery tools and the documentation of clinical feasibility, safety and efficacy through multi-center randomized trials.     

基因治疗的发展现状、问题和展望

基因治疗是一种新的治疗手段,可以治疗多种疾病,包括癌症、遗传性疾病、感染性疾病、心血管疾病和自身免疫性疾病。癌症基因治疗是基因治疗的主要应用领域。过去几年里,全球基因治疗临床试验取得了很大的进步。实际上,基因治疗也遇到了很多困难。未来,基因治疗的主要目标是发展安全和高效的基因导入系统,它们能将外源遗传物质靶向性地导入到特异的细胞。本文主要综述基因治疗所取得的突出进展、所遇到的困难和发展前景。     

Multiple potential clinical benefits for 1alpha,25-dihydroxyvitamin D3 analogs in kidney transplant recipients

Therapeutic trials of 1alpha,25(OH)(2)D(3) and related synthetic analogs are merited in diverse clinical fields, including treatment or prevention of bone disease, cancer, immune-mediated diseases, cardiovascular diseases, and prostatic hypertrophy. Potential difficulties of carrying out such trials successfully, include experimental data suggesting relatively modest therapeutic effects of 1alpha,25(OH)(2)D(3) analogs as stand-alone intervention and the likely requirement for large study group size and lengthy follow-up periods, if individual prophylactic effects are to be proven. Thus, it may be wise to identify patient groups with multiple potential benefits, accelerated disease risks, and the possibility for exploring synergistic pharmacological effects, in whom to carry out clinical trials of 1alpha,25(OH)(2)D(3) analogs. With this consideration in mind, the suitability of kidney transplant recipients for such studies is discussed. Although, highly effective in reversing end-stage renal disease, kidney transplantation continues to be limited by heightened risk of osteoporosis, persistent hyperparathyroidism, acute and chronic immunological injury, new cancer diagnosis, and cardiovascular events. In addition, kidney transplant recipients generally receive multiple immunosuppressants with a high prevalence of medication-related toxicities. Finally, it is pointed out that clinical trials carried out in organ transplant recipients provide a unique opportunity for longitudinal comparison of target tissue structural and gene expression profiles among treated and control patient groups. It is proposed that addition of a 1alpha,25(OH)(2)D(3) analog to conventional post-kidney transplant medication regimens is likely to be associated with measurable effects to prevent or retard multiple important complications and that this patient group is especially suitable for carrying out clinical trials of these compounds.     

Diabetes and other coronary heart disease risk equivalents

The close association between diabetes and cardiovascular disease suggests that current predictions of a massive increase in the prevalence of type 2 diabetes foreshadow an equally daunting rise in the incidence of vascular disease. The limited cardiovascular benefits obtained by glucose-lowering treatments, although perhaps not surprising, indicate that other cardiovascular risk factors must be given serious consideration as therapeutic targets. The impressive reductions in the number of vascular events observed in diabetic patients, albeit in small patient populations, participating in various drug trials amply justify such an approach. A necessary prerequisite, however, is a clear understanding of the clinical importance of individual risk factors to the occurrence of vascular disease in type 2 diabetic patients. This would appear essential for defining treatment strategies in the face of a bewildering array of potential therapeutic targets. The present review considers recent studies that have assessed the predictive value of risk factors against a diabetic background.     

Pharmacogenetics in Primary Care: The Promise of Personalized Medicine and the Reality of Racial Profiling

Many anticipate that expanding knowledge of genetic variations associated with disease risk and medication response will revolutionize clinical medicine, making possible genetically based Personalized Medicine where health care can be tailored to individuals, based on their genome scans. Pharmacogenetics has received especially strong interest, with many pharmaceutical developers avidly working to identify genetic variations associated with individual differences in drug response. While clinical applications of emerging genetic knowledge are becoming increasingly available, genetic tests for drug selection are not as yet widely accessible, and many primary care clinicians are unprepared to interpret genetic information. We conducted interviews with 58 primary care clinicians, exploring how they integrate emerging pharmacogenetic concepts into their practices. We found that in their current practices, pharmacogenetic innovations have not led to individually tailored treatment, but instead have encouraged use of essentialized racial/ethnic identity as a proxy for genetic heritage. Current manifestations of Personalized Medicine appear to be reinforcing entrenched notions of inherent biological differences between racial groups, and promoting the belief that racial profiling in health care is supported by cutting-edge scientific authority. Our findings raise concern for how pharmacogenetic innovations will actually affect diverse populations, and how unbiased treatment can be assured.     

Cardiovascular gene therapy with vascular endothelial growth factors

Therapeutic angiogenesis with vascular endothelial growth factors (VEGFs) is a promising approach for the treatment of ischemic myocardium and peripheral skeletal muscles. Preclinical studies in large animals have clearly demonstrated safety and efficacy of VEGF gene therapy in clinically relevant disease models. However, first clinical trials with intravascular delivery of VEGF vector constructs have only resulted in limited benefits to the patients. Second generation VEGF-based gene therapy trials are based on direct intramyocardial and intraskeletal muscle injections in order to achieve better transfection efficiency and more targeted effects. Phase I/II studies are currently ongoing to test safety, feasibility and efficacy of these improved approaches in patients with severe cardiovascular diseases.     

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral,breast and pancreatic cancer-specific profiles

Saliva is a readily accessible and informative biofluid, making it ideal for the early detection of a wide range of diseases including cardiovascular, renal, and autoimmune diseases, viral and bacterial infections and, importantly, cancers. Saliva-based diagnostics, particularly those based on metabolomics technology, are emerging and offer a promising clinical strategy, characterizing the association between salivary analytes and a particular disease. Here, we conducted a comprehensive metabolite analysis of saliva samples obtained from 215 individuals (69 oral, 18 pancreatic and 30 breast cancer patients, 11 periodontal disease patients and 87 healthy controls) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS). We identified 57 principal metabolites that can be used to accurately predict the probability of being affected by each individual disease. Although small but significant correlations were found between the known patient characteristics and the quantified metabolites, the profiles manifested relatively higher concentrations of most of the metabolites detected in all three cancers in comparison with those in people with periodontal disease and control subjects. This suggests that cancer-specific signatures are embedded in saliva metabolites. Multiple logistic regression models yielded high area under the receiver-operating characteristic curves (AUCs) to discriminate healthy controls from each disease. The AUCs were 0.865 for oral cancer, 0.973 for breast cancer, 0.993 for pancreatic cancer, and 0.969 for periodontal diseases. The accuracy of the models was also high, with cross-validation AUCs of 0.810, 0.881, 0.994, and 0.954, respectively. Quantitative information for these 57 metabolites and their combinations enable us to predict disease susceptibility. These metabolites are promising biomarkers for medical screening.     

Genetic therapies for RNA mis-splicing diseases

RNA mis-splicing diseases account for up to 15% of all inherited diseases, ranging from neurological to myogenic and metabolic disorders. With greatly increased genomic sequencing being performed for individual patients, the number of known mutations affecting splicing has risen to 50-60% of all disease-causing mutations. During the past 10years, genetic therapy directed toward correction of RNA mis-splicing in disease has progressed from theoretical work in cultured cells to promising clinical trials. In this review, we discuss the use of antisense oligonucleotides to modify splicing as well as the principles and latest work in bifunctional RNA, trans-splicing and modification of U1 and U7 snRNA to target splice sites. The success of clinical trials for modifying splicing to treat Duchenne muscular dystrophy opens the door for the use of splicing modification for most of the mis-splicing diseases.