Pharmacogenetics research on chemotherapy resistance in colorectal cancer over the last 20 years

During the past two decades the first sequencing of the human genome was performed showing its high degree of inter-individual differentiation,as a result of large international research projects(Human Genome Project,the 1000 Genomes Project International HapMap Project,and Programs for Genomic Applications NHLBI-PGA).This period was also a time of intensive development of molecular biology techniques and enormous knowledge growth in the biology of cancer.For clinical use in the treatment of patients with colorectal cancer(CRC),in addition to fluoropyrimidines,another two new cytostatic drugs were allowed:irinotecan and oxaliplatin.Intensive research into new treatment regimens and a new generation of drugs used in targeted therapy has also been conducted.The last 20years was a time of numerous in vitro and in vivo studies on the molecular basis of drug resistance.One of the most important factors limiting the effectiveness of chemotherapy is the primary and secondary resistance of cancer cells.Understanding the genetic factors and mechanisms that contribute to the lack of or low sensitivity of tumour tissue to cytostatics is a key element in the currently developing trend of personalized medicine.Scientists hope to increase the percentage of positive treatment response in CRC patients due to practical applications of pharmacogenetics/pharmacogenomics.Over the past 20 years the clinical usability of different predictive markers has been tested among which only a few have been confirmed to have high application potential.This review is a synthetic presentation of drug resistance in the context of CRC patient chemotherapy.The multifactorial nature and volume of the issues involved do not allow the author to present a comprehensive study on this subject in one review.

Pharmacogenetic considerations for optimizing tacrolimus dosing in liver and kidney transplant patients

The introduction of tacrolimus in clinical practice has improved patient survival after organ transplant.However,despite the long use of tacrolimus in clinical practice,the best way to use this agent is still a matter of intense debate.The start of the genomic era has generated new research areas,such as pharmacogenetics,which studies the variability of drug response in relation to the genetic factors involved in the processes responsible for the pharmacokinetics and/or the action mechanism of a drug in the body.This variability seems to be correlated with the presence of genetic polymorphisms.Genotyping is an attractive option especially for the initiation of the dosing of tacrolimus;also,unlike phenotypic tests,the genotype is a stable characteristic that needs to be determined only once for any given gene.However,prospective clinical studies must show that genotype determination before transplantation allows for better use of a given drug and improves the safety and clinical efficacy of that medication.At present,research has been able to reliably show that the CYP3A5 genotype,but not the CYP3A4 or ABCB1 ones,can modify the pharmacokinetics of tacrolimus.However,it has not been possible to incontrovertibly show that the corresponding changes in the pharmacokinetic profile are linked with different patient outcomes regarding tacrolimus efficacy and toxicity.For these reasons,pharmacogenetics and individualized medicine remain a fascinating area for further study and may ultimately become the face of future medical practice and drug dosing.

Pharmacogenetics of the systemic treatment in advanced hepatocellular carcinoma

Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers. To date, most patients with HCC are diagnosed at an advanced tumor stage, excluding them from potentially curative therapies (i.e., resection, liver transplantation, percutaneous ablation). Treatments with palliative intent include chemoembolization and systemic therapy. Among systemic treatments, the small-molecule multikinase inhibitor sorafenib has been the only systemic treatment available for advanced HCC over 10 years. More recently, other smallmolecule multikinase inhibitors (e.g., regorafenib, lenvatinib, cabozantinib) have been approved for HCC treatment. The promising immune checkpoint inhibitors (e.g., nivolumab, pembrolizumab) are still under investigation in Europe while in the US nivolumab has already been approved by FDA in sorafenib refractory or resistant patients. Other molecules, such as the selective CDK4/6inhibitors (e.g., palbociclib, ribociclib), are in earlier stages of clinical development, and the c- MET inhibitor tivantinib did not show positive results in a phase III study. However, even if the introduction of targeted agents has led to great advances in patient response and survival with an acceptable toxicity profile, a remarkable inter-individual heterogeneity in therapy outcome persists and constitutes a significant problem in disease management. Thus, the identification of biomarkers that predict which patients will benefit from a specific intervention could significantly affect decision-making and therapy planning. Germ-line variants have been suggested to play an important role in determining outcomes of HCC systemic therapy in terms of both toxicity and treatment efficacy. Particularly, a number of studies have focused on the role of genetic polymorphisms impacting the drug metabolic pathway and membrane translocation as well as the drug mechanism of action as predictive/prognostic markers of HCC treatment. The aim of this review is to summarize and critically discuss the pharmacogenetic literature evidences, with particular attention to sorafenib and regorafenib, which have been used longer than the others in HCC treatment.

Effects of testosterone replacement and its pharmacogenetics on physical performance and metabolism

In men, testosterone （T） deficiency is associated with decreased physical performance, as defined by adverse traits in body composition, namely increased body fat content and reduced muscle mass. Physical abilities in androgen-deficient men are further attenuated by lower oxygen supply due to decreased hemoglobin concentrations and by poor glucose utilization. Dysthymia and a lack of necessary aggressiveness also contribute to deteriorate physical effectiveness. Substitution of T can improve lipid and insulin metabolism as well as growth of muscle fibers and decreasing fat depots, which consequently will result in changes of body composition. Increment of bone density will further contribute to increase physical fitness. The effects of T replacement therapy （TRT） are strongly influenced by age, training, and also pharmacogenetics： the CAG repeat polymorphism in exon 1 of the androgen receptor （AR） gene modulates androgen effects. In vitro, transcription of androgen-dependent target genes is attenuated with increasing length of triplet residues, Clinically, the CAG repeat polymorphism causes significant modulations of androgenicity in healthy eugonadal men as well as efficacy of TRT. Thresholds at which T treatment should be initiated, as well as androgen dosage, could be tailored according to this polymorphism.

Pharmacogenetic studies update in type 2 diabetes mellitus

Type 2 diabetes mellitus(T2DM) is a silent progressive polygenic metabolic disorder resulting from ineffective insulin cascading in the body. World-wide, about 415 million people are suffering from T2DM with a projected rise to 642 million in 2040. T2DM is treated with several classes of oral antidiabetic drugs(OADs) viz. biguanides, sulfonylureas, thiazolidinediones, meglitinides, etc. Treatment strategies for T2DM are to minimize long-term micro and macro vascular complications by achieving an optimized glycemic control. Genetic variations in the human genome not only disclose the risk of T2DM development but also predict the personalized response to drug therapy. Inter-individual variability in response to OADs is due to polymorphisms in genes encoding drug receptors, transporters, and metabolizing enzymes for example, genetic variants in solute carrier transporters(SLC22A1, SLC22A2, SLC22A3, SLC47A1 and SLC47A2) are actively involved in glycemic/HbA1c management of metformin. In addition, CYP gene encoding Cytochrome P450 enzymes also play a crucial role with respect to metabolism of drugs. Pharmacogenetic studies provide insights on the relationship between individual genetic variants and variable therapeutic outcomes of various OADs. Clinical utility of pharmacogenetic study is to predict the therapeutic dose of various OADs on individual basis. Pharmacogenetics therefore, is a step towards personalized medicine which will greatly improve the efficacy of diabetes treatment.

Predicting(side) effects for patients with inflammatory bowel disease: The promise of pharmacogenetics

Inflammatory bowel disease (IBD) is a chronic and heterogeneous intestinal inflammatory disorder. The medical management of IBD aims for long-lasting disease remission to prevent complications and disease progression. Early introduction of immunosuppression forms the mainstay of medical IBD management. Large inter-individual variability in drug responses, in terms of both efficacy and toxicity, leads to high rates of therapeutic failure in the management of IBD. Better patient stratification is needed to maximize patient benefit and minimize the harm caused by adverse events. Pre-treatment pharmacogenetic testing has the potential to optimize drug selection and dose, and to minimize harm caused by adverse drug reactions. In addition, optimizing the use of cheap conventional drugs, and avoiding expensive ineffective drugs, will lead to a significant reduction in costs. Genetic variation in both TPMT and NUDT15, genes involved in thiopurine metabolism, is associated to an increased risk of thiopurine-induced myelosuppression. Moreover, specific HLA haplotypes confer risk to thiopurine-induced pancreatitis and to immunogenicity to tumor necrosis factor-antagonists, respectively. Falling costs and increased availability of genetic tests allow for the incorporation of pre-treatment genetic tests into clinical IBD management guidelines. In this paper, we review clinically useful pharmacogenetic associations for individualized treatment of patients with IBD and discuss the path from identification of a predictive pharmacogenetic marker to implementation into IBD clinical care.

Recent advances and future directions for the pharmacogenetic basis of anti-VEGF treatment response in neovascular age-related macular degeneration

Age related macular degeneration （AMD） is a complex progres- sive neurodegenerative disease causing blindness in 30-35 million people worldwide. It affects the macula region of the retina leading to severe vision loss and legal blindness in individuals 〉 50 years of age （Wong et al., 2014）. The precise aetiology of AMD is unknown but smoking, age and genetic factors are major risk factors for AMD predisposition （Ding et al., 2009）. The genetic basis of AMD is well described with a recent study from the International AMD gene consortium （IAMDGC） reporting 52 genetic variants across 34 loci associated with the risk of AMD pathogenesis and explaining more than 50% of the genetic heritabilitv of the disease （Fritsche et al., 2016）.

Pharmacogenetics of irinotecan:An ethnicity-based prediction of irinotecan adverse events

Irinotecan is now regarded as the most active drug for the treatment of colorectal cancer.However,one of the most difficult issues oncologists face is deciding the optimal dose for an individual patient,as each individual shows different outcomes even at the same dose with regard to treatment related adverse events,ranging from no toxicity to a lethal event.Inherited genetic polymorphism of a single gene or multiple genes(haplotype or linkage disequilibrium) involved in SN-38 glucuronidation,a predominant route of irinotecan detoxification,is now recognized as a significant factor that can alter the incidence of side effects.Attempts to explore such inherited genetic variability have been focused on elucidating interindividual as well as interethnic differences.Genotyping studies in relation to adverse events in an individual or in a group of similar ethnicity should contribute to establishing individualoriented or ethnicity-oriented irinotecan treatment regimens.This review highlights current single-or multi-tired approaches for the elucidation of genetic predispositions of patients to severe toxicities,especially among Asians.The purpose of this is to contribute to minimizing toxicity by dose modifications,with the consequent aim of maximizing dose intensity and efficacy,an ultimate goal of irinotecan-individualized therapy.

Pharmacogenetics of response to simvastatin in Chinese patients with hyperlipidaemia

Objective To examine the relationship of single-nucleotide polymorphisms(SNPs)in candidate genes with the lipid responses to simvastatin.Methods Chinese patients were treated with simvastatin 40 mg daily for at least 6 weeks.20 SNPs in 11 genes were genotyped.Results 95 patients age(mean±SD)57.5±10.6 years completed the treatment.The Adiponectin 45T>G polymorphism was significantly related to absolute reductions in total cholesterol(TC)and LDL-cholesterol with a trend(P=0.053)for percentage reductions in TC(TT∶TG∶GG=-38.4%∶-35.6%∶-32.6%).Similar findings were seen with LDL-Receptor(LDLR)SNPs(2052T>C and 1866C>T)with absolute reductions in TC and LDL-cholesterol significantly associated.The Breast Cancer Resistance Protein(ABCG2)421C>A polymorphism was related(P<0.05)to HDL-cholesterol response(CC∶CA∶AA=+0.50%∶-5.73%∶-11.41%).Conclusions Adiponectin,LDLR and ABCG2 SNPs had some influence on the lipid responses to simvastatin.

Pharmacogenetics as a tool to tailor antiretroviral therapy: A review

Highly active antiretroviral therapy(HAART) has substantially changed human immunodeficiency virus(HIV) infection from an inexorably fatal condition into a chronic disease with a longer life expectancy. This means that HIV patients should receive antiretroviral drugs lifelong, and the problems concerning with a chronic treatment(tolerability, side effects, adherence to treatment) have now become dominant. In this context, strategies for the treatment personalization have taken a central role in optimizing the therapeutic response and prevention of adverse drug reactions. In this setting, the study of pharmacogenetics features could be a very useful tool in clinical practice; moreover, nowadays the study of genetic profiles allows optimizations in the therapeutic management of People Living With HIV(PLWH) through the use of test introduced into clinical practice and approved by international guidelines for the adverse effects prevention such as the genetic test HLA-B*5701 to detect hypersensitivity to Abacavir. For other tests further studies are needed: CYP2B6 516 G > T testing may be able to identify patients at higher risk of Central Nervous System side effects following standard dosing of Efavirenz, UGT1A1*28 testing before initiation of antiretroviral therapy containing Atazanavir may aid in identifying individuals at risk of hyperbilirubinaemia. Pharmacogenetics represents a research area with great growth potential which may be useful to guide the rational use of antiretrovirals.

Pharmacogenetics of immunosuppressant drugs:A new aspect for individualized therapy

In recent years,pharmacogenetics has emerged as an important tool for choosing the right immunosuppressant drug and its appropriate dose.Indeed,pharmacogenetics may exert its action on immunosuppressant drugs at three levels.Pharmacogenetics identifies and studies the genes involved in encoding the proteins involved in drug pharmacokinetics and in encoding the enzymes involved in drug degradation.Pharmacogenetics is also relevant in encoding the enzymes and proteins involved in codifying the transmembrane proteins involved in transmembrane passage favoring the absorption and intracellular action of several immunosuppressants.Pharmacogenetics concern the variability of genes encoding the proteins involved as immunosuppressant triggers in the pharmacodynamic pathways.Of course,not all genes have been discovered and studied,but some of them have been clearly examined and their relevance together with other factors such as age and race has been defined.Other genes on the basis of relevant studies have been proposed as good candidates for future studies.Unfortunately,to date,clear conclusions may be drawn only for those drugs that are metabolized by CYP3A5 and its genotyping before kidney,heart and lung transplantation is recommended.The conclusions of the studies on the recommended candidate genes,together with the development of omics techniques could in the future allow us to choose the right dose of the right immunosuppressant for the right patient.

Pharmacogenetic Correlates of Antipsychotic-Induced Weight Gain in the Chinese Population

Antipsychotic-induced weight gain(AIWG) is a common adverse effect of this treatment, particularly with second-generation antipsychotics, and it is a major health problem around the world. We aimed to review the progress of pharmacogenetic studies on AIWG in the Chinese population to compare the results for Chinese with other ethnic populations, identify the limitations and problems of current studies, and provide future research directions in China. Both English and Chinese electronic databases were searched to identify eligible studies. We determined that [ 25 single-nucleotide polymorphisms in19 genes have been investigated in association with AIWG in Chinese patients over the past few decades. HTR2 C rs3813929 is the most frequently studied single-nucleotide polymorphism, and it seems to be the most strongly associated with AIWG in the Chinese population. However, many genes that have been reported to be associated with AIWG in other ethnic populations have not beenincluded in Chinese studies. To explain the pharmacogenetic reasons for AIWG in the Chinese population,genome-wide association studies and multiple-center, standard, unified, and large samples are needed.

Genomic and pharmacogenetic studies of childhood acute lymphoblastic leukemia

With the cure rate of childhood acute lymphoblastic leukemia （ALL） approaching 90%, further improvement in the treatment outcome and quality of life of patients will require better understanding of the mechanisms of drug resistance, identifying new leukemic cell genetic lesions that are amendable to available target therapy, and optimizing treatment based on host pharmacodynamics and pharmacogenomics. Deeper characterization of leukemic cell genetic abnormalities has discovered new subtypes of leukemia such as early T-cell precursor ALL and Philadelphia chromosome-like ALL, and identified many genomic alterations that have diagnostic, prognostic, or therapeutic implications. In this regard, several novel fusion transcripts are responsive to ABL tyrosine kinase inhibitors and potentially to JAK inhibitors. Genome-wide analyses have also unraveled the role of inherited cancer predisposing genes and small nucleotide polymorphisms of several genes in the development of childhood ALL. These advances promise to lead to more sophisticated personalized treatment strategies in the near future.

Pharmacogenetic activation of midbrain dopaminergic neurons induces hyperactivity

Dopaminergic neurons regulate and organize numerous important behavioral processes including motor activity.Consistently,manipulation of brain dopamine concentrations changes animal activity levels.Dopamine is synthesized by several neuronal populations in the brain.This study was carried out to directly test whether selective activation of dopamine neurons in the midbrain induces hyperactivity.A pharmacogenetic approach was used to activate midbrain dopamine neurons,and behavioral assays were conducted to determine the effects on mouse activity levels.Transgenic expression of the evolved hM3Dq receptor was achieved by infusing Creinducible AAV viral vectors into the midbrain of DATCre mice.Neurons were excited by injecting the hM3Dq ligand clozapine-N-oxide（CNO）.Mouse locomotor activity was measured in an open field.The results showed that CNO selectively activated midbrain dopaminergic neurons and induced hyperactivity in a dose-dependent manner,supporting the idea that these neurons play an important role in regulating motor activity.

Pharmacogenetics of anticancer monoclonal antibodies

Pharmacogenetics is the study of therapeutic and adverse responses to drugs based on an individual’s genetic background.Monoclonal antibodies(mAbs)are a rapidly evolving field in cancer therapy,however a number of newly developed and highly effective mAbs(e.g.,anti-CTLA-4 and anti-PD-1)possess pharmacogenomic profiles that remain largely undefined.Since the first chemotherapeutic mAb Rituximab was approved in 1997 by the US Food and Drug Administration for cancer treatment,a broad number of other mAbs have been successfully developed and implemented into oncological practice.Nowadays,mAbs are considered as one of the most promising new approaches for cancer treatment.The efficacy of mAb treatment can however be significantly affected by genetic background,where genes responsible for antibody presentation and metabolism,for example,can seriously affect patient outcome.This review will focus on current anticancer mAb treatments,patient genetics that shape their efficacy,and the molecular pathways that bridge the two.

Pharmacogenetics implementation in the clinics:information and guidelines for germline variants

The aim of this work was to supply an overview of the germline Pharmacogenetics that can be already implemented in the oncology clinical practice.An explanation of the three pillars considered necessary for determining which genetic polymorphisms should be used has been provided.These are PharmGKB single nucleotide polymorphism(SNP)-Drug Clinical Annotations with levels of evidence 1 or 2;the genetic information provided in the drug labels by the drug regulatory main agencies(Food and Drug Administration and European Medicines Agency,mainly);and the guidelines elaborated by international expert consortia(mainly Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group).A summary of the relevant SNPs and the recommendations on how to apply their results has also been compiled.

The use of pharmacogenetics to increase the safety of colorectal cancer patients treated with fluoropyrimidines

Fluoropyrimidines(FP)are given in the combination treatment of the advanced disease or as monotherapy in the neo-adjuvant and adjuvant treatment of colorectal cancerand other solid tumors including breast,head and neck and gastric cancer.FP present a narrow therapeutic index with 10 to 26% of patients experiencing acute severe or life-threatening toxicity.With the high number of patients receiving FP-based therapies,and the significant effects of toxicities on their quality of life,the prevention of FP-related adverse events is of major clinical interest.Host genetic variants in the rate limiting enzyme dihydropyrimidine dehydrogenase(DPYD)gene are related to the occurrence of extremely severe,early onset toxicity in FP treated patients.The pre-treatment diagnostic test of 4 DPYD genetic polymorphisms is suggested by the currently available pharmacogenetic guidelines.Several prospective implementation projects are ongoing to support the introduction of up-front genotyping of the patients in clinical practice.Multiple pharmacogenetic studies tried to assess the predictive role of other polymorphisms in genes involved in the FP pharmacokinetics/pharmacodynamic pathways,TYMS and MTHFR,but no additional clinically validated genetic markers of toxicity are available to date.The development of next-generation sequencing platforms opens new possibilities to highlight previously unreported genetic markers.Moreover,the investigation of the genetic variation in the patients immunological system,a pivotal target in cancer treatment,could bring notable advances in the field.This review will describe the most recent literature on the use of pharmacogenetics to increase the safety of a treatment based on FP administration in colorectal cancer patients.

iGMDR:Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research

Current pharmacogenetic studies have obtained many genetic models that can predict the therapeutic efficacy of anticancer drugs.Although some of these models are of crucial importance and have been used in clinical practice,these very valuable models have not been well adopted into cancer research to promote the development of cancer therapies due to the lack of integration and standards for the existing data of the pharmacogenetic studies.For this purpose,we built a resource investigating genetic model of drug response(iGMDR),which integrates the models from in vitro and in vivo pharmacogenetic studies with different omics data from a variety of technical systems.In this study,we introduced a standardized process for all integrations,and described how users can utilize these models to gain insights into cancer.iGMDR is freely accessible at https://igmdr.modellab.cn.

Pharmacogenetics and cancer management

The science of one’s genetic background and its impact on disease susceptibility and drug response has come of age and firmly established its proper place in the clinic.Its impact is felt more in the treatment of cancer than any other disease area several reasons:critical time,narrow therapeutic index and overlapping toxicity window.We realize that the true potential of pharmacogenetics will be realized when we have been able to integrate other variants like insertion-deletion,copy number variation,etc.,in addition to single nucleotide polymorphism for their collective influence on drug response and toxicity.Technology has rapidly evolved and has become affordable to be used in the clinic once it gets standardized and validated not only in one population but in several major world population-particularly those which are under-represented in human variant database.

Pharmacogenetic and pharmacogenomic discovery strategies

Genetic/genomic profiling at a single-patient level is expected to provide critical information for determining inter-individual drug toxicity and potential efficacy in cancer therapy.A better definition of cancer subtypes at a molecular level,may correspondingly complement such pharmacogenetic and pharmacogenomic approaches,for more effective personalized treatments.Current pharmacogenetic/pharmacogenomic strategies are largely based on the identification of known polymorphisms,thus limiting the discovery of novel or rarer genetic variants.Recent improvements in cost and throughput of next generation sequencing(NGS)are now making whole-genome profiling a plausible alternative for clinical procedures.Beyond classical pharmacogenetic/pharmacogenomic traits for drug metabolism,NGS screening programs of cancer genomes may lead to the identification of novel cancer-driving mutations.These may not only constitute novel therapeutic targets,but also effector determinants for metabolic pathways linked to drug metabolism.An additional advantage is that cancer NGS profiling is now leading to discovering targetable mutations,e.g.,in glioblastomas and pancreatic cancers,which were originally discovered in other tumor types,thus allowing for effective repurposing of active drugs already on the market.