Current Pharmacogenomics and Personalized Medicine (Formerly Current Pharmacogenomics) - Volume 17, Issue 3, 2020

Osteoporosis is a chronic disease characterized by decreased bone mass and distorted microarchitecture that leads to increased bone fragility making an individual prone to fractures. It is one of the most widely affected diseases worldwide that has the potential to cause serious morbidity, mortality and cost implications. It is a multifactorial disease that is influenced by the interaction between genetic, hormonal, nutritional and environmental factors. As it is a polygenic disorder, myriad genes influence the disease condition to a varied extent. The identification of genes or loci that effects the development of the disease will help not only in individualizing the prognosis, treatment and prevention of fractures but also in discovering novel therapeutic agents. The genetic association studies on osteoporosis have reported conflicting results. Well designed and efficiently conducted studies with enough power to detect variations in the interaction between various contributing factors of the disease in the homogenous population are needed to establish conclusive genotypic associations with the disease. The present review briefly summarizes the data published on the genes affecting osteoporosis development.

Background: Neurodegenerative disorders are one of the major health problems in Western countries. Genetic and epigenetic mechanisms play crucial roles in the origin and progression of these disorders. DNA methylation is the most widely studied epigenetic mark and is an important regulator of gene expression. Objective: Little is known about the influence of bioactive dietary components on epigenetic mechanisms in neurodegenerative diseases. In this study, we investigated the effects of E-PodoFavalin-15999 (AtreMorine®), a bioproduct with potent neuroprotective and dopamine enhancing capabilities, on DNA methylation patterns in Alzheimer’s (AD) and Parkinson’s Disease (PD). We also aimed to assess, in patients with PD, the effects that genetic variation across candidate pharmacogenes may have on dopamine synthesis and release in response to treatment with AtreMorine. Methods: We analyzed global DNA methylation and de novo DNA methyltransferase (DNMT) expression in a transgenic (3xTg) mouse model of AD, and further examined global DNA methylation in blood samples from patients with PD. Results: AtreMorine treatment increased global DNA methylation in 3xTg mice and in patients with Parkinson´s disease, and produced high DNMT3a expression in AD mice. We observed varied responses to AtreMorine across the following pharmacogenetic genophenotypes analyzed, cytochrome P450 oxidases (CYP2D6, CYP2C19, CYP2C9, CYP3A4, CYP3A5, CYP1A2), human arylamine N-acetyltransferase 2 (NAT2), the vitamin K epoxide reductase complex subunit 1 (VKORC1), ATP-binding cassette subfamily B member 1 (ABCB1), and solute carrier organic anion transporter family member 1B1 (SLCOB1). Conclusion: Our results suggest that AtreMorine regulates DNA methylation in neurodegenerative disorders and may constitute a new therapeutic option for the treatment of these pathologies.

Background: In the human population, CYP2D6 is highly polymorphic group of genes involved in metabolizing ~25% of all clinically used neuroleptic and antidepressant drugs. The CYP2D6*4 and CYP2D6*10 variants are prevalent in Asian population exhibiting variable drug metabolizing ability thereby affecting drug therapeutic responses. Objective: To determine the genotypic frequencies of CYP2D6*1 (Normal metabolizer), *4 (Poor metabolizer) and *10 (Intermediate metabolizer) variants among schizophrenic subjects and control group from a sub-set of Karachi population. Method: Genomic Deoxyribonucleic Acid (gDNA) was extracted and amplified with CYP2D6*4 and *10 primers using Polymerase Chain Reaction (PCR) and digested by Bacillus stereothermophilus (BstN1) and Hemophilus parahemolyticus (Hph1) restriction enzymes. The digested gDNA bands were identified as wild type or mutants and their genotypic frequencies were estimated by Hardy-Weinberg Equation (HWE). Results: In normal subjects, frequencies of CYP2D6*1 wild allele (57%) coded functional enzyme, CYP2D6*4 variant (9%) producing non-functional enzyme and CYP2D6*10 allele (70%) producing altered enzyme with reduced activity that was most prevalent in schizophrenic patients. Discussion: Drug response is a complex phenomenon that is governed by genetic and environmental factors. Antipsychotic drug metabolism among schizophrenic patients with variable drug responsesis related to CYP2D6 polymorphism. Clinically, it is imperative to differentiate between responders and non-responders using the treatment, otherwise the drug will be either nonefficacious or toxic to the patients. Therefore, a gene testing system needs to be established to identify patient’s genotype(s) predicting whether they are normal, poor, intermediate or ultrarapid drug metabolizer thereby allowing clinicians to adjust dose(s) of antipsychotic drug(s). Conclusion: Genotyping of CYP2D6 alleles among schizophrenic patients indicated prevalence of *4 and *10 variants in Karachi population producing non-functional (poor metabolizer) and reduced functional (intermediate metabolizer) drug metabolizing enzymes phenotypes, respectively. Hence, dose adjustment is crucial otherwise schizophrenia condition will not be improved satisfactorily. Therefore, CYP2D6 gene screening program should be included in clinical practice to help clinicians to prescribe appropriate doses according to patient’s genotype and minimize sufferings of schizophrenics including side effects of drug that might occur at high drug concentrations.

Background: Mutations in the CDH1 and the role of E-cadherin proteins are well established in gastric cancer. Several in silico tools are available to predict the pathogenicity of the mutations present in the genes with varying efficiency and sensitivity to detect the pathogenicity of the mutations. Objective: Our objective was to identify somatic pathogenic variants in CDH1 involved in Gastric Cancer (GC) by Sanger sequencing as well as using in silico tools and to find out the best efficient tool for pathogenicity prediction of somatic missense variants. Methods: Sanger sequencing of CDH1 was done for 80 GC tumor and adjacent normal tissues. Synthetic data sets were downloaded from the COSMIC database for comparison of the known mutations with the discovered mutations from the present study. Different algorithms were used to predict the pathogenicity of the discovery and synthetic mutation datasets using various in-silico tools. Statistical analysis was done to check the efficiency of the tools to predict pathogenic variants by using MEDCALC and GraphPad. Results: Six missense somatic variants were found in exons 3, 4, 7, 9, 12 and 15. Out of the 6 variants, 5 variants (chr16:68835618C>A, chr16:68845613A>C, chr16:68847271T>G, chr16:68856001T>G, chr16:68863585G>C) were novel and not reported in disease variant databases. PROVEAN, Polyphen 2 and PANTHER predicted the pathogenicity of the variants more efficiently in both the discovery and synthetic datasets. The overall sensitivity of predictions ranged from 60 to 80%, depending on the program used, with specificity from 55 to 100%. Conclusion: This study estimates the specificity and sensitivity of prediction tools in predicting novel missense variants of CDH1 in Gastric Cancer. We report that PROVEAN, Polyphen 2 and PANTHER are efficient predictors with constant higher specificity and accuracy. This study will help the researchers to explore mutations with the best pathogenicity prediction tools.

Aims: This study aims to design an angiogenesis gene expression profile; to study angiogenesis gene expression profile in breast cancer; and to map angiogenesis gene expression profile in individual participants. Background: In molecular etiology of each disease, there are some important molecules involved in the related pathways. From the viewpoint of precision medicine, molecular etiology of a disease is different person by person because of genetic variations of the genes involved in these pathways. This point of view intends researchers of drug development to design novel drugs for targeted therapy based on the exact etiology. In the case of angiogenesis, there is a drug profile parallel to the molecular profile. Bevacizumab, sunitinib and aflibercept are examples of anti-angiogenic drugs. Objectives: A hallmark of solid tumors is sustained angiogenesis. Vascular endothelial growth factors (VEGF), VEGF receptors (VEGFR) and placental growth factor (PlGF) are involved in angiogenesis. We aimed to study the gene expression profile of angiogenesis including VEGF-A, VEGF-B, VEGF-C, VEGF-D, VEGFR-1, VEGFR-2, VEGFR-3 and PlGF in an Iranian group of patients undergoing breast surgery due to breast cancer and breast fibroadenoma. Methods: Tumor tissue samples of a group of patients with invasive ductal carcinoma (IDC) and a group of patients with fibroadenoma (Fib) were used. Gene expression was studied by real-time quantitative polymerase chain reaction (q-PCR) and fold changes (FC) with their 95% confidence intervals (CI) were reported based on calibration with normal breast tissue. Results: All the genes showed significant up-regulation in IDC group. The extensive up-regulation was for VEGFR-2 (FC=52.68; 95% CI=17.96-154.47; P<0.001). In Fib group, PlGF showed a significant upregulation (FC=10.41; 95% CI=5.35-20.26; P=0.002). Comparison of IDC group with Fib group showed significant up-regulation of VEGFR-1, VEGFR-2 and VEGFR-3 in IDC group (P<0.05). Conclusion: Malignancy of breast tumors is associated with overexpression of all the genes of this profile. However, only VEGFRs showed up-regulation in comparison to benign tumors. Individualized targeted therapy, according to this profile, should be studied in the future.

Background: Dopamine plays an important role in mediating the rewarding properties in the abuse of drugs. The Taq1A polymorphism is a commonly studied DRD2 gene variant whereby carriers of the low-function T allele (T/T or T/C genotypes) show reduced brain dopamine function. Therefore, individuals who have the DRD2 Taq1A polymorphism will experience higher levels of drug addiction because the T allele is associated with a reduced number of dopamine binding sites in the brain. A study of this gene has been conducted in some areas, but there is no research for the population of Indonesia. Objective: This study will focus on the frequency of the DRD2 Taq1A gene polymorphism in the population of Indonesia and define its association with drug addiction. Methods: This is a cross sectional study in which 182 subjects were divided into 91 drugaddicted patients and 91 non-drug-addicted control subjects. The genotype analysis was carried out by a modified allele-specific Polymerase Chain Reaction (PCR) method. Results: The frequency of the T/T and C/T was significantly higher in the addicted than control subjects. They are 6.6% and 63.7% compared to 0% and 3.3%. Likewise, the T allele is more frequent in the addicted equal to 38%, compared to only 2% in the control subjects. The frequency of the T allele between the addicted and control subjects shows a significant difference (p-value < 0.0001; 95% CI), with the addicted being at a higher risk of having the T allele (OR = 37.3; 95% CI [11.46-121.29]). Conclusion: There is a significant difference in the frequency of the DRD2 Taq1A gene polymorphism between addicted patients and control subjects. Thus, there is an association between this gene polymorphism and the development of drug addiction with T allele increases the predisposition to addiction.

Background: Hereditary spastic paraplegia is a neurodegenerative disorder with a pure and complex form. More than 50 genetic types are currently known, with different ages of onset for characteristic symptoms. Data regarding hereditary spastic paraplegia remain scarce, and the rare subtype of spastic paraplegia type 5 is no exception. Objective: This report presents data regarding the case of a single family, from the city of Djerba, with five individuals affected with hereditary spastic paraplegia, the largest number of spastic paraplegia type 5 mutated family members so far reported in current literature. Methods: To emphasize the importance of genetic testing, we retrospectively reviewed a familial confirmed case of hereditary spastic paraplegia. Clinical features of family members were described. Results: The family presents a large phenotypic variation that, in part, differs from the known phenotypic presentations. Age of onset and clinical manifestation showed interfamilial variations. The alteration found in CYP7B1 (c.1081C>T; p.R361*) may help emphasize the importance of genetic testing and the much-needed treatment options already in use in current neurological practice. Conclusion: The understanding of the molecular pathways of hereditary spastic paraplegia, together with the establishment of disease biomarkers, will hopefully lead to better and more personalized treatment.