The impact of IDH and NAT2 gene polymorphisms in acute myeloid leukemia risk and overall survival in an Arab population: A case-control study

Acute myeloid leukemia (AML) is a malignancy of the myeloid cells due to the clonal and malignant proliferation of blast cells. The etiology of AML is complex and involves environmental and genetic factors. Such genetic aberrations include FLT3, DNMT3, IDH1, IDH2, NAT2, and WT. In this study, we analyzed the relationship between five, not previously studied in any Arab population, single nucleotide polymorphisms (SNPs) and the risk and overall survival of AML in Jordanian patients. The SNPs are NAT2 (rs1799930 and rs1799931), IDH1 (rs121913500), and IDH2 (rs121913502 and rs1057519736). A total number of 30 AML patients and 225 healthy controls were included in this study. Females comprised 50% (n = 15) and 65.3% (n = 147) of patients and controls, respectively. For AML patients (case group) Genomic DNA was extracted from formalin-fixed paraffin-embedded tissues and from peripheral blood samples for the control subjects group. Genotyping of the genetic polymorphisms was conducted using a sequencing protocol. Our study indicates that NAT2 rs1799930 SNP had a statistically significant difference in genotype frequency between cases and controls (p = 0.023) while IDH mutations did not correlate with the risk and survival of AML in the Jordanian population. These results were also similar in the TCGA-LAML cohorts with the notable exception of the rare NAT2 mutation. A larger cohort study is needed to further investigate our results.

Reduction of Genotoxicity of Carbamazepine to Human Lymphocytes by Pre-treatment with Vitamin B12

BACKGROUND

Carbamazepine (CBZ) is widely used as an anti-epileptic drug. Vitamin B12 has been shown to protect against DNA damage caused by several mutagenic agents.

OBJECTIVE

This study aimed to investigate the effect of vitamin B12 on CBZ-induced genotoxicity in cultured human lymphocytes.

METHODS

Sister chromatid exchanges (SCEs) and chromosomal aberrations (CAs) genotoxic assays were utilized to achieve the study objective.

RESULTS

The results showed significantly higher frequencies of CAs and SCEs in the CBZ-treated cultures (12 μg/mL) compared to the control group (P<0.01). The genotoxic effects of CBZ were reduced by pre-treatment of cultures with vitamin B12 (13.5μg/ml, P<0.05). Neither CBZ nor vitamin B-12 showed any effects on mitotic and proliferative indices.

CONCLUSION

CBZ is genotoxic to lymphocyte cells, and this genotoxicity can be reduced by vitamin B12.

Genotoxicity of nedaplatin in cultured lymphocytes: modulation by vitamin E

Nedaplatin is a chemotherapeutic agent used widely in cancer therapy. Nedaplatin has been shown to cause DNA damage to cells via the induction of oxidative stress. Vitamin E (Vit E) has an anti-mutagenic activity that can protect cells from DNA damaging agents. The objective of this study is to examine the genotoxic and cytotoxic effects of nedaplatin in human cultured lymphocytes. In addition, modulation of such effects by Vit E was also examined. The frequencies of sister chromatid exchange (SCE) and chromosomal aberrations (CAs) were used as an indicator for genotoxicity. The mitotic and proliferative indices were used to examine the cytotoxic effects of nedaplatin. The results showed that nedaplatin significantly elevated SCE and CA frequencies in human lymphocytes (p ˂ 0.01). The increases in the frequencies of SCE and CA caused by nedaplatin were lowered by pretreatment treatment with Vit E (p < 0.05). Nedaplatin significantly lowered mitotic index but Vit E pretreatment did not modulate this effect. These results suggest that Vit E has the potential to ameliorate the genotoxicity of nedaplatin in cultured lymphocytes.

Association of sodium voltage-gated channel genes polymorphisms with epilepsy risk and prognosis in the Saudi population

BACKGROUND

Epilepsy is a heterogeneous complex condition that involve the human brain. Genetic predisposition to epilepsy is a fundamental factor of the disorder aetiology. The sodium voltage-gated channel (SCN) genes variants are critical biomarker for the epilepsy development and progression. In this study, we aimed to investigate the association of several SNCs genetic polymorphisms with epilepsy risk and their intrudance of the disease prognosis.

METHODS

Blood samples were withdrawn from 296 Epilepsy patients in addition to 293 healthy matched participants prior to DNA extraction. PCR-sequencing was used for genotyping analysis. Genotyping outputs were then statistically analysed for genotype/phenotype evaluation.

RESULTS

Within SCN1A gene we found that the rs6432861 (p = 0.014) was in correlation with the risk of epilepsy. In addition, both rs4667485 and rs1469649 of SCN2A gene were significantly correlated to epilepsy risk for both allelic (4e-4 and 1e-3) and genotypic (1e-3 and 5e-3). Moreover, the haplotype analysis showed that the GATGCTCGGTTTCGCTACGCA haplotype of SCN2A gene was significantly related to epilepsy increased risk, p = 6e-3, OR (CI) = 2.02 (1.23-3.31). In relevant to our finding, many of the investigated SCNs variants in the current study were related to several clinical features of epilepsy.

CONCLUSION

In light of our results, we infer that SCN genes polymorphisms are strong candidates for epilepsy development and progression. Furthermore, these variant are essential for the disorder prognosis and medications outcomes.Key MessagesGenetic polymorphisms of sodium channels SCN1A, SCN2A and SCN3A were found to be associated with the risk of epilepsy.SCN1B polymorphisms were found to be correlated to epilepsy reduced risk.SCNs variants are involved in the epilepsy prognosis and response to treatment.

Pathological, molecular, and serological study of small ruminant lentiviruses in Jordan

Background and Aim:

Maedi-visna is a chronic viral disease of sheep with worldwide distribution causing substantial economic losses to the small ruminant industry. Pneumonia and mastitis are the main manifestations of the disease. This study aimed to investigate the occurrence of maedi-visna virus (MVV) in sheep using histopathology and nested polymerase chain reaction (PCR) techniques and also to estimate the seroprevalence of small ruminant lentiviruses (SRLVs) in sheep and goats using commercially available enzyme-linked immunosorbent assay (ELISA).

Materials and Methods:

Lung tissue samples from 380 sheep were collected and fixed in 10% formalin for histopathology and molecular diagnosis of MVV. Separately, 806 serum samples were randomly collected from 633 sheep and 173 goats to detect the seroprevalence of SRLVs using ELISA.

Results:

The results showed that 4.7% of lung samples (n=190) were positive by both histopathology and nested PCR, 5.8% (n = 380) were positive by histopathology only (have lymphoid follicular hyperplasia), and 7.4% (n = 190) were positive by nested PCR only. Statistical analysis revealed a moderate agreement between the two tests (Kappa=0.451, n = 190). Serology results revealed that sheep and/or goats herd prevalence was 59.8% (n = 87), while individual seroprevalence in sheep (40.1%, n = 633) was significantly higher than that in the other six countries and also significantly higher than that in goats (18.5%, n = 173) (at p < 0.05).

Conclusion:

The moderate statistical agreement between nested PCR and histopathological diagnosis of MVV in formalin-fixed paraffin-embedded sheep lung tissue samples (Kappa=0.451, n = 190) suggests combining both tests for more sensitive MVV detection in sheep lung samples. SRLVs seropositivity in sheep was significantly higher than in goats, thus, it is of high concern and urges the inquiry into the economic impact of the disease and the financial benefit of adopting eradication measures.

Clavulanic Acid in the Scope of Helicobacter pylori Treatment: A Literature Review and Beyond

BACKGROUND

Helicobacter pylori (H. pylori) infection is the most common cause of peptic ulcer disease and it can be associated with many complications, including malignancies. In clinical practice, some clinicians may use Clavulanic Acid (CA) in combination with amoxicillin or other beta-lactams as an addition to the standard treatment regimens. This practice may be done by habitual mistake, non-evidence based hypothetical assumptions, or by prescribing it as an alternative treatment. This review aims to expose the effect of CA against H. pylori infection and to review the possible mechanisms that may contribute to that effect.

METHODS

A PubMed and Google Scholar literature search was obtained on both pre-clinical and clinical studies related to CA and H. pylori infection.

RESULTS

Available clinical studies showed improvement in the eradication of H. pylori by about 10- 20% when CA was added to the treatment regimens. This effect for CA could be related to several mechanisms including inhibition of H. pylori growth by binding to Penicillin-Binding Proteins (PBPs), the transformation of H. pylori from the active filamentous form into coccoidal form, induction of the release of dopamine, modulation of immunological response towards H. pylori infection and its relationship with other microbiota. Randomized-controlled studies on patients with resistance to H. pylori are needed. Moreover, in vitro studies to evaluate the mechanisms by which CA may influence H. pylori are warranted.

CONCLUSION

The presented literature suggests potential avenues for the use of CA in the management of peptic ulcer disease and H. pylori infection.

RAD51-UTR haplotype genetic polymorphisms and susceptibility to breast cancer in women from Jordanian population

BACKGROUND

Genetic predisposition to breast cancer (BC) has been extensively explored to achieve an enhanced understanding of the biology of BC. Targeting candidate genes to screen different genetic variants such as RAD51 gene that plays a critical role in DNA repair pathways including the double-strand break repair system is an important task.

AIM

To study several single nucleotide polymorphisms (SNPs) within RAD51-UTR gene and to find their relationship with BC risk and prognosis among Jordanian females.

MATERIALS AND METHODS

In this case-control study, DNA sequencing technique was used to screen SNPs within the untranslated region (UTR) of RAD51 in 206 cases and 185 controls and the resulting data were statistically analyzed using different types of genetic analyses. Patients' clinical and pathological features were obtained from their medical records to perform genotype-phenotype association analysis.

RESULTS

Our findings show a significant association between both SNPs rs528590644, rs1801320 and BC risk (p = 0.016). We estimated the correlation between many of BC prognostic factors and BC risk, and we found an association between rs1801321 and age at first menstruation (p = 0.032) in addition to a strong correlation between age at BC diagnosis and rs1801320 (p = 0.008).

CONCLUSION

RAD51-UTR polymorphisms may be involved in BC development and progression.

Association of CYP2C19, TNF-α, NOD1, NOD2, and PPARγ polymorphisms with peptic ulcer disease enhanced by Helicobacter pylori infection

OBJECTIVES

To assess the correlation between a number of genetic variations of CYP2C19, TNF-α, NOD1, NOD2, and PPARγ genes with the severity of Helicobacter pylori (H. pylori) infections and peptic ulcers (PU).

METHODS

A retrospective cross-sectional design was used in this study. Formalin-fixed paraffin-embedded (FFPE) tissue was used to extract genomic DNA that was collected from Jordanian patients who visited endoscopy clinics between 2014 to 2018 at the King Abdullah University Hospital (KAUH), Irbid, Jordan. Genotyping of the studied single nucleotide polymorphisms (SNPs) were applied using the sequencing protocol. Results:  A total of 251 patients (mean age: 42.12 ± 16.09 years) and healthy controls (mean age: 52.76 ± 19.45 years) were enrolled in this study. This study showed no significant association between patients and the studied polymorphisms except for rs2075820 of the NOD1 (p=0.0046). It is hypothesized that the heterozygous genotype (TC); 44.8% in patients versus 61.3% in controls has a decreased risk of peptic ulcers (OR:  0.49). The alleles frequency association was insignificant in all studied SNPs with a p-value more than 0.05.

CONCLUSION

This study provided evidence regarding the association of the rs2075820 with H. pylori infections. The other studied SNPs were not statistically significant.

Improving public stigma, sociocultural beliefs, and social identity for people with epilepsy in the Aseer region of Saudi Arabia

•

An update of the data reported previously in 2016 in Aseer region.

•

The level of education and awareness regarding epilepsy in Aseer region has improved recently.

•

The belief in spiritual and traditional therapies has decreased, considering them as additional options.

Differences in the sociocultural practice and biases against people with epilepsy (PWE) largely contribute to the development of stigmatization. In this study, we evaluated factors that impact stigma for PWE involved in evolution and maintenance to report changes in the public awareness and cultural practices. We performed a cross-sectional study in which data were collected from a self-administered electronic survey composed of 33 items targeting the population in the Aseer region. Feedback response was obtained from 937 respondents. Of these, 921 participants (98.3%) had heard or read about the disorder previously. Approximately 84.8% believed that epilepsy was one of the brain disorders. 95.8% disagreed that epilepsy was due to a contagious disease. However, 40.1% of the responders were convinced that it was the result of a spiritual reason. Still, more than 9% believed treating PWE should be approached spiritually. About 75% felt that epilepsy could be the results of a test delievered by God. In addition to the clinical impact from seizures in PWE, it carries a social label and public stigma that influences one's social prognosis. Raising awareness through campaigns would improve the knowledge and practices of the population and hence provide a healthier environment for PWE, alleviating feelings of stigma, and improving their quality of life.

Association of DRD4 exon III and 5-HTTLPR VNTR genetic polymorphisms with psychiatric symptoms in hemodialysis patients

Mental illness is prevalent among hemodialysis (HD) patients. Given that the dopaminergic and serotonergic pathways are involved in the etiology of psychiatric disease, this study evaluated the genetic association of dopamine D4 receptor (DRD4) and serotonin transporter (SLC6A4) genes with psychiatric symptom susceptibility among HD patients. Hospital Anxiety and Depression Scale (HADS) was used to assess anxiety and depressive symptoms among patients (n = 265). Genetic polymorphisms of DRD4 (48 bp VNTR) and SLC6A4 (5-HTTLPR VNTR and rs25531) were examined using a conventional polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique, as appropriate. Significant differences were observed in the distribution of 5-HTTLPR genotypes, SLC6A4 tri-allelic-phased genotype, and DRD4-Exon III VNTR genotypes/alleles between patients with anxiety symptoms versus those with normal/borderline conditions (p<0.05). Binary logistic regression analyses showed that the heterozygous 4,5 VNTR genotype of DRD4 was associated with a higher risk of anxiety symptoms after adjusting for other covariates (odds ratio = 4.25, p = 0.028). None of the studied polymorphisms was linked to depression in HD patients. Collectively, the current findings provide genetic clues to psychopathology in HD patients and suggest that the DRD4 exon III VNTR polymorphism is involved in the etiology of anxiety in this patient population.

Impact of PCSK9, WDR12, CDKN2A, and CXCL12 Polymorphisms in Jordanian Cardiovascular Patients on Warfarin Responsiveness and Sensitivity

Background

The main objective of this study is sought to determine the impacts of PCSK9, WDR12, CDKN2A, and CXCL12 polymorphisms on warfarin sensitivity and responsiveness in Jordanian cardiovascular patients during the initiation and stabilization phases of therapy.

Methods

This study took place at the anticoagulation clinic at Queen Alia Heart Institute (QAHI) in Jordan. DNA samples were collected from 212 cardiovascular patients and 213 healthy controls. Genomic SNPs genotyping was conducted using the MassARRAY System at the Australian Genome Research Facility.

Results

This study assessed 10 polymorphisms (rs11206510 within the PCSK9 gene, rs6725887 and rs7582720 within the WDR12 gene, rs4977574, rs10757278, and rs1333049 within the CDKN2A gene, rs2862116, rs7906426, rs1746048, and rs268322 within the CXCL12 gene) in 212 Jordanian cardiovascular patients. Carriers of CDKN2A rs1333049, rs10757278, and PCSK9 rs11206510 polymorphisms had an increased risk of resistance during the initiation phase of warfarin therapy compared to those who do not carry it, or those who are carrying one polymorphism only (P < 0.05), while carriers of CXCL12 rs7906426 polymorphism had similar increased risk but during the stabilization phase of warfarin therapy (P < 0.05).

Conclusion

Carriers of CXCL12 rs2862116 polymorphism had an increased risk to be warfarin extensive responders compared to those with no or only one polymorphism (P = 0.01). However, the presence of PCSK9 rs11206510 polymorphism affects the warfarin maintenance doses (P ˃ 0.0001).

Influence of CYP4F2, ApoE, and CYP2A6 gene polymorphisms on the variability of Warfarin dosage requirements and susceptibility to cardiovascular disease in Jordan

Cardiovascular diseases are among the leading causes of death worldwide. Many of those diseases require treatment with warfarin, an anticoagulant that has a large high inter and intra-variability in the required doses. The aim of this study is to find if there are any associations between rs2108622 of CYP4F2, rs7412 and rs405509 of ApoE, and rs1801272 of CYP2A6, and CVD and warfarin dose variability. The selected genes and their polymorphisms are involved in many GWAS associated with cardiovascular disease and variability in warfarin treatment. The study sample consisted of 212 Jordanian Cardiovascular patients and 213 healthy controls. DNA was extracted and the Mass ARRAY™ system was used to genotype four selected SNPs within three genes (CYP4F2, ApoE, and CYP2A6). Only one out of the four selected SNPs (ApoE rs7412 SNP) was found to be associated with the risk of cardiovascular disease. Also, this SNP showed significant differences in warfarin initial doses. CYP2A6 rs1801272 SNP was found to be associated with warfarin sensitivity during the initiation phase of therapy and with warfarin responsiveness and INR measurement during the stabilization phase of therapy. This study improves the current understanding of the high inter and intra-variabilities in response to warfarin, including the variety of dosing requirements and the susceptibility to cardiovascular disease in the Jordanian Arab population. Further study on a larger sample and in different ethnic groups could help in improving our understanding of warfarin's pharmacogenetics and its application in personalized medicine.

WITHDRAWN: Evaluation of the factors that may contribute to the responsiveness of anti-epileptic treatments in pediatric patients, a study from Jordan

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The Association Between Serum Vitamin D3 Levels and Autism Among Jordanian Boys

This study assesses the correlation between vitamin-D deficiency and autism spectrum disorder (ASD) in Jordan. We performed a case-controlled cross-sectional analysis to assess vitamin D levels in 83 children with ASD aged less than 8 years old compared to 106 healthy controls. In addition, the association between vitamin D deficiencies and gastrointestinal (GI) complains and electroencephalogram (EEG) abnormalities commonly found in children with ASD was investigated. Vitamin D levels in ASD patients were significantly lower. Also, Vitamin D levels in ASD patients had significant correlation with GI complains, but no correlation between vitamin D levels and Ca²⁺or EEG abnormalities was detected. These data suggest a possible role for vitamin D deficiency in the pathophysiology of ASD.

Pharmacogenomics of genetic polymorphism within the genes responsible for SARS-CoV-2 susceptibility and the drug-metabolising genes used in treatment

The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) represents a significant challenge to international health. Pharmacogenomics aims to identify the different genetic variations that exist between individuals and populations in order to determine appropriate treatment protocols to enhance the efficacy of drugs and reduce their side‐effects. This literature review provides an overview of recent studies of genetic polymorphisms in genes that mediate the SARS‐CoV‐2 infection mechanism (ACE1, ACE2, TMPRSS2 and CD26). In addition, genetic variations in the drug‐metabolising enzyme genes of several selected drugs used in the treatment of COVID‐19 are summarised. This may help construct an effective health protocol based on genetic biomarkers to optimise response to treatment. Potentially, pharmacogenomics could contribute to the development of effective high‐throughput assays to improve patient evaluation, but their use will also create ethical, medical, regulatory, and legal issues, which should now be considered in the era of personalised medicine.

Influence of PSRC1, CELSR2, and SORT1 Gene Polymorphisms on the Variability of Warfarin Dosage and Susceptibility to Cardiovascular Disease

Background

Cardiovascular disease is one of the most common causes of morbidity and mortality worldwide. Several cardiovascular diseases require therapy with warfarin, an anticoagulant with large interindividual variability resulting in dosing difficulties. The selected genes and their polymorphisms have been implicated in several Genome-Wide Association Study (GWAS) to be associated with cardiovascular disease.

Objective

The goal of this study is to discover if there are any associations between rs646776 of PSRC1, rs660240 and rs12740374 of CELSR2, and rs602633 of SORT1 to coronary heart disease (CHD) and warfarin dose variability in patients diagnosed with cardiovascular disease undergoing warfarin therapy.

Methods

The study was directed at the Queen Alia Hospital Anticoagulation Clinic in Amman, Jordan. DNA was extracted and genotyped using the Mass ARRAY™ system, statistical analysis was done using SPSS.

Results

The study found several associations between the selected SNPs with warfarin, but none with cardiovascular disease. All 4 studied SNPs were found to be correlated to warfarin sensitivity during the stabilization phase except rs602633 and with warfarin dose variability at the initiation phase. CELSR2 SNPs also showed association with dose variability during the stabilization phase. Also, rs646776 and rs12740374 were linked to warfarin sensitivity over the initiation phase. Only rs602633 was associated with INR treatment outcomes.

Conclusion

The findings presented in this study found new pharmacogenomic associations for warfarin, that warrant further research in the field of genotype-guided warfarin dosing.

Genetic Association of Epilepsy and Anti-Epileptic Drugs Treatment in Jordanian Patients

Purpose

The aim of this study was to investigate the possible effects of single-nucleotide polymorphisms (SNPs) within SLC1A1, SLC6A1, FAM131B, GPLD1, F2, GABRG2, GABRA1, and CACNG5 genes on response to anti-epileptic drugs (AEDs) and the genetic predisposition of epilepsy in Jordanian patients.

Patients and Methods

A total of 299 healthy individuals and 296 pediatric patients from the Jordanian population were recruited. Blood samples are collected, and genotyping was performed using a custom platform array analysis.

Results

The SLC1A1 rs10815018 and FAM131B rs4236482 polymorphisms found to be associated with epilepsy susceptibility. Moreover, SLC1A1 rs10815018 and GPLD1 rs1126617 polymorphisms were associated with generalized epilepsy (GE), while FAM131B rs4236482 is associated with the focal phenotype. Regarding the therapeutic response, the genetic polymorphisms of FAM131B rs4236482, GABRA1 rs2279020, and CACNG5 rs740805 are conferred poor response (resistance) to AEDs. There was no linkage of GLPD1 haplotypes to epilepsy, its subtypes, and treatment responsiveness.

Conclusion

Our findings suggested that SLC1A1, FAM131B, and GPLD1 polymorphisms increasing the risk of generating epilepsy, while FAM131B, GABRA1, and CACNG5 variants may play a role in predicting drug response in patients with epilepsy (PWE).

LTA, LEP, and TNF-a Gene Polymorphisms are Associated with Susceptibility and Overall Survival of Diffuse Large B-Cell lymphoma in an Arab Population: A Case-Control Study

Objective:

In this study, we aimed to explore the relationship between five selected proinflammatory and immune-mediated genes (TNF rs1800629G>A, rs361525G>A, rs1799964T>C, LTA rs1800683G>A, rs909253A>G, TNFAIP8 rs1042541C>T, LEPR rs1327118G>C, and LEP rs2167270G>A) and the risk and overall survival of DLBCL patients within the Jordanian Arab population.

Methods:

One hundred twenty-five patients (125) diagnosed with DLBCL at the King Abdullah University Hospital (KAUH) between 2013 and 2018 and 238 healthy cancer-free control subjects with similar geographic and ethnic backgrounds to the patients were included in the study. Genomic DNA was extracted from the formalin-fixed paraffin-embedded tissues of the subjects and from peripheral blood samples of the controls. The Sequenom MassARRAY^® sequencer system (iPLEX GOLD) was used. The analyses included assessments of population variability and survival.

Results:

Our study showed significant differences in the distribution of the studied polymorphisms of DLBCL between the patients and controls for TNF rs1800629G>A, LTA rs909253 G>A and LEP rs2167270 G>A. TNF rs1800629G>A (p = 0.01), in which the G allele harbors a higher risk of DLBCL (GG and GA genotypes when compared with AA genotype) (p = 0.044). The LTA rs909253 A>G polymorphism is associated with a higher risk of DLBCL in the allelic model (p = .004). LEP rs2167270 G>A polymorphism is associated with a decreased risk of DLBCL in the recessive mode models (p = .03). Subjects with the dominant model for TNF-a rs1799964 (TT genotype in comparison with the combined TT/TC genotype) and patients with the homozygous genotype (GG) of rs361525 have better overall survival rates.

Conclusion:

Our results confirmed the diversity and the heterogeneity of the disease. Although the study has a limitation because of its relatively small size, it clearly emphasizes the significance of ancestry and genetic composition as the determinants of DLBCL risk and behavior.

Analysis of Comprehensive Pharmacogenomic Profiling of VIP Variants Among the Genetically Isolated Chechen Subpopulation from Jordan

Background

Profiling rare variants in isolated populations can significantly clarify and understand the development of a clinically relevant process. Therefore, leading to a better identifying novel targeted treatment.

Objective

This study aimed to determine the allele frequencies of 56 single nucleotide polymorphisms (SNPs) within several important pharmacogenes.

Methods

This study consisted of 166 unrelated subjects from a genetically isolated group (Chechen) who were living in Jordan. In this study, the distribution of the variants among Chechen was compared to other ethnic groups available at two databases (Genome 1000 and (ExAC)). The frequency of genotypes and alleles was calculated and tested using the chi-square test and the Hardy–Weinberg equilibrium equation (HWE).

Results

Our results revealed that the distribution of allele frequencies within different pharmacogenes among Chechen showed different similarities with other populations. The CEU and TSI showed the highest resemblance with the Chechen population (75% similarity), in contrast to LWK which had the lowest similarity (30%).

Conclusion

This study sheds light on clinically relevant SNPs to enhance medical research and apply pharmacogenomics in clinical settings.

Aberrant right subclavian artery in a cadaver: a case report of an aortic arch anomaly

In early embryogenesis, aortic anomalies occur as a consequence of disorders in the development of the primitive aortic arches system. Aberrant right subclavian artery, also known as arteria lusoria, is one of the important congenital anomalies of the aortic arch, in which the right subclavian artery arises from the arch of aorta instead of the brachiocephalic trunk. During routine dissection of a female cadaver, we observed retro-oesophageal aberrant right subclavian artery arising as the fourth branch from the aortic arch. In this case, the brachiocephalic trunk was absent. Early detection of aortic arch anomalies through diagnostic interventions is helpful to avoid complications during surgical procedures.

Possible mechanisms for the renoprotective effects of date palm fruits and seeds extracts against renal ischemia/reperfusion injury in rats

PURPOSE

This work investigates the possible renoprotective effects of date palm fruits and seeds extract against renal ischemia and their underlying mechanisms.

METHODS

108-Sprague Dawle male rats were randomly allocated into 6 equal groups differently receiving aqueous or methanolic fruit and seed extracts. Assay of serum creatinine, BUN and TNF-α, morphological examination of the left kidney, markers of the redox state (MDA, CAT, and GSH), the expression of TNFα and Nrf2 genes at the level of mRNA, the expression of caspase-3 and TGF-β proteins by immunohistochemistry were performed.

RESULTS

45-min renal I/R caused significant deterioration of kidney functions (increase in serum creatinine and BUN) and morphology (P < 0.001) and significant reduction in CAT activity and GSH levels with significant increase in serum TNF-α and MDA concentration and the expression of Nrf2, caspase-3, TNF-α, and TGF-β in kidney tissues. Pre-treatment with either date palm fruit or seed extracts significantly improved kidney functions and morphology (P ≤ 0.001) with a significant increase in the expression of Nrf2 and CAT activity, and GSH concentration and a reduction in serum TNF-α and expression of caspase-3, TNF-α, and TGF-β (P < 0.001).

CONCLUSIONS

Administration of date palm extracts exhibited a renoprotective effect against renal I/R injury.This renoprotective action might be due to their antioxidants, anti-apoptotic and anti-inflammatory actions. Moreover, aqueous fruit extracts offered powerful renoprotective effect than aqueous seed extracts, and aqueous fruit and seed extracts were generally more effective than methanolic extracts.

Genome-wide identification of methylated CpG sites in nongenital cutaneous warts

BACKGROUND

Low-risk HPV infection has not been the subject of epigenetic investigation. The present study was carried out in order to investigate the methylation status of CpG sites in non-genital cutaneous warts.

METHODS

Genomic DNA was extracted from 24 paired epidermal samples of warts and normal skin. DNA samples were bisulfite converted and underwent genome-wide methylation profiling using the Infinium MethylationEPIC BeadChip Kit.

RESULTS

From a total of 844,234 CpG sites, 56,960 and 43,040 CpG sites were found to be hypo- and hypermethylated, respectively, in non-genital cutaneous warts. The most differentially methylated CpG sites in warts were located within the C10orf26, FAM83H-AS1, ZNF644, LINC00702, GSAP, STAT5A, HDAC4, NCALD, and EXOC4 genes.

CONCLUSION

Non-genital cutaneous warts exhibit a unique CpG methylation signature.

The Impact of the Genetic Polymorphism in DNA Repair Pathways on Increased Risk of Glioblastoma Multiforme in the Arab Jordanian Population: A Case-Control Study

Introduction

Among the Jordanian population, brain tumors are the tenth most common type of cancers in both males and females, comprising 2.8% of all newly diagnosed neoplasms. Diffuse gliomas are the most prevalent and the most aggressive primary brain tumors in adults. The incidence of diffuse gliomas varies among different populations; this variation is partially linked to genetic polymorphisms. The purpose of the study is to examine the association between (BRCA1 rs799917G>A, rs1799966T>C, EXO1 rs1047840G>A, EME1 rs12450550T>C, ERCC2 rs13181T>G, rs1799793C>T, and XRCC1 rs1799782G>A) DNA repair gene polymorphisms and glioblastoma multiforme (GBM) susceptibility, and survival in the Jordanian Arab population.

Methods

Eighty-four patients diagnosed with glioblastoma multiforme at the King Abdullah University Hospital (KAUH) between 2013 and 2018 and 225 healthy cancer-free control subjects with similar geographic and ethnic backgrounds to the patients were included in the study. Genomic DNA was extracted from the formalin-fixed paraffin-embedded tissues of the subjects. The Sequenom MassARRAY^® sequencer system (iPLEX GOLD) was used. The analyses included assessments of population variability and survival.

Results

This study is the first to address the relationship between BRCA1 rs1799966 and rs799917 SNP, and the risk of GBM among the Arab Jordanian population. The findings of the study show that BRCA1 rs799917 is associated with decreased risk of GBM in the recessive model (AA vs G/G-A/G: OR, 0.46, 95% CI, 0.26-0.82, p=0.01) and the same SNP is associated with increased risk of GBM in the overdominant model (AG vs G/G-A/A: OR, 1.72, 95% CI, 1.02-2.89, p=0.04).

Pharmacogenomic landscape of VIP genetic variants in Jordanian Arabs and comparison with worldwide populations

The pharmacogenomics has lately become a focal field of research that investigates the influence of genetic variations of drug-metabolizing enzymes and their receptors and downstream proteins on the interindividual variability in response to medications and adverse drug reactions. Therefore, it is significantly important to study and analyze the variations in drug response between different ethnic groups and populations. The current study aimed to detect the distribution of the genotype and allele frequencies in several very important pharmacogenetic (VIP) gene polymorphisms in the Jordanian population of Arab descent. This study involved 500 unrelated Jordanian individuals of Arab descent. A total of 65 VIP variants located within 33 candidate genes were randomly selected from the PharmGKB database and genotyped using the MassARRAY (iPLEX GOLD) system. The chi-square test was used to evaluate the significant differences of minor allele and genotype frequencies between the Jordanian and other populations including CHE, ASW, CEU, CHB, CDX, GIH, GBR, JPT, LWK, MXL, TSI, YRI, CAR, and ACB. This study revealed six variants were not in Hardy Weinberg equilibrium (HWE) (P-value > 0.05) and ten SNPs showed monomorphic features. Most of the remaining forty-nine variant frequencies were significantly different from the compared ethnic groups (P-value < 0.05). The results of this study may be helpful to develop safer treatment by applying the concept of personalized medicine based on the profile of VIP pharmacogene variants of the Jordanian population of Arab descent.

Epigenome-wide analysis of common warts reveals aberrant promoter methylation

Epigenetic alteration of host DNA is a common occurrence in both low- and high-risk human papillomavirus (HPV) infection. Although changes in promoter methylation have been widely studied in HPV-associated cancers, they have not been the subject of much investigation in HPV-induced warts, which are a temporary manifestation of HPV infection. The present study sought to examine the differences in promoter methylation between warts and normal skin. To achieve this, DNA was extracted from 24 paired wart and normal skin samples and inputted into the Infinium MethylationEPIC BeadChip microarray. Differential methylation analysis revealed a clear pattern of hyper- and hypomethylation in warts compared to normal skin, and the most differentially methylated promoters were found within the EIF3EP2, CYSLTR1, C10orf99, KRT6B, LAMA4, and H3F3B genes as well as the C9orf30 pseudogene. Moreover, pathway analysis showed that the H3F3A, CDKN1A, and MAPK13 genes were the most common regulators among the most differentially methylated promoters. Since the tissue samples were excised from active warts, however, this differential methylation could either be a cellular response to HPV infection or an HPV-driven process to establish the wart and/or promote disease progression. Conclusively, it is apparent that HPV infection alters the methylation status of certain genes to possibly initiate the formation of a wart and maintain its presence.

Candidate Gene Analysis Of Alopecia Areata In Jordanian Population Of Arab Descent: A Case-Control Study

Background

Alopecia areata (AA) is a non-cicatricial patchy hair loss on the scalp, face or other parts of the body. AA was found to be responsive to immunosuppressive therapies, a finding that supports an autoimmune basis for the disease. Several genetic studies have shown the significance of immunological factors as key genetic components in AA.

Objective

In this study, we aimed to investigate the genetic association of 7 single-nucleotide polymorphisms (SNPs) within five candidate genes including TAP1, CXCL1, CXCL2, HSPA1B, and TNFα with AA susceptibility in the Jordanian Arab population.

Methods

A case–control genetic association study conducted in 152 patients and 150 healthy individuals was performed using the sequenom MassARRAY system (iPLEX GOLD) to genotype the selected SNPs.

Results

rs1800629 SNP of the TNFα gene was significantly associated with AA in the heterozygous and rare homozygous genotypes (P=0.022 and P=0.0079, respectively) with no linkage of the TAP1, CXCL1, CXCL2 and HSPA1B variants.

Conclusion

This is the first study of its kind among the Jordanian population providing evidence of genetic association of the TNFα with AA susceptibility. Further genetic studies on Arab descent including other variants are required to clarify and strengthen the association of these genes with susceptibility to develop AA.

Correlation between a variable number tandem repeat (VNTR) polymorphism in SMYD3 gene and breast cancer: A genotype-phenotype study

Genetic predisposition to breast cancer (BC) has become one of the most studied aspects of the disease. Advances in the field of cancer research have revealed the role of different genetic polymorphisms within genes of interest in the development of BC. This study aimed to explore the impact of a variable number tandem repeat (VNTR) genetic variant found within the SET and MYND domain containing protein 3 (SMYD3) gene on BC risk in Jordan and examine key clinical and pathological prognostic factors. Genotyping of blood samples from 180 cases with breast cancer and 180 healthy individuals from the Jordanian population was carried out via a combination of PCR and agarose gel electrophoresis. A highly significant association was found at level of genotype (P-value = 0.009) and allele (P-value = 0.0001) between BC development and the VNTR variant in the SMYD3 gene among Jordanian women. Moreover, we found that the VNTR of SMYD3 gene may interfere with BC risk among patients with different immunohistochemistry (IHC) profiles (P-value < 0.05). This study reported that there is a significant correlation between BC development and the VNTR in the SMYD3 gene. These findings can help alleviate the burden of BC in developing countries including Jordan and to fill the gaps in current literature. Since this study was carried out on Jordanian Arabs, more studies on the link between BC and the SMYD3 VNTR variant are recommended to determine this polymorphism's impact on other ethnic groups.

Investigation of the forensic GlobalFiler loci in the genetically isolated Circassian subpopulation in Jordan

Circassians are a Caucasian ethnic group who make up a significant minority in Jordan. Although other ethnic groups have been the subject of forensic genetic analysis, no published study has investigated the forensic genetic efficiency of short tandem repeats (STRs) in Circassians, neither in Jordan nor in any other country. The main objective of the current study is to determine the allelic frequencies and evaluate the forensic efficiency parameters of 21 highly polymorphic autosomal STR loci among the Circassian subpopulation in Jordan. The GlobalFiler loci were amplified using DNA extracted from the whole blood samples of 150 Jordanian Circassians. The SE33 locus was found to be the most informative and polymorphic STR marker while TPOX was the least informative. However, allele 8 of TPOX was the most common across all of the investigated 21 loci in Jordanian Circassians. The combined matching probability (CMP) and combined power of discrimination (CPD) were 5.02E-24 and 0.9999999, respectively.

Vitamin E protects against cisplatin-induced genotoxicity in human lymphocytes

Cisplatin is an anticancer drug that is widely used in treatments of human malignancies such as ovaries,' testes,' and solid tumors of the head and neck. However, the use of cisplatin in the treatments can be associated with DNA damage and high risk to the development of secondary malignancies. Vitamin E is a strong lipophilic antioxidant that has the ability to protect normal cells from chromosomal damage and promote the repair of the damaged DNA. In the current study, the possible protective effect of vitamin E on DNA damage induced by cisplatin was investigated. For that, chromosomal aberrations (CAs) frequency and the number of sister chromatid exchanges (SCEs) were measured in cultured human lymphocytes. Results showed that cisplatin statistically significant increases in the number of cells with CAs (P < 0.05) and in the frequency of SCEs (P < 0.05) as compared to the control group. These increases were significantly lowered by pretreatment of cells with vitamin E. Additionally, cisplatin reduced mitotic index at used concentrations (P < 0.05), which was normalized by vitamin E. Therefore, we conclude that vitamin E can prevent the genotoxicity of cisplatin on cultured human lymphocyte.

Genetic polymorphisms of CYP3A5, CHRM2, and ZNF498 and their association with epilepsy susceptibility: a pharmacogenetic and case-control study

Background

A total of 50 million persons were diagnosed worldwide with epilepsy. One-third of them are experiencing debilitating seizures despite optimum anti-epileptic drugs (AEDs) treatment. Several studies have suggested that CYP3A5, CHRM2, and ZNF498 influence the pharmacokinetics of AEDs. Therefore, the severity of the disease as well as the degree of response to the AEDs could be affected by the genetic polymorphisms within these genes.

Objectives

In this study, we assessed the effect of certain single nucleotide polymorphisms (SNPs) within CYP3A5, CHRM2, and ZNF498 genes on the susceptibility to develop epilepsy and the responsiveness to AEDs treatment.

Methods

A case-control and pharmacogenetic study was conducted on samples of 299 healthy individuals in addition to 296 epileptic patients. Genotypic, allelic, and clinical data association were performed for the selected polymorphisms within the (rs324649, rs420817, rs15524, and rs1859690) in the Jordanian population.

Results

The analysis revealed no significant association of the investigated SNPs with epilepsy in general, partial and generalized epilepsy as well as drug responsiveness. CYP3A5 and ZNF498 were associated with family history (P=0.003 and P=0.002, respectively) and the classification of epilepsy for the ZNF498 variant (P=0.009). On the other hand, CHRM2 was not linked to either disease severity or treatment responsiveness.

Conclusion

Our results failed to confirm the association of CYP3A5, ZNF498, and CHRM2 variants with either disease development or treatment response. Clinical pharmacogenetic studies may contribute to treatment personalization, appropriate drug dose selection, minimizing drug adverse reactions, increasing drug efficacy, and reducing the costive burdens.

Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection

HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield's tissue-clustered DNase hypersensitive sites, ENCODE's segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission.

Genetic association of XRCC5 gene polymorphisms with breast cancer among Jordanian women

Purpose

Breast cancer (BC) is a complex disease that is governed by several different environmental and inherited factors. There are many genes have been linked with BC development by screening specific genetic variants within these genes. In this study, we aim to investigate the correlation between Variable Number Tandem Repeat (VNTR) in XRCC5 gene and BC.

Materials and methods

Polymerase Chain Reaction (PCR) and Gel electrophoresis were used to genotype the XRCC5 gene polymorphism in 200 cases with breast cancer and 200 healthy individuals. All participants were Jordanian women from Arab descents. Clinical and pathological characteristics for BC patients were summarized and categorized according to their medical records.

Results

In this study, we found a strong correlation between the VNTR polymorphism in the XRCC5 gene and BC risk (P-value<0.0001). Remarkably, three different genotypes (2R\2R, 3R\2R and 3R\3R) showed significant association with BC (P-value<0.0001). This study also reported a significant difference in the distribution of allele frequencies between BC patients and healthy individuals (3R; P-value<0.0001 and 2R; P-value<0.001). However, we propose that VNTR of XRCC5 gene did not interfere with BC prognosis.

Conclusion

We speculate that the VNTR of XRCC5 gene may influence BC development. More investigations are needed in this regard to clarify the underlying role of the XRCC5 genetic variant in tumorgenesis including BC development.

Association Of GSTM1, GSTT1 And GSTP1 Polymorphisms With Breast Cancer Among Jordanian Women

Purpose

Genetic predisposition to disease has become one of the most investigated risk factors in recent years, and breast cancer (BC) is no exception. In this study, we investigated specific genetic variants of three candidate genes belonging to the glutathione-S-transferase superfamily that have been implicated in increased risk of cancers.

Materials and methods

This case-control study comprised 241 Jordanian women who were diagnosed with BC in addition to 219 matched controls. Gel electrophoresis of PCR products was used to visualize and genotype both the GSTM1 and GSTT1 genes, while PCR-RFLP was employed to genotype the rs1695 of the GSTP1 gene.

Results

Our findings did not reveal any correlation between the investigated polymorphisms of GST genes and BC risk among Jordanian women. Otherwise, the combination of GSTM1 entire gene deletion and (GG) genotype of GSTP1 polymorphism (rs1695) was significantly associated with BC with p-value <0.05 (i.e. p-value was not significant after correcting for multiple comparison).

Conclusion

We suggest that the interaction between GSTM1 polymorphism and rs1695 of GSTP1 may influence BC development and progression among Jordanian women. More epidemiological studies are needed to provide a baseline for the underlying role of GSTs polymorphisms in tumorigenesis.

Association of CYP gene polymorphisms with breast cancer risk and prognostic factors in the Jordanian population

Background

Single nucleotide polymorphisms (SNPs) in several CYP genes have been associated with altered breast cancer (BC) risk in different populations. Despite this, there is a dearth of information on the roles of these SNPs in Jordanian BC patients. Therefore, this study aims to determine if there is any single nucleotide polymorphism (SNP) within CYP19A1, CYP2C19, CYP2C9, CYP1B1, CYP3A4, and CYP1A2 genes associated with BC in the Jordanian population. In addition, this work investigates the association between selected BC prognostic factors and variants of the aforementioned CYP candidate genes.

Methods

Blood samples were withdrawn from 221 BC patients and 218 healthy volunteers recruited from the Jordanian population. Genomic DNA was withdrawn and, after quantification and quality control, was genotyped using the Sequenom MassARRAY® system (iPLEX GOLD). Statistical analysis was then carried out to assess allelic and genotypic frequencies as well as genetic association between cases and controls.

Results

The CYP19A1 SNP rs7176005 (p < 0.0045) and the CYP1A2 SNP rs762551 (p = 0.004) were significantly associated with BC risk. However, no such association was found for the screened SNPs of the CYP2C9, CYP1B1, CYP2C19 and CYP3A4 genes. Regarding the prognostic factors of BC, several of the screened SNPs were associated with different pathological and clinical features.

Conclusions

Certain CYP genes, particularly CYP19A1 and CYP1A2, were associated with BC risk and development in the Jordanian population.

Investigating the Contribution of NPSR1, IL-6 and BDNF Polymorphisms to Depressive and Anxiety Symptoms in Hemodialysis Patients

AIMS

Psychological symptoms are prevalent in hemodialysis (HD) patients. Previous investigations showed that brain-derived neurotrophic factor (BDNF) and interleukin-6 (IL-6) as well as the interaction with neuropeptide S receptor 1 (NPSR1) are linked to the development of psychological distress. This study examined the association of polymorphisms of genes encoding these proteins with depression and anxiety in a representative group of Jordanian HD patients.

METHODS

A total of 302 HD patients were involved in the study and categorized into three groups based on the Hospital Anxiety and Depression Scale, HADS-D or HADS-A scores as follows: normal (<7), mild (8-10) and moderate-severe (11-21). Single nucleotide polymorphism (SNP) of NPSR1 Asn107Ile (rs324981), IL-6 G174C (rs1800795), and BDNF Val66Met (rs6265) was genotyped using blood samples.

RESULTS

The frequency of Ile-allele of NPSR1 Asn107Ile was significantly higher in patients with moderate-severe HADS-A scores versus normal (53% vs. 40.8%, p = .035). Using ordinal regression analysis, Asn-allele of NPSR1 polymorphism was nominally significantly associated with a lower risk of anxiety (OR = 0.57, CI: 0.33-0.97, p = .038) after adjusting for other covariates. A marginally significant difference in genotype distribution of IL-6 G174C was observed among patients according to HADS-D scores (p = .05). Furthermore, carriers of IL-6174 CC genotype showed lower median IL-6 serum concentration versus carriers of GG genotype (5.2 vs. 1.35 pg/mL, p < .05).

CONCLUSIONS

The results support the genetic role of NPSR1 in the pathogenesis of anxiety and suggest that carriers of NPSR1 Ile-allele are at increased risk of anxiety in HD patients. Neither BDNF Val66Met nor IL-6 G174C were linked to psychological symptoms. Future studies among other ethnicities are necessary to verify the observations.

The influence of an IL-4 variable number tandem repeat (VNTR) polymorphism on breast cancer susceptibility

Backgrounds

Breast cancer (BC) is one of the most widespread cancers globally. Understanding the etiology of BC may help in determining the various risk factors involved in its malignancy. Certain genetic mutations are considered to play a key role in increasing the risk of BC.

Objectives

In this study, we explored the correlation between a variable number tandem repeat (VNTR) polymorphism in the IL-4 gene and BC.

Methods

PCR and subsequent gel electrophoresis were used to genotype this variant in 360 Jordanian women (180 BC patients and 180 controls). In addition, phenotype–genotype analysis was carried out.

Results

Our findings illustrate that there is no significant relationship between the variant genotypes in the IL-4 gene and BC among Jordanian females. Other than body mass index and tumor differentiation (p< 0.05), none of the clinical and pathological parameters of BC patients exhibited any association with the variant genotypes.

Conclusions

From this study, we propose that the IL-4 genetic variant does not impact BC development and progression but that it could influence the disease prognosis.

Correlation between Candidate Single Nucleotide Variants and Several Clinicopathological Risk Factors Related to Breast Cancer in Jordanian Women: A Genotype-Phenotype Study

This study aim to investigate the association of breast cancer risk and prognostic factors with single nucleotide variants of the BRCA1, BRCA2, DAPK1, MMP9, TOX3, and TP53 genes in Jordanian women. Blood samples were collected from 230 Jordanian breast cancer patients for use in DNA extraction followed by genotyping and subsequent statistical analysis. We found that two single nucleotide variants (SNVs) of the BRCA2 gene, namely rs1799944 and rs766173, were significantly associated with breastfeeding status. Likewise, the rs11141901 and rs1041326 SNVs of the DAPK1 gene were linked with co-morbidity (p-value = 0.002) and family history of BC (p-value = 0.015), while the rs1045042 SNV of the same gene was associated with both allergy (p-value = 0.001) and family history of BC (p-value = 0.02). Tumor differentiation was correlated with the DAPK1 SNVs rs11141901 (p-value = 0.041) and rs1041326 (p-value = 0.005). Additionally, the rs2250889 SNV of the MMP9 gene was significantly associated with HER2 status, whereas the TP53 SNVs rs12951053 and rs1042522 were associated with age at menarche (p-value = 0.043) and breastfeeding status (p-value = 0.013), respectively. In contrast, the TP53 SNV rs2287497 was significantly linked to age at first pregnancy (p-value = 0.001), smoking (p-value = 0.041), and axillary lymph node status (p-value = 6e^-4). No such association was found for the BRCA1 and TOX3 SNVs. The current findings suggest significant associations between certain SNVs and breast cancer risk and prognosis in Jordanian women.

Genetic Polymorphisms of Pharmacogenomic VIP Variants in the Circassian Subpopulation from Jordan

BACKGROUND

It has been suggested that genetic variation within candidate pharmacogenes contributes to the differences in drug safety and efficacy as well as risk of adverse drug reactions among different ethnic groups. Illustrating the polymorphic distribution of Very Important Pharmacogenes (VIPs) in various ethnic groups will contribute to the development of personalized medicine for those populations.

OBJECTIVE

The present study aimed to identify the polymorphic distribution of VIPs in the Circassian subpopulation of Jordan and compare their allele frequencies with those of other populations.

METHODS

A total of 130 healthy and unrelated Circassian adults from Jordan were randomly recruited and genotyped for eleven VIP variants within the thiopurine S-methyltransferase (TPMT), ATP-binding cassette, sub-family B, member 1 (ABCB1), and vitamin D receptor (VDR) genes via Sequenom's MassARRAY® genotyping platform (iPLEX GOLD).

RESULTS

Our data on the allelic frequencies of the investigated VIP variants were compared to those of 18 other populations, comprising 11 HapMap populations, 6 Exome Aggregation Consortium populations, and the Chechen- Jordanian population from Jordan. Circassian-Jordanians were found to most resemble the African, Chechen- Jordanian, European (Finnish), European (non-Finnish), and South-Asian populations.

CONCLUSION

Circassians from Jordan significantly differ from other populations in terms of the allelic frequencies of selected VIP variants. The present findings constitute the first set of pharmacogenetic data for Circassian population from Jordan, providing a basis for safe drug administration that may be useful in diagnosing and treating diseases in this ethnic group.

Effects of MTHFR and ABCC2 gene polymorphisms on antiepileptic drug responsiveness in Jordanian epileptic patients

Background

Epilepsy is one of the most common neurological diseases with unclear etiology where its genetic background and treatment regime still need further exploration.

Objectives

This study designed to evaluate the pharmacogenomics of MTHFR and ABCC2 genes, and their association with epilepsy susceptibility among Jordanian population.

Methods

A case-control study was conducted on Jordanian cohort of 296 epileptic patients and 299 healthy individuals. Custom platform array was used to genotype the genetic polymorphisms within MTHFR (rs1801133) and ABCC2 (rs717620, rs3740066, rs2273697) genes.

Results

This study revealed a significant genetic association of MTHFR rs1801133 polymorphism with susceptibility to generalized in general and generalized tonic-clonic epilepsy (GTCE)(p=0.018 and 0.01, respectively). Regarding ABCC2 gene, rs717620 was of linkage with generalized and GTCE subtypes (p=0.045 and 0.048, respectively), while rs717620 was associated with poor responder patients (p=0.036) with no linkage of the ABCC2 haplotypes.

Conclusions

MTHFR and ABCC2 polymorphisms showed an association with either epilepsy types in general or subtypes and treatment response among Jordanian population. This study also suggested that these gene polymorphisms have an important role in epilepsy development and drug effectiveness and could be of a great impact in the era of epilepsy diagnosis and treatment.

Effects of GRM4, SCN2A and SCN3B polymorphisms on antiepileptic drugs responsiveness and epilepsy susceptibility

Background

Pharmacotherapy of epilepsy including antiepileptic drugs (AEDs) is one of the main treatment approaches. As a biological target, sodium channels (Nav channels) and glutamate receptor genes are playing a major role in the etiology and treatment of epilepsy.

Objective

This study aims to investigate the genetic associations of certain genetic polymorphisms with increased risk of epilepsy susceptibility and variability in response to AEDs treatment in a Jordanian Arab population.

Method

A pharmacogenetics and case-control study on 296 unrelated epileptic Jordanian patients recruited from the pediatric neurology clinic at the Queen Rania Al-Abdullah Hospital (QRAH) in Amman, Jordan and 299 healthy individuals was conducted. Children up to 15 years old which receiving AEDs for at least three months were scanned for genetic association of 7 single nucleotide polymorphisms (SNPs) within three candidate genes (SCN2A, SCN3B and GRM4) with epilepsy susceptibility.

Results

SCN2A rs2304016 (P = 0.04) and GRM4 rs2499697 (P = 0.031) were statistically significant with generalized epilepsy. Haplotype of CAACG GRM4 was genetically associated with epilepsy and partial epilepsy (P = 0.036; P = 0.024, respectively). This study also found that TGTAA genetic haplotype formed within GRM4 gene was associated with generalized epilepsy susceptibility (P = 0.006). While, no significant linkage of SCN3B rs3851100 to either disease susceptibility or drug responsiveness was found.

Conclusion

This study identified no significant associations of allelic or genotypic SNPs with the susceptibility of epilepsy and medication response with an exception of rs2304016 and rs2499697 SNPs that were associated with the generalized type of epilepsy among Jordanian population. Further studies are required in different populations to confirm our results and identify genetic factors that involved in susceptibility and treatment response.

Impact of a variable number tandem repeat in the CYP2C9 promoter on warfarin sensitivity and responsiveness in Jordanians with cardiovascular disease

Purpose

The purpose of this study was to investigate the influence of CYP/CYP450 2C9 (CYP2C9) promoter variable number tandem repeat (p-VNTR) polymorphism on susceptibility to cardiovascular disease and on warfarin sensitivity and responsiveness, in Jordanians with cardiovascular disease during initiation and stabilization phases of therapy.

Patients and methods

A total of 211 cardiovascular patients who were being treated with warfarin anticoagulants and 205 healthy individuals were enrolled in this study. PCR-based methods were performed to analyze the effects of CYP2C9 p-VNTR polymorphism on warfarin metabolism. The p-VNTR polymorphism was composed of tandem repeat motifs sorted into three alleles based on the length and structure: short (p-VNTR-S), middle (p-VNTR-M), and long (p-VNTR-L).

Results

We found that the genotypic and allelic frequencies differ significantly between patients and healthy individuals; therefore, our results suggest that this polymorphism is associated with cardiovascular disease in the Jordanian population. Moreover, during the initiation phase of therapy, 20% of warfarin-sensitive patients were homozygous for a short allele (p-VNTR-S), and 12.2% were heterozygous for this allele (p-VNTR-M/p-VNTR-S). During the stabilization phase, no significant differences were found between these groups and their genotypic frequencies. Additionally, we did not confirm any relationship between the CYP2C9 p-VNTR polymorphism and warfarin response during either the initiation or the stabilization phases of therapy.

Conclusion

Our data show a significant difference between the CYP2C9 p-VNTR polymorphism and risk of cardiovascular disease, in addition to significant association between this polymorphism and sensitivity to warfarin at the initiation phase of therapy in a Jordanian population. However, there is no correlation between this polymorphism and warfarin response, international normalized ratio (INR) values, or required warfarin dose to achieve a target INR either at the initiation or stabilization phases of therapy. To further corroborate our results, additional studies are required with a larger number of samples and different ethnic groups.

Association of genetic variants with level of asthma control in the Arab population

Background

Rates of asthma in Jordan have been doubled in the past decade, but this increased prevalence was not met with improved asthma control protocols. The aim of the present study was to assess whether there was any significant association between the level of asthma control and certain single-nucleotide polymorphisms (SNPs) in five genes: (ADRB2; rs1042713 and rs1042714), (CRHR1; rs1876828, rs242939, and rs242941), (STIP1; rs2236647), (ADH5, rs1154400), and (ARG1; rs2781659). These SNPs were selected based on their involvement in enzymes and receptors that are related to asthma pathways and subsequent response to medication and based on a high degree of linkage disequilibrium.

Patients and methods

A cross-sectional genetic association study was conducted from June 2016 to June 2017 in the two major hospitals in Jordan. The present study involved sampling from adult asthmatic patients of Arab descent who were selected from two phenotypic groups, ie, controlled and uncontrolled asthma. The blood samples and medical data were collected from the participants. DNA samples were extracted, quantified, and genotyped according to standard operating procedure. Allelic and haplotypic analyses were performed using the Haploview^®.

Results

A total of 245 Arab asthmatic patients were enrolled in this study. Genotyping analysis revealed that the two SNPs (rs1042713 and rs1042714) in ADRB2 gene, along with their related haplotypes, were nominally significantly associated with asthma control in the Jordanian population. The A-allele of rs1042713 and the C-allele of rs1042714 were more common in the uncontrolled asthma group than in the controlled asthma group (P=0.048 and P=0.017, respectively).

Conclusion

This was the first study that identified the nominal significant association between the level of asthma control and genetic variants in ADRB2 gene in Arab population. Further studies in other Arab region with larger sample size are recommended to confirm the relationship.

Effects of coagulation factor VII polymorphisms on warfarin sensitivity and responsiveness in Jordanian cardiovascular patients during the initiation and maintenance phases of warfarin therapy

Purpose

This study aims to investigate the relationships between genetic polymorphisms of the coagulation factor VII (FVII) gene and warfarin responsiveness and sensitivity.

Patients and methods

The study population consisted of 417 subjects (207 Jordanian cardiovascular patients and 210 healthy individuals). Cardiovascular patients were classified into two groups: those sensitive to warfarin dosage (sensitive, moderate, and resistant) and those responsive to warfarin based on International Normalized Ratios (INRs; poor, good, and extensive responders). The HVR4 polymorphism of the FVII gene was genotyped.

Results

Our results showed that there are significant differences between patients and controls according to both genotypic and allelic frequencies (P<0.0001) in the genetic susceptibility study. Moreover, the pharmacogenetics study reported that HVR4 had no association with warfarin sensitivity or responsiveness during the initiation and maintenance phases of therapy, the only significant differences were in the INR outcome measured during the maintenance phase of therapy (P=0.012).

Conclusion

Our data suggests lacking of association between the HVR4 polymorphism in the FVII gene and warfarin sensitivity and responsiveness during the initiation and maintenance phases of therapy. It is possible that these patients carry additional mutations in genes involved in the coagulation pathway.

Effects of CYP2C9 and VKORC1 polymorphisms on warfarin sensitivity and responsiveness during the stabilization phase of therapy

The main objective of this study is to assess the effects of CYP2C9 and VKORC1 polymorphisms on warfarin sensitivity and responsiveness in a Jordanian population during the stabilization phase of treatment. This study was conducted at the Queen Alia Heart Institute (QAHI) anticoagulation clinic in Amman, Jordan. We assessed three CYP2C9 (rs1799853, rs1057910, rs4086116) and four VKORC1 (rs10871454, rs8050894, rs9934438, rs17708472) polymorphisms in 139 Jordanian cardiovascular patients. Demographic and clinical data were also collected. Of the 139 patients in the cohort, 80% had the VKORC1 polymorphisms rs10871454 and rs9934438, while 22.3% and 24.5% of patients had the rs1799853 and rs1057910 CYP2C9 alleles, respectively. Carriers of the CYP2C9 polymorphisms rs1057910 and rs4086116 had an increased risk of warfarin sensitivity compared to subjects with no or only one polymorphism. Similarly, carriers of all four VKORC1 variants had an increased risk of warfarin sensitivity (over anticoagulation) compared to those with no or only one polymorphism. Patients with a CYP2C9 or VKORC1 polymorphism required significantly lower doses than patients with no polymorphisms. The presence of any of CYP2C9 or VKORC1 polymorphisms is associated with sensitivity to warfarin during the stabilization period. Being a CYP2C9 or VKORC1 polymorphism carrier is associated with a variation in doses required to achieve the therapeutic INR compared to non-carrier patients.

Gas chromatographic-mass spectrometric analysis of sunscreens and their effects on mice liver and kidney enzyme function

Background

Sunscreens are one of the most widely used products among cosmetics and personal care products. Recent studies have shown that some of sunscreen formulations may contain toxic, carcinogenic, or even nonallowed chemicals that may affect skin, cells, and hormones.

Materials and methods

This study aimed to develop and validate a method that allows the determination of sunscreen ingredients by gas chromatography-mass spectrometry (GC-MS). Analysis of original sunscreen products (n=5) from a licensed pharmacy and counterfeit sunscreen products (n=5) from local markets in Jordan was performed using GC-MS. pH stability of the sunscreen samples were also monitored under different storage temperatures. Topical application of sunscreens on mice skin was conducted to study their effects on liver and kidney enzymes' function.

Results

In terms of pH stability, there is a significant change in pH at different degrees of temperature between the products. Diethyl phthalate (DEP) was detected in two counterfeit products and was not mentioned on the ingredients' label. DEP was reported for its percutaneous absorption and systemic uptake in the literature. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were significantly increased with a P<0.005 in some groups treated with original sunscreens under sun radiation. Creatinine showed a significant decrease in some groups treated with original and counterfeit sunscreens, while blood urea nitrogen (BUN) showed no differences.

Conclusion

This study presents a method that allows the scanning and profiling of sunscreen ingredients as well as investigates their stability, permeation, and toxicity. Profiling of sunscreen product, changing in pH stability, and analyzing kidney and liver enzymes' level would be of a great impact on products' safety and consumers' health.

Impact of CYP2C9 and VKORC1 Polymorphisms on Warfarin Sensitivity and Responsiveness in Jordanian Cardiovascular Patients during the Initiation Therapy

Warfarin is an oral anticoagulant frequently used in the treatment of different cardiovascular diseases. Genetic polymorphisms in the CYP2C9 and VKORC1 genes have produced variants with altered catalytic properties. A total of 212 cardiovascular patients were genotyped for 17 Single Nucleotide Polymorphisms (SNPs) within the CYP2C9 and VKORC1 genes. This study confirmed a genetic association of the CYP2C9*3 and VKORC1 rs10871454, rs8050894, rs9934438, and rs17708472 SNPs with warfarin sensitivity. This study also found an association between CYP2C9 and VKORC1 genetic haplotype blocks and warfarin sensitivity. The initial warfarin dose was significantly related to the CYP2C9*3 polymorphism and the four VKORC1 SNPs (p < 0.001). There were significant associations between rs4086116 SNP and TAT haplotype within CYP2C9 gene and rs17708472 SNP and CCGG haplotype within VKORC1 gene and warfarin responsiveness. However, possessing a VKORC1 variant allele was found to affect the international normalized ratio (INR) outcomes during initiation of warfarin therapy. In contrast, there was a loose association between the CYP2C9 variant and INR measurements. These findings can enhance the current understanding of the great variability in response to warfarin treatment in Arabs.

Diabetes mellitus in two genetically distinct populations in Jordan. A Comparison between Arabs and Circassians/Chechens Living with Diabetes

OBJECTIVES

To compare clinical, anthropometric, and laboratory characteristics in diabetes type 2 patients of 2 genetically-distinct ethnicities living in Jordan, Arabs and Circassians/Chechens.  Methods: This cross sectional ethnic comparison study was conducted in King Abdullah University Hospital, Irbid and The National Center for Diabetes, Endocrinology, and Genetics, Amman, Jordan between June 2013 and February 2014. A sample of 347 (237 Arab and 110 Circassian/Chechen) people living with diabetes were included in the study. Data were collected through direct interviews with the participants. Clinical data were collected using a questionnaire and anthropometric measurements. Laboratory data were extracted from the patients' medical records. Results: More Arabs with diabetes had hypertension as a comorbidity than Circassians/Chechens with diabetes. Arabs living with diabetes were generally more obese, whereas Circassians/Chechens living with diabetes had worse lipid control. Arabs with diabetes had higher means of glycated haemoglobin (HbA1c) and fasting blood sugar, and more Arabs with diabetes had unsatisfactory glycemic control (60.6%) than Circassians/Chechens with diabetes (38.2%) (HbA1c ≥7.0%). Most participants (88.8%) had at least one lipid abnormality (dyslipidemia).  Conclusion: Multiple discrepancies among the 2 ethnic diabetic populations were found. New diabetes management recommendations and policies should be used when treating people living with diabetes of those ethnicities, particularly in areas of glycemic control, lipid control, and obesity.

Candidate Gene Analysis of Breast Cancer in the Jordanian Population of Arab Descent: A Case-Control Study

This study aimed to investigate whether there are specific polymorphisms within six genes (BRCA1, BRCA2, TP53, DAPK1, MMP9 promoter, and TOX3) that are associated with breast cancer among the Jordanian population. Sequenom MassARRAY system was used to genotype 17 single nucleotide polymorphisms (SNPs) within these genes in 230 Jordanian breast cancer patients and 225 healthy individuals. Three SNPs (MMP9 (rs6065912), TOX3 (rs1420546), and DAPK1 (rs11141901) were found to be significantly associated with an increased risk of breast cancer (p < .05). This study is the first to provide evidence that genetic variation in MMP9, TOX3, and DAPK1 genes contribute to the development of breast cancer in the Jordanian population.

Candidate gene analysis of asthma in a population of Arab descent: a case-control study in Jordan

AIM

To evaluate whether SNPs (n = 15) in ten candidate genes (ADRB2, ADH5, ARGI, CRHR1, STIP1, LTA4H, LTC4S, ALOX5, ABCC1 and OATP2B1) are associated with asthma in Jordanian population of Arab descent.

METHODS

A case-control study included 245 adult asthmatics and 249 controls.

RESULTS

Significant genetic association was identified at the rs2236647 (T/C) SNP in STIP1 and risk of asthma (p < 0.001). The C allele and CC genotype of this SNP were significantly higher in asthmatics compared with controls. The rs1141370 SNP (Val34Met) in ADRB2 is not polymorphic in our cohort.

CONCLUSION

The rs2236647 SNP could act as a reliable tool to identify individuals at risk of developing asthma and provision of early intervention in population of Arab descent.