Refractory Mutation System-polymerase Chain Research Articles

Role of genetic variations of DNA damage response pathway genes and heat-shock proteins in increased head and neck cancer risk.

Aim: The present study was designed to evaluate the role of DNA damage response pathway genes and heat-shock proteins in head and neck cancer (HNC) risk. Methods: For this purpose, two study cohorts were used. Cohort 1 (blood samples of 250 HNC patients and 250 controls) was used for polymorphism screening of selected genes using tetra-primer amplification refractory mutation system-polymerase chain (Tetra-ARMS PCR). Cohort 2 (200 HNC tumors and adjacent controls) was used for expression analysis, using quantitativePCR. Results: Analysis showed that mutant allele frequency of selected polymorphisms was found associated with increased HNC risk. Expression analysis showed the significant deregulation of selected genes in patients. Conclusion: The present study showed that selected genes (CHK1, CHK2, HSP70 and HSP90) can act as good diagnostic/prognostic markers in HNC.

Comparison of Nonsequencing Techniques for Identification of NPM1 Mutations and Associated Blast Morphology in Patients With Acute Myeloid Leukemia.

Nucleophosmin 1 (NPM1) mutations affect 20% to 30% of all acute myeloid leukemia (AML) patients; several methods are employed to analyze NPM1 mutations, each of them with its advantages and limitations. To compare 3 nonsequencing protocols capable of detecting the main NPM1 mutations and to evaluate nuclear morphometric analysis (NMA) as an alternative to cuplike blast detection. We selected multiparameter flow cytometry (MFC), amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), and a quantitative PCR (qPCR) kit to identify NPM1 mutations in AML patients at diagnosis. We also evaluated the presence of cuplike blasts and assessed nuclear morphometry using NMA. MFC appears as a screening method for NPM1 mutations because of its lower specificity. ARMS-PCR demonstrated specificity similar to that of the qPCR kit, although it was more laborious. qPCR testing, conversely, is relatively fast and easy to standardize. Of these methods, qPCR was the only one capable of identifying the type of NPM1 mutation. With regard to morphology, NMA could be used as an alternative for the evaluation of cuplike blasts in AML smears. qPCR appears to be the best option to identify NPM1 mutations, with ARMS-PCR representing a cheaper alternative. MFC may be used as a screening method, in which results falling within and above the gray zone should be confirmed by molecular testing.

Genetic Polymorphisms in MicroRNA-196a2 and the Risk of Human Abortion Related to Mycoplasma hominis.

Mutations in some miRNAs are associated with human recurrent pregnancy loss (RPL). In parallel, Mycoplasma spp. are one of the most common infections in pregnant women. The objective of this study was to identify the relationship between miRNA196a-2 gene polymorphism and Mycoplasma hominis (M. hominis) infection as a possible cause of human abortion. A total of 160 cervical swab specimens were collected from women (80 samples with at least one abortion as case, and 80 samples without abortion as control). A PCR-based method using 16S rRNA gene and tetra primer amplification refractory mutation system-polymerase chain (Tetra-ARMS-PCR) were used to identify the presence of M. hominis infections and miRNA196a-2 genotypes of studied women, respectively. Results showed that 22.5% of women with abortion and 7.5% of women without abortion were infected with M. hominis, thereby suggesting a significant difference between the two groups (P < 0.05). Tetra-ARMSPCR indicated that no significant difference in frequency of genotypes existed between women experimenting abortion and control group. Independently to the presence of M. hominis infection, a significant difference (P < 0.05) was observed in genotypic frequencies of miRNA196a-2 between RPL women and those with one abortion. Estimation of the Odds Ratios indicated that the chance of recurrent abortions in TT genotypes of miRNA196a-2 was about three times more likely than CC in non-infected individuals and about five times more likely than CC in M. hominis-infected patients. Our results proposed the role of miRNA196a-2 genotypes in RPL either in M. hominis-infected or non-infected individuals.

The role of deiodinase type 1 polymorphism, rs11206244 (C785T), in clinical management of a sample of Iraqi hypothyroidism patients treated with levothyroxine

BackgroundLevothyroxine (LT4) is the drug that is frequently recommended for the treatment of hypothyroidism. Many patients still have symptoms and disease-complaints even after a long time of maintaining treatment with this drug. Deiodinase type1 (DIO1) gene encodes for the DIO1 enzyme that regulates the metabolism of thyroid hormones and LT4 as well. Polymorphisms in this genes could be responsible for altered DIO1 enzymatic activity and accordingly altered response to LT4. MethodsA total of 220 primary hypothyroidism unrelated female patients aged 40 years and above were enrolled in this cross-sectional study. The single nucleotide polymorphism (SNP) rs11206244 (C785T) in the DIO1 gene was detected using tetra primers amplification refractory mutation system polymerase chain reaction (tetra ARMS PCR) technique. The thyroid hormones (thyroxin (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diiodothyronine (T2)) and thyroid stimulating hormone (TSH) in addition to some glycemic indices were determined. ResultThe distribution of the rs11206244 (C785T) alleles indicated the prevalence of the C allele, the genotype frequency was106 (48.2%) for CC, 75 (34.1%) for CT and 39 (17.7%) for TT. The patients were divided into three groups according to their detected genotype. Both TSH and rT3 were elevated in the carriers of T allele (p = 0.018 and p = 0.028, respectively). There were no significant differences in the other thyroid hormones (T3, T4 and T2) among the three groups. The glycemic indices were in close limits among the three groups of the patients as well. ConclusionSince the rs11206244 (C785T) SNP of DIO1 gene has no impact on the T3 and T4 hormones levels, this SNP could has no contribution to the therapeutic response to LT4 in our sample of Iraqi hypothyroidism female patients. However, this SNP could be associated with the decreased clearance of rT3 from the body.

P071 Isolate profiling and antifungal susceptibility determination for terbinafine and itraconazole among dermatophytes in a tertiary care hospital of western rajasthan

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM ObjectiveTo determine the species distribution of causative agents causing dermatophytosis, and their antifungal susceptibility pattern for terbinafine and itraconazole in trichophyton spp among samples collected in patients with dermatophytosis clinical suspicion during the period of December 1, 2020 to January 31, 2022.Materials and MethodsThis is a prospective study conducted in the Department of Microbiology of a tertiary care super specialty and referral Centre of western Rajasthan from December 1, 2020 to January 31, 2022.Skin scraping, nail clipping, and hair pluckings were collected in mycology lab from clinically suspected cases of dermatophytosis presenting to the department of dermatology for conventional identification, and antifungal susceptibility testing.The specimens were subjected to direct KOH and calcofluor white microscopy and conventional fungal culture on SDA at 25 ͦ C and 37 ͦ C.The cultures positive for dermatophytes were speciated by microslide culture lactophenol cotton blue mount, hair perforation test, and urease test.The isolates identified as Trichophyton spp were taken up for antifungal susceptibility testing against terbinafine and itraconazole by microbroth dilution according to CLSI-M38 A2 guidelines. Further terbinafine resistance gene evaluation for detection of C1191A and T1189C single nucleotide polymorphism in Squalene epoxide by Amplified Refractory Mutation System-Polymerase chain Reaction (ARMS-PCR) is undergoing for trichophyton spp.ResultsOver the 14-month study period, the laboratory processed total of 174 specimens: 134 skin scraping, 36 nail clipping, and 4 hair pluckings. Of them, 106 (61.62%) specimens were microscopy positive and 111 (63.79%) were culture positive. Out of the 111 culture-positive agents isolated, 94 (84.68%) were found to be dermatophytes. On isolate profiling of 94 dermatophytes T. mentagrophyte was found to be most common 45 (48%) followed by T. rubrum 27 (29%), T. tonsurans 20 (21%), T. verrucosum 1 (1.1%), and Microsporum spp 1(1.1%). Antifungal susceptibility of 93 Trichophyton spp against terbinafine showed resistance among 58.06% isolates with 83.33% isolates among terbinafine resistant cases showing ≥4 μg/ml minimum inhibitory concentration. There was no resistance detected for itraconazole with microbroth dilution.ConclusionA total of (54.02%) skin, hair, nail infections were found to be caused by dermatophytes.On isolate profiling, T. mentagrophyte, T. rubrum, and T. tonsurans were found to be predominant species among our isolates showing altered trend of local isolates from T. tonsurans being second most common spp isolated in past.On antifungal susceptibility >55% isolates showed resistance for Terbinafine with >80% having higher MIC of ≥4 μg/ml on the contrary there was no observed resistance for itraconazole.There is a need for encouraging dermatologists for prescribing routine fungal microscopy, culture, and AFST for dermatophytes in Western Rajasthan, to reduce the indiscriminate use of antifungals.

Detection of Benzimidazole Resistance-Associated Single-Nucleotide Polymorphisms in the Beta-Tubulin Gene in Trichuris trichiura from Brazilian Populations.

Preventive chemotherapy is recommended by the WHO as the main strategy for controlling infections caused by nematodes in humans, aiming to eliminate the morbidity associated with these infections. This strategy consists of routine periodic administration of benzimidazoles, among other drugs. Although these drugs decrease the intensity of infections, they have the potential to exert selection pressure for genotypes bearing mutations associated with drug resistance, which may result in the establishment of resistant worm populations. There is evidence in the literature of resistance to these drugs in nematodes that infect humans, including in the species Trichuris trichiura. Single-nucleotide polymorphisms (SNPs) in the beta-tubulin gene located at codons 167, 198, and 200 are associated with the mechanism of resistance to benzimidazoles in nematodes. Here, we standardized a molecular technique based on an amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) to analyze codons 167, 198, and 200 of T. trichiura. The ARMS-PCR methodology was successfully established to evaluate the codons of interest. A total of 420 samples of individual eggs were analyzed from populations obtained from five Brazilian states. A mutation in codon 198 was observed at a frequency of 4.8% (20/420), while for the other two codons, no polymorphism was observed. This is the first report of the presence of this mutation in populations of T. trichiura in Brazil. This fact and the emergence of the problem already observed in other species reinforces the need for regular monitoring of SNPs related to benzimidazole resistance using techniques that are highly sensitive and specific.

Lack of association between the eNOS rs1800779 (A/G) polymorphism and the myocardial infarction incidence among the Iraqi Kurdish population

ObjectivesThe genetic polymorphisms of the endothelial nitric oxide synthase (eNOS) gene are strongly associated with several cardiovascular diseases (CVDs) in various populations. The current study aimed to investigate the association of the eNOS rs1800779 (A/G) polymorphism with the progress of myocardial infarction (MI). MethodsEighty-five healthy subjects and 80 patients with MI admitted to the Erbil Cardiac Centre in the Kurdistan Region of Iraq were enrolled in the study. All participants were Kurdish from the same ethnic group. The amplification refractory mutation system polymerase chain reaction (ARMS-PCR) was used to determine the rs1800779 (A/G) polymorphism of eNOS, and the nitric oxide (NO) serum level was detected by spectrophotometer. ResultsThe genotypic frequencies of the eNOS rs1800779 AA (wild type), AG, and GG were 58.75%, 33.75%, and 7.50%, respectively, in the MI patients, and 49.41%, 43.53%, and 7.06%, respectively, for the control group. The frequencies of the A and the G alleles were 75.6% and 24.4%, respectively, in the MI group, and 71.2% and 28.8%, respectively, in the control subjects. The results revealed a lack of association of the rs1800779 genotype distribution with the level of NO serum and increased risk of MI. ConclusionThe study concluded that there is a lack of association between the genotypes and alleles of the rs1800779 eNOS and susceptibility to MI in the studied population.

The impact of deiodinase type II gene on the therapeutic response to levothyroxine in a sample of Iraqi hypothyroidism patients

BackgroundThere is a clinical observation in the local population of hypothyroid patients that many patients still have symptoms and disease-complaints even after they treated with levothyroxine as a replacement therapy. Deiodinase type II enzyme play a central role in the conversion of thyroxin to the active form triiodothyronine. This study searches the effect of rs225014; 274 T>C single nucleotide polymorphism (SNP) of deiodinase type II (DIO2) gene on the clinical response to levothyroxine replacement therapy in Iraqi hypothyroidism patients. MethodologyIn this cross –sectional study, one hundred fifty Iraqi female patients with primary hypothyroidism of the age of 40 and above, who were treated with levothyroxine were recruited. Thyroid hormones were assessed and the genetic analysis to detect rs225014 SNP was done using the tetra primers amplification refractory mutation system-polymerase chain reaction technique. ResultsThe genotypes distribution of rs225014; 274 T>C SNP was 22(14.66 %), 19 (12.66 %) and 72(72.66 %) as TT, TC and CC, respectively. Total T4 was significantly higher in TC carriers than in CC carriers, while there were no significant differences in the levels of TSH, total T3, free T3 and free T4 in TT, TC and CC groups of patients. The TC group also had significantly higher fasting serum insulin and homeostatic model assessment for insulin resistance (HOMA-IR) than the carriers of CC genotype. ConclusionsSince the rs225014 SNP of DIO2 gene is not associated with the most of the thyroid hormones levels, it could not affect the response to levothyroxine treatment in our sample of Iraqi hypothyroidism patients. Although this SNP cannot be excluded from being related to the hypothyroidism because the homozygous mutant type (CC) of it is the most frequent genotype in our sample of Iraqi hypothyroidism patients. Since TC genotype is associated with elevated levels of fasting serum insulin and HOMA-IR, it could have an impact in developing insulin resistance and type 2 diabetes mellitus.

MET overexpression in EGFR L858R mutant treatment-naïve advanced lung adenocarcinoma correlated with poor prognosis: a real-world retrospective study.

Mesenchymal epithelial transition (MET) overexpression has been reported in approximately 50-60% of epidermal growth factor receptor (EGFR)-mutant non-small-cell lung cancers. However, the prognostic significance of MET overexpression has not been established in advanced lung adenocarcinoma (ADC) patients with EGFR-sensitive mutations. A retrospective study was performed on a total of 406 treatment-naïve advanced ADC patients with EGFR mutation detection and MET expression information. EGFR mutations were detected by next-generation sequencing or amplification refractory mutation system-polymerase chain reaction. Immuno-histochemistry staining of MET expression was evaluated by H-score and overexpression was defined as an H-score ≥ 200. Overall survival (OS) and progression-free survival (PFS) were analyzed according to MET expression. Among the 406 patients, 208 patients had EGFR mutations, including 102 exon 19_del mutations, 94 L858R mutations and 12 other types of mutations. Of 110 patients with concomitant EGFR mutations and MET overexpression, 61 (59.8%) patients had 19_del mutations, 44 (46.8%) patients had L858R mutations and five (41.7%) patients had others. Patients with MET overexpression had a markedly shorter PFS and OS than patients with MET H-score < 200 in the EGFR L858R mutation subgroup (median PFS: 12 versus 26months, p = 0.001; median OS: 24 versus 32months, p = 0.038), whereas no significant difference was observed in 19_del mutation subgroup. Multivariate Cox analysis showed that MET overexpression was an independent poor prognostic factor for PFS and OS in patients with the L858R mutations (HR = 3.064, 95% CI 1.705-5.507, p < 0.001; HR = 2.043, 95% CI 1.000-4.172; p = 0.049), rather than 19_del. MET overexpression is a poor prognostic factor for advanced ADC patients with the EGFR L858R mutation.

Association of rs3212220 G/T single nucleotide polymorphism of IL-12B with tuberculosis in the population of Punjab, India

Many single nucleotide polymorphisms (SNPs) in the cytokine genes are reported to be associated with altered host susceptibility to tuberculosis (TB). Interleukin (IL)-12 has crucial role in immunity against Mycobacterium tuberculosis (MTB), the causative organism of TB. IL-12 is a key cytokine required for the release of IFN-γ by NK and Th1 cells, which is regarded as pivotal cytokine against TB. IL-12 has two subunits IL-p35 and IL-12p40 encoded by IL-12A and IL-12B gene respectively. Present study was designed for evaluating the association of rs3212220 G/T SNP of IL-12B and to check plasma levels of IL-12p40 in TB patients from population of Punjab, India. This case-control study was conducted on 300 TB patients and 150 normal healthy controls (NHCs). Genotyping of selected SNP of IL-12B was done by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method. Plasma levels of IL-12p40 were measured by enzyme linked immunosorbent assay (ELISA). Statistical significance level was calculated at 0.05. No statistically significant difference was found between genotypic and allelic frequencies of rs3212220 G/T SNP of IL-12B among TB patients and NHCs. IL-12p40 levels were found to be significantly elevated in TB patients when compared with NHCs (p < 0.0001). These levels declined with the course of anti-tuberculosis therapy (ATT). GG and GT genotypes were found to be associated with increased level of IL-12p40 in TB patients when compared to NHCs.

Cut-off values for diagnosis of G6PD deficiency by flow cytometry in Thai population

In heterozygous females, X-inactivation causes a change in glucose-6-phosphate dehydrogenase (G6PD) activity from normal to deficient. Most G6PD screening tests are used to accurately diagnose hemizygous males, but they are less reliable for diagnosing heterozygous females. This study established flow cytometric cut-off values for screening of G6PD deficiency in hemizygous males and heterozygous or homozygous females. We studied 205 (125 females, 80 males) leftover blood samples from quantitative methemoglobin reduction (MR) screening. G6PD gene mutations determined by multiplex amplification refractory mutation system-polymerase chain reaction and direct DNA sequencing were used as the gold standard reference. Accuracy of the test, including the sensitivity, specificity, and positive and negative predictive values, was analyzed using MedCalc software. The optimal cut-off values for classification of %red blood cells with normal G6PD activity or %bright cells into homozygous normal, heterozygous, and homozygous deficiency in females were 85.4–100%, 6.3–85.3%, and 0–6.2%, respectively (sensitivity 93.2%, specificity 100%). The cut-offs for classification into hemizygous normal and hemizygous deficiency in males were 76.5–100% and 0–76.4%, respectively (sensitivity 100%, specificity 96.5%). Flow cytometry can be used to differentiate heterozygous females with intermediate phenotype from homozygous females, but cannot distinguish between heterozygous females with extreme phenotype and homozygous females. By flow cytometry, heterozygous and homozygous deficiency was detected in 29.6% and 3.2% of females, respectively. Among males, hemizygous deficiency was found in 31.3%. Flow cytometry can be used to screen patients with G6PD deficiency, and reliably and efficiently identify heterozygous and homozygous females, and hemizygous males based on cellular G6PD activity.

Genomics Analysis and Nomogram Risk Predictionof Occult Lymph Node Metastasis in Non-Predominant Micropapillary Component of Lung Adenocarcinoma Measuring ≤ 3 cm.

BackgroundThe efficacy of sublobar resection and selective lymph node dissection is gradually being accepted by thoracic surgeons for patients within early-stage non-small cell lung cancer (NSCLC). Nevertheless, there are still some NSCLC patients develop lymphatic metastasis at clinical T1 stage. Lung adenocarcinoma with a micropapillary (MP) component poses a higher risk of lymph node metastasis and recurrence even when the MP component is not predominant. Our study aimed to explore the genetic features and occult lymph node metastasis (OLNM) risk factors in patients with a non-predominant micropapillary component (NP-MPC) in a large of patient’s cohort with surgically resected lung adenocarcinoma.MethodsBetween January 2019 and December 2021, 6418 patients who underwent complete resection for primary lung adenocarcinoma at the Qilu Hospital of Shandong University. In our study, 442 patients diagnosed with lung adenocarcinoma with NP-MPC with a tumor size ≤3 cm were included. Genetic alterations were analyzed using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Abnormal protein expression of gene mutations was validated using immunohistochemistry. A nomogram risk model based on clinicopathological parameters was developed to predict OLNM. This model was invalidated using the calibration plot and concordance index.ResultsIn our retrospective cohort, the incidence rate of the micropapillary component was 11.17%, and OLNM was observed in 20.13% of the patients in our study. ARMS-PCR suggested that EGFR exon 19 del was the most frequent alteration in NP-MCP patients compared with other gene mutations (frequency: 21.2%, P<0.001). Patients harboring exon 19 del showed significantly higher risk of OLNM (P< 0.001). A nomogram was developed based on five risk parameters, which showed good calibration and reliable discrimination ability (C-index = 0.84) for evaluating OLNM risk.Conclusions.Intense expression of EGFR exon 19 del characterizes lung adenocarcinoma in patients with NP-MCP and it’s a potential risk factor for OLNM. We firstly established a nomogram based on age, CYFRA21-1 level, tumor size, micropapillary and solid composition, that was effective in predicting OLNM among NP-MCP of lung adenocarcinoma measuring ≤ 3 cm.

Frequency of Hereditary Hemochromatosis Gene (HFE) Variants in Sri Lankan Transfusion-Dependent Beta-Thalassemia Patients and Their Association With the Serum Ferritin Level.

IntroductionCo-inheritance of hereditary hemochromatosis (HFE) gene variants p. C282Y and p.H63D worsen iron overload in transfusion-dependent thalassemia. Data on the HFE gene variants in Sri Lankan patients with thalassemia have not been extensively studied. This study aimed to analyze the p.C282Y and p.H63D variants in transfusion-dependent beta (β) and HbE/β-thalassemia patients and establish an association between these variants and their serum ferritin levels.Materials and MethodsA total of 125 transfusion-dependent β-thalassemia major and HbE/β thalassemia patients were tested for the c.845G>A (p.C282Y) and c.187C>G (p.H63D) HFE gene variants using the multiplex Amplification Refractory Mutation System Polymerase Chain Reaction method. For phenotype-genotype correlation, serum ferritin levels, the erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) levels were measured. The standard descriptive statistics were used for data analysis.ResultsThe study cohort consisted of transfusion-dependent 123 β-thalassemia and 2 HbE/β-thalassemia patients. The p.C282Y variant was not detected in any patient; allele frequency for the wild type (c.845GG) was 100%. Twenty-three patients were heterozygous for the p.H63D variant allele, and the allele frequencies were c.187CC 91.8%, c.187CG 9.2%, and c.187GG 0%. The mean serum ferritin level was relatively higher (mean level 4,987 ng/ml) in the p.H63D heterozygous (c.187CG) group compared to the wild type (c.187CC) group (mean level 4,571 ng/ml), but the difference was statistically not significant (p = 0.865). Among the total study population, CRP, ESR, and serum glutamine aspartate transaminase (SGPT) were elevated in 9 (7.2%), 65 (52%), and 82 (65.6%) patients, respectively. Among the p.H63D c.187CG group, elevated CRP, ESR, and SGPT were present in 5 (5%), 15 (12%), and 18 (14.4%) patients, respectively. The detected sample number was low to correlate with the confounding effect of inflammatory disorders and liver damage on the serum ferritin levels.ConclusionsThe HFE gene variant p.C282Y is unlikely to cause iron overload in the Asian β-thalassemia patients; the rarity of this variant in the study cohort replicates the findings of other South Asian population studies of this variant. The presence of the p.H63D variant could be a potential risk factor for iron overload in the β-thalassemia patients. A more extensive cohort study is required to validate this finding.

Genetic Variant of Vascular Endothelial Growth Factor (VEGF)-A rs699947 is Associated with Preeclampsia

Background: Preeclampsia remains as the leading cause of maternal-neonatal mortality and morbidity worldwide. Vascular endothelial growth factor A (VEGF-A) is a proangiogenic factor related to endothelial dysfunction and plays an important role in the preeclampsia pathophysiology. Genetic variants of VEGF-A are associated with VEGF-A expression and preeclampsia risk, however there are still inconsistent results between different populations. The aim of this study was to determine the association of this genetic variant as preeclampsia risk factor.Materials and methods: A cross-sectional study was performed with 76 pregnant women (29 preeclampsia and 47 normotensive) Jambi-Malay ethnic subjects. Sample DNA was extracted from subject’s blood. To determine the genotype, one-step tetra amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) method for VEGF-A rs699947 C/A was used.Results: We found that pregnant woman with AC genotype (p-value=0.045; OR=2.76 ; 95% CI=1.01-7.58) and AA genotype (p-value=0.026; OR=12.44; 95% CI=1.23-126.18) had higher risk of preeclampsia than the CC genotype.Conclusion: Genetic variant VEGF-A rs699947 C/A is associated with preeclampsia. The AC and AA genotype is the risk genotype for preeclampsia in Jambi-Malay ethnics.Keywords: preeclampsia, VEGF-A, genetic variant, Jambi-Malay, Indonesia

Impact of interferon-induced transmembrane protein 3 gene rs12252 polymorphism on COVID-19 mortality

Background and aimsInterferon-induced transmembrane protein 3 (IFITM3) plays a critical role in the adaptive and innate immune response by preventing membrane hemifusion between the host and viral cell cytoplasm. This study aimed to evaluate whether IFITM3 rs12252 polymorphism is related to an increased mortality rate of coronavirus disease 2019 (COVID-19). MethodsThe IFITM3 rs12252 polymorphism was genotyped using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) in 548 dead and 630 improved patients positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ResultsIn the present study, the minor allele frequency of IFITM3 rs12252 (C) was significantly more frequent in dead patients than in improved cases. The results of the multivariate logistic regression analysis indicated that the lower lipid profiles, PCR Ct value, 25-hydroxyvitamin D, and uric acid and higher levels of erythrocyte sedimentation rate (ESR), liver enzymes, and creatinine, and IFITM3 rs12252 CC genotypes were related to the COVID-19 infection mortality. ConclusionsIn summary, our findings suggested a possible link between the mortality of COVID-19 infection, the CC genotypes of IFITM3 rs12252, and clinical parameters. Further investigations are required worldwide to prove the link relationship of COVID-19 mortality with host genetic factors.

The risk of relapse in breast cancer patients is associated with MMP-9 gene polymorphism: a prospective study in a sample of the Iranian population

We investigated the association of MMP-9 rs1056628 and rs17576 polymorphisms with breast cancer (BC) relapse in a cohort of prospectively observed BC patients. The polymorphisms were genotyped in 200 BC subjects with(case) and without(control) relapse by Tetra-primer Amplification Refractory Mutation System-Polymerase Chain Reaction (T-ARMS-PCR) method. A significant association was found between the rs1056628C allele and increased risk of BC relapse (OR = 1.8, P = 0.006). Also, rs17576 allele and genotypes were shown protective effects against BC relapse. Increased risk of relapse was observed in haplotype CG (OR = 2.1, P = 0.001). Our results suggest for the first time that rs1056628 and rs17576 polymorphisms may influence BC relapse.

Impact of cytokines genes polymorphisms and their serum levels on childhood asthma in Egyptian population

BackgroundAsthma is chronic immune-mediated airway inflammation, and it is affected by a complex network of interacting cytokines. To date, the exact role of each cytokine and its genetic polymorphisms in childhood asthma development and its severity has remained poorly understood. The purpose of this study was to explore potential roles of four cytokine genes polymorphism and serum levels l [(T helper-2 (Th2) cytokine); Interleukin-4 (IL-4) 590, (Th3 cytokine); and transforming growth factor β1 (TGF-β1) 509T; (Th17) including tumor necrosis factor-alpha (TNF-α), and IL17A rs8193036] in childhood asthma risk and control in Egyptian children, for the 1st time. Materials and methodsThis case-control study included two children subgroups; Group1 included 216 non-asthmatic controls and (Group 2) 216 cases diagnosed with asthma (clinically and spirometry-based) were classified as controlled, partly controlled, and uncontrolled. Polymorphisms of TGF-β1-509, IL-4 590, and TNF-α-308 genes were detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). IL-17 was genotyped using tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR). Serum cytokines levels were measured by enzyme-linked immunosorbent assay (ELISA). ResultsSerum total IgE, TGF-β1, IL4, TNF-α, and IL17A levels were significantly higher in asthmatic compared to controls. Also, significant increases in serum total IgE, IL-4, TGF-β1, and TNF-α levels are combined with poor asthma control, while no significant IL17A changes. There were significant changes of IL-4-590, TNF-α-308, and IL17A genotypes and allele distributions between asthmatic and controls groups as well as different asthma control levels; while no impact of TGF-β1 SNP on asthma risk and control level. Four cytokines SNPs affected their serum levels among asthmatic patients. ConclusionThere are impacts of cytokine gene polymorphisms (IL-4-590, TNF-α-308, and IL17A); but not TGF-β1 on asthma susceptibility and poor asthma control in Egyptian children.

A Novel Study of Protein Kinase C Beta Gene Polymorphism (rs3760106) and Protein Kinase C Activity Levels as a Predictor of Nephropathy Complications in Iraqi Diabetic Patients

Objective: This study aimed to investigate the relation between the risk of (PRKCB-1504 C/T) gene polymorphisms and diabetic nephropathy pathogenesis and its association with its levels and some other biomarkers in serum of Iraqi diabetic nephropathy patients.&#x0D; Methods: A cross-sectional study was performed on 130 samples obtained from Al-Hussein Teaching Hospital / Kerbala – Iraq during Feb., 2020 to March. 2021. Seventy three patients of them with type 2 diabetes mellitus (T2D) and the remaining patients with type 2 diabetes mellitus with nephropathy complications (DN). Phenotypic analysis included determination of protein kinase C (PKC) activity levels, HbA1c%, serum insulin levels and renal function tests. Five ml of whole blood was obtained from each patients, 4.0 ml was centrifuged for serum separation used for biomarkers determinations and the remaining 1.0 ml was used for genomic DNA extraction for molecular analysis and polymorphism of PRKCB (rs3760106) by allele specific-amplification refractory mutational system-polymerase chain reaction (allele specific ARMS-PCR), followed by electrophoresis on 1% agarose gel. Various statistical analyses were applied to analyze the obtained data.&#x0D; Results: The amplification of the PRKCB gene gives one genotypes as indicated by (200 bp) bands for those with homozygous wild type (CC), homozygous mutant (TT) genotypes and two genotypes bands (200 bp) for those with heterozygous (CT). Genotype frequencies of rs3760106 polymorphism were found to be consistent with Hardy–Weinberg equilibrium. Allele frequencies (23.3 %, 26.7 %, 50 %) of CC, CT, TT in cases of DN group. While the frequencies in the non-DN group were (30 %, 45%, 25%) and for healthy control group were (50%, 33.4%, 16.6%) for wild, heterozygous, and homozygous in an order. In healthy control group, the risk of diabetic nephropathy was significantly higher among carriers of T allele under codominant TT (OR=6.42, 95%CI=(1.66-24.85), P=0.007), dominant CT+TT (OR=3.2, 95%CI = (1.08-9.95),P=0.03) and recessive model (OR=5, 95%CI = (1.51-16.56), P=0.008) while in T2DM without nephropathy the risk of diabetic nephropathy was significantly higher among carrier of T allele under recessive model (0R=3, 95%CI = (1.09-28.25), P= 0.003). Serum level of PKC-B1 activity was significantly higher among DN group than T2DM and control groups (43.35 ± 18.69, 30.35 ± 11.96, 27.42 ± 10.31, P=0.001), also PKC-B1 activity in DN group was significantly correlated with fasting blood glucose, HOMA-IR and renal function tests such as GFR, urea and creatinine.&#x0D; Conclusion: This study indicates that the PRKCB (C/T-1504) rs3760106 single nucleotide polymorphism was significantly associated with increased diabetic nephropathy susceptibility of Iraqi patients with T2DM and serum level of PKCB activity was associated with increase the risk of diabetic nephropathy complications.

The STAT4 SNP (rs7574865) and systemic lupus erythematosus

Introduction: Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease affecting several systems and organs in the body. The association of STAT4 transcription factor with SLE risk remains unclear. Objectives: The aim of this study was to investigate the association of STAT4 gene polymorphism (rs7574865) with the incidence of SLE. Patients and Methods: One hundred and sixty participants (80 patients with SLE and 80 healthy individuals) were included in this study. Gene analysis was conducted by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) in peripheral blood samples. Results: Fifty-seven percent (n=45) of patients with SLE had SLE disease activity index (SLEDAI) above six and had active disease. In the SLE group, the frequency of G and T alleles were 81% and 19%, respectively. Moreover, 72.50% (n=58) of patients carried the GG genotype, 17.5% (n=14) had the GT genotype and 10.1% (n=8) carried the TT genotype. There was no significant difference between allele frequency and genotypic distribution for rs7574865 polymorphism (P&gt;0.05) between SLE and control groups. Significant differences were observed between the distribution of genotypes and clinical manifestations including leukopenia (P=0.04), pulmonary (P=0.01) and ophthalmic (P=0.049) problems. The T allele with an odd ratio of 1.47 and confidence interval of 0.80 to 2.6 could increase the risk of SLE; however, it was not statistically significant (P=0.20). Conclusion: The T allele and TT genotype of the STAT4 rs7574865 polymorphism could increase the risk of lupus; however, these observations were not statistically significant.

IL-17 gene polymorphism (rs763780) in kidney recipients with post-transplant diabetes

Introduction: New-onset diabetes mellitus after transplantation (NODAT) is a common complication of organ transplantation, leading to allograft dysfunction. Genetic alterations of inflammatory cytokines have been reported to be associated with glucose homeostasis and diabetes. Objectives: This study evaluated the rs763780 polymorphism of IL-17F gene in transplant recipients with and without NODAT. Patients and Methods: The present retrospective study was conducted on ninety-one patients who have had a kidney transplant for at least three months. Patients were divided into two subgroups; recipients with NODAT (n=32) and kidney recipients without NODAT (n=59). After DNA extraction from patients’ blood samples, amplification and evaluation of specific polymorphism of the gene were performed using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Clinical and demographic data of patients were collected. Results: The NODAT was detected in 81.3% (n=26) of TT genotype carriers, 12.5% of TC genotype carriers and 6.3% of CC genotype carriers. No statistically significant differences between the studied groups in the frequency of C and T alleles and the distribution of the abovementioned genotypes were detected (P≥0.721). In the NODAT group, graft rejection and age of patients were higher significantly (P≤0.017). Conclusion: No significant correlation between the incidence of diabetes and rs763780 polymorphism of IL-17F gene was observed.