Significant Genotypic Association Research Articles

Significant Association of Cyclin D1 Promoter Genotypes With Asthma Susceptibility in Taiwan.

The molecular mechanisms underlying the association between cell cycle and asthma are poorly understood, and cyclin D1 (CCND1) is found to be upregulated in asthma airway smooth muscle. We investigated whether the most frequently examined functional variants in CCND1 determine asthma susceptibility. We genotyped 651 participants for single-nucleotide polymorphisms (SNPs) at rs9344 and rs678653 on CCND1 and assessed the association of these SNPs with asthma risk. Significant differences were found in the distributions of genotypic (p=0.0064) and allelic (p=0.0021) frequencies of CCND1 rs9344. In addition, AG or GG carriers had 0.63- or 0.48-fold adjusted odds ratios for asthma risk (95%confidence intervals=0.48-0.92 and 0.22-0.78, respectively) than those who carried the AA wildtype. Our results suggest that cell cycle regulation may play a role in asthma initiation and development, and the CCND1 rs9344 genotype may serve as an early detection marker for asthma.

Association of interleukin-17A rs2275913 polymorphism with rheumatoid arthritis susceptibility in Sudanese population.

Objectives:Rheumatoid arthritis is a chronic inflammatory autoimmune disease. This study aimed to determine the association of interleukin-17A-197G/A polymorphism with rheumatoid arthritis in Sudanese patients.Methods:A case–control study was conducted between March and December 2018. Clinical and demographic data of the study participants were collected and analyzed. Polymerase chain reaction restriction fragment length polymorphism molecular technique was done to investigate interleukin-17A-197G/A polymorphisms. All statistical tests were considered statistically significant when p < 0.05.Results:The study population included 266 participants aged between 1 and 85 years, with an average of 40 years, classified into 85 (31.2%) cases (mean age 48.5 ± 11.3 years), and 181 (68.8%) controls (mean age 35.3 ± 15.9 years). The interleukin-17A homozygote AA genotype was more frequent among the control group compared to the case group; 95 (52.5%) and 7 (8.2%), respectively. The homozygote GG and the heterozygote AG genotypes were proportionally not different among the cases and control groups; 13 (54.2%) and 11 (45.8%), and 65 (46.4%) and 75 (53.6%), respectively. According to the distribution of interleukin-17A genotypes, a statistically significant difference was observed among cases with the interleukin-17A AA and AG genotypes, p values 0.001 and 0.004, respectively. For the association interleukin-17A genotypes and family history a negatively significant association was reported (95% confidence interval, –0.219, p value = 0.001). There was also a negatively significant association of interleukin-17A genotypes and anti-cyclic citrullinated peptide (95% confidence interval, −0.141, p value = 0.002).Conclusion:This study is the first study in Sudan established the association between interleukin-17A-197G/A (rs2275913) polymorphisms and susceptibly to rheumatoid arthritis. These findings appeal for further research in Sudan to investigate the exact role of IL-17A in immunopathology and disease severity among Sudanese rheumatoid arthritis

Correlation and Path Coefficient Analysis in Coffee (&amp;lt;i&amp;gt;Coffea arabica &amp;lt;/i&amp;gt;L.) Germplasm Accessions in Ethiopia

Sufficient information on the nature and magnitude of traits association will facilitate effective selection and hybridization to develop high yielding coffee progenies. The study was conducted at Metu Agricultural Research Sub Center to determine the extent of association among yield and yield related traits of coffee. Sixty four Coffee (Coffea arabica L.) germplasm including two standard check varieties (74110 and 74112) were used for this study. The field experiment was superimposed during 2018 cropping seasons on six years old coffee trees, which was laid down in 8x8 simple lattice design. The orchard was managed as per the coffee agronomic production practices. Data on 19 quantitative traits were recorded from four representative trees per row for each accession. Yield per tree exhibited significant (P<0.05) and positive phenotypic and genotypic association with fruit width (r_ph=0.19; r_g=0.19) and fruit thickness (r_ph=0.18; r_g=0.15). On the other hand, number of primary branches showed positive and significant (P<0.05) phenotypic and genotypic correlations with fruit width (r_ph=0.23; r_g=0.12) and fruit thickness (r_ph=0.21; r_g=0.07). Hence, indirect selection in favor of this trait can improve yield in coffee. Coffee berry disease mainly attacks fruits and beans, however, the disease showed negative phenotypic and genotypic correlation with fruit and bean quantitative traits. Average inter-node length of main stem, number of nodes on primary branches, Number of primary branches, fruit width and thickness, bean width and thickness and hundred beans weight exerted positive direct effect and also had positive genotypic association with yield per tree, while the other traits affected yield indirectly, mainly through average inter-node length of primary branches production. Therefore, these traits could be used as a reliable indicator in indirect selection for higher tree yield.

Genetic Variability and Associations of Yield and Yield Related Traits for Fieldpea (&amp;lt;i&amp;gt;Pisum stivum L.&amp;lt;/i&amp;gt;) Genotypes in Arsi Zone, Southeastern Ethiopia

Field pea is an important pulse crops in Ethiopia, however the production is reduced due to many constraints including limited availability of improved variety and traditional farming systems. Twenty five advanced field pea genotypes were evaluate for ten traits at three locations during 2015/16 main cropping season using RCBD with two replications. Thus the objectives of this study were to estimate genetic variability of the genotypes and to assess the associations of yield and yield related traits. The ANOVA result showed that significant variation among genotypes. Mean square from genotype by environment interaction showed that highly significant variation among the genotypes for all traits. The genotypic and phenotypic coefficient of variation ranged from 2.4 to 12.9 and 2.9 to 22 respectively. Heritability estimates and genetic advance as present of mean also ranged from 20% to 90% and from 2.2% to 25.8% respectively. Higher estimate of heritability recorded from days to 50% flowering and thousand seed weight. Grain yield showed a significant and negative genotypic association with plant height and stand count. Stand count, days to 50% flowering, thousands seed weight and powdery mildew have a negative direct effects on grain yield while plant height has appositive direct effect on grain yield. The first two principal components explained about 58.36% of the total variation among the genotypes. The first components explained about 38.97% of the total variation and mostly explained by stand count, powdery mildew and days to 50% flowering. So the research gives as clear information about the 25 field pea genotypes for future breeding strategy.

Genotypic and Phenotypic Correlation and Path Coefficient for Quantitative Traits in Field Pea (&amp;lt;i&amp;gt;Pisum sativum&amp;lt;/i&amp;gt; L.) Genotypes at Arsi Highland of Ethiopia

In Ethiopia, field pea (<i>Pisum sativum</i> L.) is the main source of protein for resource poor growers. The improvement of varieties for yield and disease resistance is one of the important activities to support farmers and improve the productivity of the crop. Consequently, this study was showed to evaluate the genotypic correlations, phenotypic correlations and path coefficient analysis between the field pea genotypes for yield and yield associated traits. Forty-nine field pea genotypes were evaluated in simple lattice design at two locations Bekoji and Asasa in 2018/2019 cropping time of year. Grain yield per plot had positive and highly significant genotypic association through plant height whereas highly significant phenotypic correlation observed between grain yield and plant height and biomass yield. At Bekoji genotypic path analysis, days to 50% flowering, plant height, grain filling period, thousand seed weight, harvest index and total biomass showed strong positive direct effect on grain yield per plot. At Asasa the path analysis for grain yield at genotypic level showed that harvest index, thousand seed weight, plant height, days to 50% flowering and days to 95% physiological maturity and total biomass yield exerted positive direct effect on grain yield per plot. Path coefficient analysis at genotypic levels of the combined data exhibited that days to 50% flowering and total biomass per plot had strong positive direct effect on grain yield per plot. The phenotypic path analysis of the combined data revealed total biomass yield, thousand seed weight, plant height and days to maturity has strong positive direct effect on grain yield per plot. The study showed the existence of reasonable genetic variability between the field pea genotypes that can be exploited in breeding programs.

Single-nucleotide polymorphisms (SNPs) of antioxidant enzymes SOD2 and GSTP1 genes and SLE risk and severity in an Egyptian pediatric population

BackgroundSystemic lupus erythematosus (SLE) is a chronic autoimmune disease associated with increased oxidative stress that participates in immune dysregulation, and injury resulting in loss of immune tolerance and increased auto-antibody production. This study was designed to investigate the effects of genetic polymorphisms of the antioxidant enzymes genes that code for SOD2 (rs2758332) and GSTP1 (rs1695) on SLE risk and severity in Egyptian children and adolescents cohort from Delta region. MethodsThe frequencies of these genes polymorphic variants were compared between 100 SLE children and adolescents and 100 healthy control subjects. Single-nucleotide polymorphisms (SNPs) of the two antioxidants were determined using TaqMan SNP genotyping assay. ResultsIndividuals with the TT and CT genotypes of rs2758332 in the SOD2 gene were of significant risk for SLE patients (OR = 1.831, 95% CI = 1.082–3.101, P = 0.024) and (OR = 1.864, 95% CI = 1.136–3.059, P = 0.014), respectively. Cases who have combined CT + TT genotype were of significant higher risk of SLE (OR = 1.851, 95% CI = 1.156 – 2.962, P = 0.010). While, they did not show any significant association between SOD2 genotypes or alleles with SLE clinical features. In case of the SNP rs1695 in the GSTP1 gene, no significant associations of genotypes or alleles with SLE risk or with SLE clinical features were detected. ConclusionsThis study among Egyptian children and adolescents showed a strong association of the SOD2 rs2758332 not GSTP1 rs1695 polymorphism with the risk of SLE disease.

The impact of BDNF variant on bipolar susceptibility, suicidal behavior, and response to lithium carbonate in bipolar patients

Synaptic plasticity is intimately involved in the pathophysiology and treatment of bipolar disorder and disruptions in neuroplasticity can play an important role in the process of suicide behavior in bipolar patients. One of the major neurotrophic factors with essential role in the maintenance and survival of neurons and synaptic plasticity is Brain-Derived Neurotrophic Factor (BDNF) which is encoded by BDNF gene. The impact of BDNF variant on predisposition to bipolar disorder, suicidal behavior and response of patients to lithium carbonate was investigated in this study on 201 bipolar patients compared with 201 healthy controls. The tetra primers -Amplification Refractory Mutation System-PCR method was used for genotyping. Results were confirmed by Sanger sequencing method. The obtained results showed significant association of different genotypes of rs6265 with bipolar susceptibility, suicide tendency, suicide ideation as well with various responses of patients to the treatment.Overall, it appears that BDNF variant may serve as an important biological risk factor in bipolar pathogenesis, suicidality, and various responses to lithium carbonate in bipolar patients in Iranian population.

Evaluation of candidate genotype of leptin gene associated with fertility and production traits in Hardhenu (Bos taurus×Bos indicus) cattle.

The present study was conducted on Hardhenu cattle to screen genomic region of leptin gene with an objective to find the association of genotypes with fertility and production traits. The association analysis with traits under study was analysed by least squares analysis of variance by taking SNPs genotype as fixed effects in the statistical model. The genotypic frequencies with respect to targeted loci g.92450765 G>A indicated that AG (0.54) genotype was highest in Hardhenu cattle. Chi-squared tests showed that g.92450765G>A SNP meet with the Hardy-Weinberg equilibrium (p>.05).The association analysis revealed significant association of genotypes with total milk yield (TMY) and 305days milk yield (MY) (p<.05). Service period (SP) and calving interval (CI) were also found significantly associated with genotypes (p<.05). Whereas, lactation length (LL), dry days (DD) and age at first calving (AFC) did not divulge any significant association with genotype. The AG and GG genotypes were associated with higher milk yields as compared to AA genotype, indicating that allele G was associated with superior milk performance. However, AA genotyped cattle found to be favourable with SP, CI and artificial insemination (AI) per conception compared to AG and GG genotyped cows. Chi-square analysis revealed that genetic variants of g.92450765 G>A SNP of leptin gene differ significantly with regard to reproductive disorders incidence (p<.05). The frequency of GG genotype (88.89%) in the affected animal group was very high followed by AG. The animals with GG genotype were found to be more susceptible to reproductive disorders as suggested by the higher odd ratio value (16.00) in logistic model. These observations and their differential association with the fertility and production traits can be utilized as an aid to selection for genetic improvement of antagonistic traits in dairy cows.

Inteurleukin-8 gene variations and the susceptibility to schizophrenia

The relevance of Interleukin-8 (IL-8) cytokine alteration in the peripheral and central system has been widely shown in psychosis while variation in the IL-8 gene remains largely unexplored and to the best of our knowledge, IL-8 polymorphisms have never been specifically targeted in Schizophrenia (Scz). Thus, we set out to search a potential correlation between rs4073, rs2227306 and rs1126647 polymorphisms in IL-8 gene and the development of Scz in a sample of the Tunisian population in a candidate gene approach. Targeted polymorphisms were analysed in 206 patients and 195 controls using PCR-RFLP method. Among all analysed polymorphisms, only rs1126647 showed a significant risk for Scz. After stratification analysis, we noted a significant association of TT genotype and T allele at rs1126647 with paranoid form, and more specifically with female sex. We find that the rare haplotypes at rs4073-rs2227306-rs1126647 of TTT, ACT and TCT, each containing the risk allele rs1126647T, were associated with increased risk for paranoid Scz while only the TCT combination constituted a risk factor for Scz more generally. Our findings support that IL-8 gene may be involved in susceptibility to Scz but this still preliminary and needs to be strengthened by further independent analyses.

COL1A2 Polymorphism contributes to Oral submucous fibrosis: A possible role in inducing alternative splicing in areca chewers

AbstractOral submucous fibrosis (OSMF) is a chronic inflammatory disease of the oral cavity but the pathogenesis of the disease is still uncertain among the areca nut chewers. Every chewer does not show up with fibrotic changes that further extend to genetic basis of OSMF pathogenesis. Genetic predisposition has been now identified as a major risk factor for increasing the susceptibility toward the disease among these chewers. In this study, two single nucleotide polymorphism (SNP) of COL1A2 rs42542 (Exon 28, G1645C) and rs421587 (Intron 28, 665+15A&gt;G) showing mRNA splice variant trait with exon 28 skipping, extended exon 28 and intron 28 retention. The polymorphisms of the COL1A2 gene was identified by polymerase chain reaction‐direct genomic DNA sequencing from 187 patients with OSMF and 188 control participants matched on age, gender, and ethnicity. COL1A2 alternative splice variants from mRNA in human oral biopsy tissues obtained from OSMF patient and controls were confirmed by using reverse transcription PCRs (RT‐PCRs). Significant genotypic associations were observed for an exon 28 SNP (GC; P &lt; [OR‐2.35; CI {1.44‐3.83}; P &lt; .001] and CC [OR‐6.99; CI {1.83‐31.24}; P = .001) induces Ala to Pro substitution at amino acid 459 of COL1A2 in OSMF patients. Exon skipping is significantly associated with both the SNPs. Our results confirm the role of rs42542 and rs421587 in COL1A2 alternative splicing and support a strong role in susceptibility to OSMF, and could have served as surrogate markers.

Selection for yield and its component traits in interspecific recombinant inbred lines of tef

Forty recombinant inbred lines (RILs) of interspecific cross of Eragrostis tef x E. pilosa were evaluated to study variability and interrelationships among agronomic traits using randomized complete block design. The RILs were evaluated for 17 traits. The result showed panicle length, rind penetrometer resistance of the first and the second basal internodes, 100-kernel weight, kernel weight per panicle, plant height and grain yield per plant had high estimates of genetic coefficient of variation, broad sense heritability and genetic advance. Thus, improvement of these traits could be attained through direct selection without the masking effect of the environment. The correlation study showed positive and significant (p&lt;0.01) phenotypic and genotypic associations of grain yield per plant with days to heading and maturity, panicle length, 100-kernel weight, kernel weight per panicle, biomass yield per plant and harvest index. Genotypic path coefficient analysis revealed that panicle length, biomass yield per plant, crushing strength of the second basal internode, harvest index, days to heading and kernel weight per panicle exerted appreciable positive direct effect on grain yield per plant. These traits could, therefore, be considered as indirect selection criteria while selecting lines in order to improve grain yield of the interspecific population.

Nuclear factor NF-κB1 functional promoter polymorphism and its expression conferring the risk of Type 2 diabetes-associated dyslipidemia.

Type 2 diabetes mellitus (T2DM) accompanied by hyperlipidemia confers higher risk for diabetes as well as cardiovascular diseases. NF-κB is actively involved in generating low-grade inflammation and oxidative stress triggering the development of diabetic complications. In this study, we have attempted to investigate the association between NF-κB1 functional promoter polymorphism-94 ATTG insertion/deletion (rs28362491) with inflammatory markers in developing diabetes-linked dyslipidemia. We performed a case-control study in a total of 401 individuals belonging to three categories such as Type 2 diabetes with dyslipidemia, Type 2 diabetes without dyslipidemia, and normal healthy controls. Experiments were carried out using genotyping, real-time PCR, and western blot. Pearson's correlation, analysis of variance, and logistic regression were utilized for statistical analysis. As per genetic association conducted in this study the SNP rs28362491 showed significant allelic and genotypic associations (Allelic: OR = 1.374, CI 0.9797-1.927, p = 0.003, and Genotypic in dominant model: OR = 1.77, CI 1.04-2.99, p = 0.002) with the risk of diabetes and associated dyslipidemia. The -94 ATTG insertion/insertion (ins/ins) genotype was associated with significantly increased level of serum TNF-α (p = 0.002), serum IL-6 (p = 0.067) in diabetes-induced dyslipidemia. Multiple linear regression analysis identifies independent correlation of Total cholesterol, HDL, LDL, TNF-α, and rs28362491 ATTG ins/ins with triglyceride in diabetic dyslipidemic condition. T2DM with dyslipidemia having ins/ins genotype showed significant increased expression of pro-inflammatory cytokines such as TNF-α, IL-6, and activation of NF-κB. Our study reports that individuals with ATTG insertion allele and ATTG ins/ins genotype at NF-κB1 promoter regulatory gene predicts the risk and severity of T2DM-linked dyslipidemia.

Condyle modeling stability, craniofacial asymmetry and ACTN3 genotypes: Contribution to TMD prevalence in a cohort of dentofacial deformities.

Craniofacial asymmetry, mandibular condylar modeling and temporomandibular joint disorders are common comorbidities of skeletally disproportionate malocclusions, but etiology of occurrence together is poorly understood. We compared asymmetry, condyle modeling stability and temporomandibular health in a cohort of 128 patients having orthodontics and orthognathic surgery to correct dentofacial deformity malocclusions. We also compared ACTN3 and ENPP1 genotypes for association to clinical conditions. Pre-surgical posterior-anterior cephalometric and panometric radiographic analyses; jaw pain and function questionnaire and clinical examination of TMD; and SNP-genotype analysis from saliva samples were compared to assess interrelationships. Almost half had asymmetries in need of surgical correction, which could be subdivided into four distinct morphological patterns. Asymmetric condyle modeling between sides was significantly greater in craniofacial asymmetry, but most commonly had an unanticipated pattern. Often, longer or larger condyles occurred on the shorter mandibular ramus side. Subjects with longer ramus but dimensionally smaller condyles were more likely to have self-reported TMD symptoms (p = 0.023) and significantly greater clinical diagnosis of TMD (p = 0 .000001), with masticatory myalgia most prominent. Genotyping found two significant genotype associations for ACTN3 rs1671064 (Q523R missense) p = 0.02; rs678397 (intronic SNP) p = 0.04 and one significant allele association rs1815739 (R577X nonsense) p = 0.00. Skeletal asymmetry, unusual condyle modeling and TMD are common and interrelated components of many dentofacial deformities. Imbalanced musculoskeletal functional adaptations and genetic or epigenetic influences contribute to the etiology, and require further investigation.

Impact of single nucleotide polymorphisms in the OGG1 and XRCC1 genes on modulation of DNA damage in pesticide-exposed agricultural workers in Punjab, North-West India

Pesticide-induced DNA damage is primarily repaired by base excision repair (BER) pathway. However, polymorphism in DNA repair genes may modulate individual’s DNA repair capacity (DRC) leading to increased genotoxicity and adverse health effects. Our first study in North-West Indian population aimed to evaluate the impact of OGG1 rs1052133 (Ser326Cys; C1245G), XRCC1 rs1799782 (Arg194Trp; C26304T) and XRCC1 rs25487 (Arg399Gln; G28152A) polymorphisms on the modulation of pesticide-induced DNA damage in a total of 450 subjects (225 pesticide-exposed agricultural workers and 225 age- and sex-matched controls). DNA damage was estimated by alkaline comet assay using silver-staining method. Genotyping was carried out by PCR-RFLP using site-specific restriction enzymes. Mann-Whitney U-test revealed elevation in DNA damage parameters (p < 0.01) in pesticide-exposed agricultural workers than controls. Chi-square test showed significant (p < 0.05) differences in the XRCC1 Arg194Trp (C26304T) and Arg399Gln (G28152A) genotypes among two groups. Multivariate logistic-regression analysis revealed that heterozygous genotypes of OGG1 rs1052133 (326Ser/Cys; 1245CA), XRCC1 rs1799782 (194Arg/Trp; 26304CT) and XRCC1 rs25487 (399Arg/Gln; 2815GA) were positively associated (p < 0.05) with elevated DNA damage parameters in pesticide-exposed agricultural workers. Our results strongly indicate significant positive association of variant OGG1 and XRCC1 genotypes with reduced DRC and higher pesticide-induced DNA damage in North-West Indian agricultural workers.

Association of Single-Nucleotide Polymorphism (rs833061) of Vascular Endothelial Growth Factor with Breast Cancer Risk

Background: Breast cancer is the most common cancer among women and one of the most important causes of death among them. Angiogenesis is an important step for primary tumor growth, invasiveness, and metastases. Vascular endothelial growth factor (VEGF) is involved in angiogenesis associated with tumors. Objective: To investigate the association of single nucleotide polymorphisms (SNPs) of VEGF gene located in the promoter region at position 460T/C (rs833061) with the risk of breast cancer. Patients and Methods: This study was conducted on (40) Egyptian female patients who were diagnosed as breast cancer according to histopathological examination of breast biopsy (Group 1, Patients), in addition to (40) age-matched apparently healthy females serving as controls (Group II, Controls). Detection of SNP of VEGF gene located in the promoter region 460T/C (rs833061) was done by real-time polymerase chain reaction technique. Results: There was no significant difference in frequency of the (C/C, T/C and T/T) genotypes of VEGF 460T/C (rs833061) in group I compared with group II (p>0.05). None of the studied VEGF genotypes had shown significant difference in distribution related to clinico-pathological parameters as tumor size, histological grade, hormone receptors, HER2/new status, regional lymph node and distant metastasis (p>0.05). Conclusion: This study revealed that there was no significant association of the (C/C, T/C and T/T) genotypes of VEGF 460T/C (rs833061) and breast cancer risk. Moreover, VEGF polymorphism 460T/C (rs833061) was not associated with breast cancer patients’ clinico-pathological characteristics and tumor markers levels.

Genetic Polymorphisms in Transforming Growth Factor-β, Interferon-γ and Interleukin-6 Genes and Susceptibility to Behcet's Disease in Saudi Population.

BackgroundBehcet’s disease (BD) is a complex, inflammatory, immune-mediated multi-systemic disease of unknown etiology. Cytokines play major roles in the pathophysiology of BD, and its production may be affected by polymorphism in cytokine genes. Hence, the present study was planned to investigate any possible association between the polymorphism in TGF-β, IFN-γ, and IL-6 genes and BD in the Saudi population.Materials and MethodsThe present study includes 79 BD cases and 117 age-matched controls. Polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation systems (ARMS) PCR methods were used for polymorphic analysis.ResultsThe heterozygous (CT) and (CT+TT) combined genotypes of TGF-β (509-C/T), heterozygous (AT), variant (TT), and (AT+TT) combined genotypes of IFN-γ (874-A/T) were significantly (P<0.05) associated with BD in the Saudi population. No significant differences were observed for IL-6 (174-G/C) genotypes and alleles between BD cases and controls. Gender does not reflect any significant genotypic and allelic association with males and females.ConclusionCT genotype of TGF-β, and AT and TT genotypes of IFN-γ could be associative genetic risk factors for BD in Saudis. Regulatory region polymorphism in cytokines gene can increase inflammation and deregulated immune response, which could be risk factor for BD.

Targeted genotype analyses of GWAS-derived lean body mass and handgrip strength-associated single-nucleotide polymorphisms in elite master athletes.

Recent large genome-wide association studies (GWAS) have independently identified a set of genetic loci associated with lean body mass (LBM) and handgrip strength (HGS). Evaluation of these candidate single-nucleotide polymorphisms (SNPs) may be useful to investigate genetic traits of populations at higher or lower risk of muscle dysfunction. As such, we investigated associations between six SNPs linked to LBM or HGS in a population of elite master athletes (MA) and age-matched controls as a representative population of older individuals with variable maintenance of muscle mass and function. Genomic DNA was isolated from buffy coat samples of 96 individuals [consisting of 48 MA (71 ± 6 yr, age-graded performance 83 ± 9%) and 48 older controls (75 ± 6 yr)]. SNP validation and sample genotyping were conducted using the tetra-primer amplification refractory mutation system (ARMS). For the three SNPs analyzed that were previously associated with LBM (FTO, IRS1, and ADAMTSL3), multinomial logistic regression revealed a significant association of the ADAMTSL3 genotype with %LBM (P < 0.01). For the three HGS-linked SNPs, neither GBF1 nor GLIS1 showed any association with HGS, but for TGFA, multinomial logistic regression revealed a significant association of genotype with HGS (P < 0.05). For ADAMTSL3, there was an enrichment of the effect allele in the MA (P < 0.05, Fisher's exact test). Collectively, of the six SNPs analyzed, ADAMTSL3 and TGFA showed significant associations with LBM and HGS, respectively. The functional relevance of the ADAMTSL3 SNP in body composition and of TGFA in strength may highlight a genetic component of the elite MA phenotype.

Polymorphisms in XPC and XPD genes modulate DNA damage in pesticide-exposed agricultural workers of Punjab, North-West India.

The genetic susceptibility of individuals to the genotoxic effect of pesticides may be modulated by variations in genes involved in nucleotide excision repair (NER) pathway and therefore plays an important role in the evaluation of occupational risk. We aimed to evaluate the role of xeroderma pigmentosum complementation group C (XPC) Lys939Gln (A2920C, rs2228001), XPC Ala499Val (C2151T, rs2228000), xeroderma pigmentosum complementation group D (XPD) Asp312Asn (G23591A, rs1799793) and XPD Lys751Gln (A35931C, rs13181) in the modulation of DNA damage. A total of 450 subjects (225 pesticide-exposed agricultural workers and 225 age- and sex-matched controls) from Punjab, North-West India were recruited to study DNA damage by alkaline comet assay. Genotyping was carried out by PCR-RFLP using site-specific restriction enzymes. We found significant elevation in DNA damage parameters in pesticide-exposed agricultural workers as compared to the controls (p < 0.01). Association of comet tail length with XPC 939Gln/Gln (CC), XPD 312Asp/Asn (GA) and XPD 312Asn/Asn (AA) genotypes was observed. Frequency of cells showing DNA migration was significantly higher in exposed workers with variant XPC 939Gln/Gln (CC), XPD 312Asp/Asn (GA) and XPD 312Asn/Asn (AA) genotypes. Mean tail length was significantly increased in agricultural workers carrying XPD 312Asn/Asn (AA) genotype. Elevation in total comet DNA migration was also observed in exposed workers carrying variant XPC 939Lys/Gln (AC), XPC 939Gln/Gln (CC), XPC 499Val/Val (TT) and XPD 312Asn/Asn (AA) genotypes. Our results strongly indicate significant positive association of variant XPC and XPD genotypes with higher pesticide-induced DNA damage in North-West Indian agricultural workers.

Glutathione S-Transferase Theta 1 / Mu 1 Null Genotype and Risk of Development of Actinic Keratosis in Pakistani Population.

To assess the frequency and association of Glutathione S-Transferase Theta 1 and Glutathione S-Transferase Mu 1 null genotypes in development of actinic keratosis (AK) in a group of Pakistani population. Case-control analytical study. Department of Biochemistry, Islamic International Medical College, Rawalpindi in collaboration with Department of Dermatology, Railway Hospital and Rural Health Center, District Health Office, Rawalpindi from September 2018 to September 2019. Methodology: A total of 86 participants were included in this study with 27 biopsy proven cases of AK and 59 matched controls. Blood samples were collected after obtaining written informed consent; and DNA was extracted by Chelex™ method. Multiplex PCR (M-PCR) was done to find respective allelic frequencies of GSTM1 and GSTT1 genes in both cases and controls. Results: Mean age of participants in cases and controls was 62.93 ±10.29 years and was 61.42 ±9.96 years, respectively. There were 18 males (66.7%) and 9 females (33.3%); and 43 males (72.9%) and 16 females (27.1%) in cases and controls, respectively. There was a significant association of GSTT1 null genotype with AK (OR: 2.72, 95% CI: 1.05-7.05, p = 0.037). There was a positive correlation between GSTT1 null genotype and AK (r = 0.225, p = 0.037). GSTT1 null genotype has a significant association for AK development in the studied Pakistani population. Key Words: Actinic keratosis, Glutathione S-Transferase Mu 1, Glutathione S-Transferase Theta 1, Polymerase chain reaction, Squamous cell carcinoma.

Promoter Hypermethylation of Wnt/β-catenin Signaling Pathway Inhibitor WIF-1 Gene and its Association with MTHFR C677T Polymorphism in Patients with Colorectal Cancer.

ObjectivesColorectal cancer (CRC) is a common malignancy with a high rate of mortality. The dysregulation of genes involved in the Wnt/β-catenin signaling pathway is a common finding in cancers. Wnt-inhibitory factor-1 (WIF-1) suppresses the Wnt/β-catenin signaling pathway and its inactivation by genetics and epigenetic changes may cause cancer. We investigated the DNA methylation status of the WIF-1 gene in patients with CRC and its interaction with MTHFR C677T polymorphism, a known modifier of methylation reaction.MethodsWe investigated 50 cancerous tissues and the adjacent non-cancerous tissue. Genomic DNA was extracted using a commercial kit and was treated by sodium bisulfite. Methylation-specific PCR was used for methylation analysis, and restriction fragment length polymorphism PCR to analyze the C677T polymorphism of the MTHFR gene.ResultsThe frequency of WIF1 promoter DNA methylation was significantly higher in cancerous tissue than adjacent non-cancerous tissue (52.0% vs. 8.0%; p < 0.001). WIF1 promoter DNA methylation status showed a significant association only with tumor location (p = 0.009). Carriers of TT genotype and T allele of MTHFR C677T polymorphism had a significantly higher frequency of unmethylated WIF1 gene than methylated WIF-1 gene in cancerous tissue (p = 0.025 and p = 0.001, respectively).ConclusionsPromoter DNA hypermethylation of the WIF-1 gene is a significant risk factor for CRC development, which was significantly associated with tumor location only. The significant association of TT genotype and T allele of MTHFR C677T polymorphism with unmethylated WIF-1 gene suggests a protective role for this common polymorphism against methylation-induced development of CRC.