Single nucleotide polymorphism within chromosome 8q24 is associated with prostate cancer development in Saudi Arabia

Objective: Genome-wide association studies have demonstrated that single nucleotide polymorphisms (SNPs) are important risk factors for the development of prostate cancer (PCa). Preliminary studies have suggested that the incidence of PCa in Saudi males is low but is probably familial or genetically related.Methods: To identify any possible association of SNP with PCa development in Saudi patients, we investigated a group of SNPs in Saudi PCa patients (n=85) and compared the outcomes to healthy normal controls (n=115) and nodular hyperplasia patients (n=120). DNA was extracted from paraffin-embedded formalin fixed tissue or whole blood from both patients’ groups and healthy control group. A total of thirteen SNPs were genotyped using TaqMan® minor groove binder polymerase chain reaction assay.Results: The rs16901979A, s629242T and rs1447295A alleles were found at significantly higher frequency in PCa patients than controls (p< 0.05). The rs16901979 CA genotype was found at significantly greater frequency in PCa patients than in healthy controls (43% vs. 14%, odds ratio=4.6, p=0.0001) and benign hyperplasia group (43% vs. 25%, odds ratio=2.2, p=0.009).Conclusion: Our study has highlighted the association of rs16901979 SNP with PCa in Saudi males. Such findings have important implications in the PCa diagnosis and in screening unaffected family members of Saudi patients.

No association between cyclooxygenase-2 and uridine diphosphate glucuronosyltransferase 1A6 genetic polymorphisms and colon cancer risk

AIM：To investigate the association of variations in the cyclooxygenase-2 （COX2） and uridine diphosphate glucuronosyltransferase 1A6 （UGTIA6） genes and non-steroidal anti-inflammatory drugs （NSAIDs） use with risk of colon cancer.METHODS： NSAIDs, which are known to reduce the risk of colon cancer, act directly on COX2 and reduce its activity. Epidemiological studies have associated variations in the COX2 gene with colon cancer risk, but others were unable to replicate this finding. Similarly,enzymes in the UGT1A6 gene have been demonstrated to modify the therapeutic effect of NSAIDs on colon adenomas. Polymorphisms in the UGTIA6 gene have been statistically shown to interact with NSAID intake to influence risk of developing colon adenomas, but not colon cancer. Here we examined the association of tagging single nucleotide polymorphisms （SNPs） in the COX2 and UGTIA6 genes, and their interaction with NSAID consumption, on risk of colon cancer in a population of 422 colon cancer cases and 481 population controls.RESULTS： No SNP in either gene was individually statistically significantly associated with colon cancer, nor did they statistically significantly change the protective effect of NSAID consumption in our sample. Like others, we were unable to replicate the association of variants in the COX2 gene with colon cancer risk （P 〉 0.05）,and we did not observe that these variants modify the protective effect of NSAIDs （P 〉 0.05）. We were able to confirm the lack of association of variants in UGT1A6 with colon cancer risk, although further studies will have to be conducted to confirm the association of these variants with colon adenomas.CONCLUSION： Our study does not support a role of COX2 and UGTIA6 genetic variations in the development of colon cancer.

Impact of IL28B and OAS gene family polymorphisms on interferon treatment response in Caucasian children chronically infected with hepatitis B virus

AIM To investigate the impact of IL28 B and OAS gene polymorphisms on interferon treatment responses in children with chronic hepatitis B.METHODS We enrolled 52 children(between the ages of 4 and 18) with hepatitis B e antigen-negative chronic hepatitis B(CHB), who were treated with pegylated interferon alfa for 48 wk. Single nucleotide polymorphisms in the OAS1(rs1131476), OAS2(rs1293747),OAS3(rs2072136), OASL(rs10849829) and IL28B(rs12979860, rs12980275 and rs8099917) genes were studied to examine their associations with responses to IFN treatment in paediatric patients. We adopted two criteria for the therapeutic response, achieving an hepatitis B virus(HBV) DNA level < 2000 IU/m L and normalization of ALT activity(< 40 IU/L). To perform the analyses, we compared the patients in terms of achieving a partial response(PR) and a complete response(CR) upon measurement at the 24-wk posttreatment follow-up. RESULTS The PR and CR rates were 80.8% and 42.3%, respectively. Factors such as age, gender and liver histology had no impact on the type of response(partial or complete). A statistically significant relationship between higher baseline HBV DNA and ALT activity levels and lower rates of PR and CR was shown(P < 0.05). The allele association analysis revealed that only the IL-28 B rs12979860(C vs T) and IL28 B rs12980275(A vs G) markers significantly affected the achievement of PR(P = 0.021, OR = 3.3, 95%CI: 1.2-9.2 and P = 0.014, OR = 3.7, 95%CI: 1.3-10.1, respectively). However, in the genotype analysis, only IL-28 B rs12980275 was significantly associated with PR(AA vs AG-GG, P = 0.014, OR = 10.9, 95%CI: 1.3-93.9). The association analysis for CR showed that the TT genotype of IL28 B rs12979860 was present only in the no-CR group(P = 0.033) and the AA genotype of OASL rs10849829 was significantly more frequent in the noCR group(P = 0.044, OR = 0.26, 95%CI: 0.07-0.88). The haplotype analysis revealed significant associations between PR and CR and OAS haplotype(P = 0.0002 and P = 0.001, respectively), but no association with IL28 B haplotype was observed.CONCLUSION IL28 B and OAS polymorphisms are associated with different clinical outcomes in CHB children treated with interferon.

Single nucleotide polymorphism in the tumor necrosis factor-alpha gene affects inflammatory bowel diseases risk

AIM: To investigate the role that single nucleotide polymorphisms (SNPs) in the promoter of the tumour necrosis factor-alpha (TNF-α) gene play in the risk of inflammatory bowel diseases (IBDs) in a New Zealand population, in the context of international studies. METHODS: DNA samples from 388 patients with Crohn's disease (CD), 405 ulcerative colitis (UC), 27 indeterminate colitis (IC) and 201 randomly selected controls, from Canterbury, New Zealand were screened for 3 common polymorphisms in the TNF-α receptor: -238 G→A, -308 G→A and -857C→T, using a TaqmanR assay. A meta-analysis was performed on the data obtained on these polymorphisms combined with that from other published studies. RESULTS: Individuals carrying the -308 G/A allele had a significantly (OR = 1.91, χ2 = 17.36, P < 0.0001) increased risk of pancolitis, and a 1.57-fold increased risk (OR = 1.57, χ2 = 4.34, P = 0.037) of requiring a bowel resection in UC. Carrying the -857 C/T variant decreased the risk of ileocolonic CD (OR = 0.56, χ2 =4.32, P = 0.037), and the need for a bowel resection (OR = 0.59, χ2 = 4.85, P = 0.028). The risk of UC was reduced in individuals who were smokers at diagnosis, (OR = 0.48, χ2 = 4.86, P = 0.028). CONCLUSION: TNF-α is a key cytokine known to play a role in inflammatory response, and the locus for the gene is found in the IBD3 region on chromosome 6p21, known to be associated with an increased risk for IBD. The -308 G/A SNP in the TNF-α promoter is functional, and may account in part for the increased UC risk associated with the IBD3 genomic region. The -857 C/T SNP may decrease IBD risk in certain groups. Pharmaco- or nutrigenomic approaches may be desir- able for individuals with such affected genotypes.

TRAF6 polymorphisms not associated with the susceptibility to and severity of sepsis ina Chinese population

BACKGROUND： The tumor necrosis factor recepter associated factor （TRAF） 6 is an important intracellular adapter protein that plays a pivotal role in activating multiple inflammatory and immune related processes induced by cytokines. TRAF6 represents a strong candidate susceptibility factor for sepsis. We investigated whether polymorphisms at the TRAF6 gene are associated with the susceptibility to and severity of sepsis.METHODS： A hospital-based case-control study was conducted with 255 patients with sepsis and 260 controls who were recruited from Zhengzhou, China. Haplotype tagging single nucleotide polymorphisms （htSNPs） were selected from the HapMap database and genotyped using the SNPstream genotyping platform. The associations with the susceptibility and disease severity of sepsis were estimated by logistic regression, and adjusted for age, sex, smoking, drinking, chronic diseases status, APACHEII score and critical illness status.RESULTS： A total of 13 TRAF6 SNPs were tagged by 7 htSNPs. Five htSNPs （rs5030490, rs5030411, rs5030416, rs5030445 and rs3740961） were genotyped in the case control study. Genotype frequencies of the htSNPs were conformed to the Hardy-Weinberg equilibrium in both patients and controls. No significant association was found between the 5 htSNPs and the susceptibility to and severity of sepsis. Compared with the main haplotype -11120A/-10688T/-9423A/805G/12967G, no certain haplotype was associated with the signi？ cantly susceptibility to or severity of sepsis.CONCLUSION： TRAF6 gene polymorphisms might not play a major role in mediating the susceptibility to and severity of sepsis in the Chinese population. A larger population-based case-control study is warranted.

Multidrug resistance protein 3 R652G may reduce susceptibility to idiopathic infant cholestasis

AIM:To evaluate the role of genetic factors in the pathogenesis of idiopathic infant cholestasis.METHODS:We performed a case-control study,in-cluding 78 infants with idiopathic infant cholestasis and 113 healthy infants as controls.Genomic DNA was extracted from peripheral venous blood leukocytes us-ing phenol chloroform methodology.Polymerase chain reaction was used to amplify the multidrug resistance protein 3(MDR3)R652G fragment,and products were sequenced using the ABI 3100 Sequencer.RESULTS:The R652G single nucleotide polymorphism(SNP)was significantly more frequent in healthy infants(allele frequency 8.0%)than in patients(allele frequency 2.60%)(P < 0.05),odds ratio,0.29;95% confidence interval,0.12-0.84.The conjugated bilirubin in patients with the AG genotype was significantly lower than in those with the AA genotype(44.70 ± 6.15 μmol/L vs 95.52 ± 5.93 μmol/L,P < 0.05).CONCLUSION:MDR3 R652G is negatively correlated with idiopathic infant cholestasis.Children with the R652G SNP in Guangxi of China may have reduced susceptibility to infant intrahepatic cholestasis.

Genetic Diversity and Drug Susceptibility of Mycobacterium tuberculosis Isolates in a Remote Mountain Area of China

Objective We determined the genetic diversity of Mycobacterium tuberculosis（MTB） in a remote mountainous area of southwest China and evaluated the resolving ability of single nucleotide polymorphism（SNP） genotyping combined with variable number tandem repeat（VNTR） genotyping for Beijing family strains in association with drug resistance status.Methods Three hundred thirty-one MTB strains were isolated from patients living in mountainous regions of southwest China,and 8-loci SNP,VNTR-15 genotyping assays,and drug susceptibility testing of 9 drugs were performed.Results A total of 183 [55.29%（183/331）] strains were classified into the Beijing family.Of the 183 strains,111（60.66%） were defined as modern Beijing strains.The most predominant modern Beijing sub-lineage and ancient Beijing sub-lineage were Bmyc10 [39.34%（72/183）] and Bmyc25 [20.77%（38/183）],respectively.Of the isolates,19.64%（65/331） were resistant to at least 1 of the 9 anti-TB drugs and 17 [4.98%（17/331）] MTB isolates were multi-drug resistant tuberculosis（MDR-TB）.Two hundred sixty-one isolates showed a clustering rate of 14.18%（37/261） and a discriminatory index of 0.9990.The Beijing lineage exhibited a significantly higher prevalence of MDR-TB,as well as resistance to isoniazid（INH）,rifampin（RIF）,and para-aminosalicylic acid（PAS） when analyzed independently（P = 0.005,P = 0.017,P = 0.014,and P = 0.006 respectively）.The Beijing lineage was not associated with genetic clustering or resistance to any drug.In addition,genetic clustering was not associated with drug resistance.Conclusion MTB strains demonstrate high genetic diversity in remote mountainous areas of southwest China.Beijing strains,especially modern Beijing strains,are predominant in remote mountainous area of China.The combination of 8-loci SNPs and VNTR-15 genotyping is a useful tool to study the molecular epidemiology of MTB strains in this area.

Impact of metabolism-related mutations on the heart rate of gastric cancer patients after peritoneal lavage

BACKGROUND During surgery for gastric cancer,peritoneal lavage using warm distilled water can cause temporary hemodynamic changes.AIM To examine the associations between changes in heart rate and single nucleotide polymorphisms(SNPs).METHODS This was a prospective observational study of patients with gastric cancer who underwent gastrectomy and peritoneal hypotonic lavage at the Third Afliated Hospital of Soochow University from March 2018 to March 2019.Related SNPs were selected,and the verified exons were analyzed.Heart rate and blood pressure(BP)were measured before and after lavage.The patients were grouped as heart rate change≥30%vs<30%.Comparison and regression analyses of the selected SNPs were performed between the two groups.RESULTS According to the inclusion/exclusion criteria,194 patients were included in the analysis.Of these patients,138 were male,with a mean age of 65.9±0.8 years,and 56 were female,with a mean age of 65.0±1.3 years.Heart rate dropped by 0%-10%in 65 participants,by 10%-15%in 29,by 15%-20%in 23,by 20%-50%in 39,by 50%-100%in four,six had a cardiac arrest,and 28 had an increase in heart rate.Considering the possible impact of exonic SNPs on the phenotypes,TEP1(rs938886),TEP1(rs1713449),and RECQL5(rs820196)were analyzed.The haplotype analysis suggested that the haplotypes CTT[odds ratio(OR)=2.018,95%confidence interval(CI):1.012-4.025,P=0.0430]and GCC(OR=2.293,95%CI:1.174-4.477,P=0.0131)of TEP1(rs938886),TEP1(rs1713449),and RECQL5(rs820196)increased the risk of a drop in heart rate>30%.CONCLUSION The TEP1(rs938886),TEP1(rs1713449),and RECQL5(rs820196)SNPs were associated with changes in heart rate≥30%during intraperitoneal lavage using distilled water after gastrectomy for gastric cancer.

Genes Related to Oxytocin and Arginine-Vasopressin Pathways:Associations with Autism Spectrum Disorders

Autism spectrum disorder（ASD） is a highly heritable neurodevelopmental disorders characterized by impaired social interactions, communication de？cits, and repetitive behavior. Although the mechanisms underlying its etiology and manifestations are poorly understood,several lines of evidence from rodent and human studies suggest involvement of the evolutionarily highly-conserved oxytocin（OXT） and arginine-vasopressin（AVP）, as these neuropeptides modulate various aspects of mammalian social behavior. As far as we know, there is no comprehensive review of the roles of the OXT and AVP systems in the development of ASD from the genetic aspect. In this review, we summarize the current knowledge regarding associations between ASD and single-nucleotide variants of the human OXT-AVP pathway genes OXT, AVP, AVP receptor 1a（AVPR1a）, OXT receptor（OXTR）, theoxytocinase/vasopressinase（LNPEP）, and ADP-ribosyl cyclase（CD38）.

Super-assembly of integrated gold magnetic assay with loopmediated isothermal amplification for point-of-care testing

With the increasing global threat of various diseases and infections,it is essential to develop a fast,low-cost,and easy-to-use point-of-care testing(POCT)system for inspections at all levels of medical institutions and self-examination at home.In this work,gold magnetic nanoparticles(GMNPs)are used as the key material,and a rapid visual detection method is designed through integrating loop-mediated isothermal amplification(LAMP)and lateral flow assay(LFA)biosensor for detecting a variety of analytes which includes whole blood,buccal swabs,and DNA.It is worth to note that the proposed method does not need DNA extraction.Furthermore,uracil DNA glycosylase(UDG)is employed to eliminate carrier contamination for preventing false positive results.The whole detection process can be finished within 25 min.The accuracy of detection is measured by assessing the polymorphisms of the methylenetetrahydrofolate reductase(MTHFR)C677T.The detection limit of the newly developed extraction-free detection system for MTHFR C677T is 0.16 ng/μL.A preliminary clinical study of the proposed method is carried out by analyzing 600 clinical samples(including 200 whole blood samples,100 buccal swabs,and 300 genomic DNA samples).The results indicate that the proposed method is 100%consistent with the sequencing results which provides a new choice for POCT and shows a broad application prospect in all levels of medical clinics and at home.