目的探讨维生素D受体(VDR)基因Fox I、Bsm I、Apa I和Tap I位点多态性与梅毒易感性之间是否存在关联。方法应用质谱分析的方法检测106例梅毒患者及134名健康对照者VDR基因Fox I、Bsm I、Apa I和Tap I位点基因型及等位基因分布频率。结...目的探讨维生素D受体(VDR)基因Fox I、Bsm I、Apa I和Tap I位点多态性与梅毒易感性之间是否存在关联。方法应用质谱分析的方法检测106例梅毒患者及134名健康对照者VDR基因Fox I、Bsm I、Apa I和Tap I位点基因型及等位基因分布频率。结果病例组和对照组间VDR基因Fox I、Bsm I、Apa I和Tap I 4个基因位点基因型分布无明显差异(Fox I:P=0.922;Bsm I:P=0.460;Apa I:P=0.287;Tap I:P=0.093);两组间等位基因分布也均无统计学差异(Fox I C vs.T:P=0.742;Bsm I C vs.T:P=0.345;Apa I G vs.T:P=0.113;Tap I A vs.G:P=0.345);两组间在隐性遗传模型和显性模型下比较也未发现有统计学差异(Fox I CC vs.CT+TT:P=0.687;Fox I TT vs.CT+CC:P=0.905;Bsm I CC vs.CT+TT:P=0.336;Apa I TT vs.GT+GG:P=0.438;Apa I GG vs.GT+TT:P=0.123;Tap I AA vs.AG+GG:P=0.204)。结论 VDR基因Fox I、Bsm I、Apa I和Tap I位点多态性与梅毒易感性之间无显著相关。展开更多
Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assist...Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.展开更多
The authors investigated the possible association of -4522C/T variation of adiponectin gene with coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Genotyping of SNP --4522C/T in 304 patients with C...The authors investigated the possible association of -4522C/T variation of adiponectin gene with coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Genotyping of SNP --4522C/T in 304 patients with CHD, 389 patients with T2DM, and 405 age and sex-matched healthy control subjects was carried out by means of PCR-RFLP approach. No significant difference in the genotype or allele frequencies was found, either between patients with CHD and control subjects, or between patients with T2DM and control subjects. However, in the subgroup analysis, an association of the TAr genotype and T allele with type 2 diabetes combined with obesity （BMI ≥ 25 kg/m2） was found （P = 0.014 and P = 0.034, respectively）. Also the homeostasis model assessment of insulin resistance （HOMA-IR） in T2DM patients with T/T genotype was significantly higher than that in T2DM patients carrying C allele （P = 0.0069）. The authors＇ findings for the first time demonstrated that SNP --4522 in the adiponectin gene was associated with T2DM that combined with obesity and higher insulin resistance index in patients with T2DM. This indicated that the variation might associate with an increased susceptibility to type 2 diabetic obesity and insulin resistance. But -4522C/T polymorphism did not contribute to the susceptibility of CHD.展开更多
Previous research on gene expression analysis and association tests have suggested that RELN is a risk gene for schizophrenia in world populations.Based on the reported down-regulation of RELN in schizophrenia patient...Previous research on gene expression analysis and association tests have suggested that RELN is a risk gene for schizophrenia in world populations.Based on the reported down-regulation of RELN in schizophrenia patients compared with normal subjects,we speculated that variants in the RELN promoter region may confer risk for schizophrenia.In this study,we investigated the associations of three SNPs in the promoter region of RELN with schizophrenia in a case-control sample from southwestern China（940 cases and 13 69 controls）.The results suggested that none of the SNPs showed significant associations in our sample,indicating the risk variants for schizophrenia in RELN may not be located in the promoter region.We also performed meta-analysis by combining our data with previously reported data on the Chinese population with a total sample size of 2 843 individuals,and the result remained nonsignificant.Collectively,our results suggested variants in the RELN promoter may not harbor risk SNPs associated with schizophrenia in the Chinese population.展开更多
Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q ...Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q tel with 3-cM. The purpose of this study was to narrow down the genetical distance on chromosomal 22q tel with MLC. Methods: Thirty-nine MLC patients in 33 families were collected,and the linkage analysis and haplotype analysis of twelve informative families were done, using seven microsatellite markers and four SNP markers. Results: The maximum tow-point LOD score for marker 355c18 was 6.65 at recombination fraction 0.02. The haplotype analysis narrowed down the critical region of MLC to 250 kb on chromosomal 22q tel. Conclusion: One of the causing genes of MLC was located on chromosomal 22q tel with 250 kb. Four candidate genes were considered. The heterogeneity of one informative family indicated possible existence of a second locus for MLC.展开更多
AIM:To study the (functional) relevance of single nucleotide polymorphisms (SNPs) in genes encoding matrix metalloproteinases (MMP)-1,-2,-3,-9,tissue inhibitors of metalloproteinases (TIMP)-1,-2 and tumor necrosis fac...AIM:To study the (functional) relevance of single nucleotide polymorphisms (SNPs) in genes encoding matrix metalloproteinases (MMP)-1,-2,-3,-9,tissue inhibitors of metalloproteinases (TIMP)-1,-2 and tumor necrosis factor (TNF)-α in the etiopathogenesis of inflammatory bowel diseases (IBD),that may enhance susceptibility and/or disease severity. METHODS:Genomic DNA from 134 Crohn's disease (CD),111 ulcerative colitis (UC) patients and 248 control subjects was isolated from resected intestinal tissue or blood. Allelic composition at SNP loci was determined by PCR-RFLP or tetra primer ARMS PCR. RESULTS:The TIMP-1 genotype TT in women and T in men at SNP +372 T/C was found to increase CD susceptibility (39% vs 23.8%,P=0.018 and 67.9% vs 51.6%,P=0.055,respectively),while women with this genotype were less prone to development of fistulae during follow-up (41.4% vs 68.3%,P=0.025). Male IBD or CD patients carrying the TIMP-1 +372 T-allele expressed lower levels of TIMP-1 in surgically resected macroscopically inflamed tissue (0.065 < P < 0.01). The 5T5T genotype at MMP-3 SNP -1613 5T/6T increased the chance of stenotic complications in CD during follow-up (91.2% vs 71.8%,P = 0.022) but seemed to protect against colonic involvement of this disease at first endoscopic/radiologic examination (35.3% vs 59.5%,P=0.017). CONCLUSION:Allelic composition at the examinedSNPs in genes coding for TIMP-1 and MMP-3 affect CD susceptibility and/or phenotype,i.e.,fistulizing disease,stricture pathogenesis and first disease localisation. These findings reinforce the important role of these proteins in IBD.展开更多
Genome-wide and candidate gene association studies have identified several variants that predispose indi- viduals to developing nonalcoholic fatty liver disease （NAFLD）. However, the gene that has been consis- tentl...Genome-wide and candidate gene association studies have identified several variants that predispose indi- viduals to developing nonalcoholic fatty liver disease （NAFLD）. However, the gene that has been consis- tently involved in the genetic susceptibility of NAFLD in humans is patatin-like phospholipase domain contain- ing 3 （PNPLA3, also known as adiponutrin）. A nonsyn- onymous single nucleotide polymorphism in PNPLA3 （rs738409 C/G, a coding variant that encodes an amino acid substitution I148M） is significantly associated with fatty liver and histological disease severity, not only in adults but also in children. Nevertheless, how PNPLA3 influences the biology of fatty liver disease is still an open question. A recent article describes new aspects about PNPLA3 gene/protein function and suggests that the I148M variant promotes hepatic lipid synthesis due to a gain of function. We revise here the published data about the role of the I148M variant in lipogen- esis/lipolysis, and suggest putative areas of future research. For instance we explored in silico whether the rs738409 C or G alleles have the ability to modify miRNA binding sites and miRNA gene regulation, and we found that prediction of PNPLA3 target miRNAs shows two miRNAs potentially interacting in the 3＇ UTR region （hsa-miR-769-3p and hsa-miR-516a-3p）. In addition, interesting unanswered questions remain to be explored. For example, PNPLA3 lies between two CCCTC-binding factor-bound sites that could be tested for insulator activity, and an intronic histone 3 lysine 4 trimethylation peak predicts an enhancer element, cor- roborated by the DNase I hypersensitivity site peak. Finally, an interaction between PNPLA3 and glycerol- 3-phosphate acyltransferase 2 is suggested by data miming.展开更多
Nonalcoholic fatty liver disease （NAFLD） is common worldwide. The importance of genetic and epigen- eric changes in etiology and pathogenesis of NAFLD has been increasingly recognized. However, the ex- act mechanism...Nonalcoholic fatty liver disease （NAFLD） is common worldwide. The importance of genetic and epigen- eric changes in etiology and pathogenesis of NAFLD has been increasingly recognized. However, the ex- act mechanism is largely unknown. A large number of single nucleotide polymorphisms （SNPs） related to NAFLD has been documented by candidate gene studies （CGSs）. Among these genes, peroxisome pro- liferatoractivated receptor-γ, adiponectin, leptin and tumor necrosis factor-α were frequently reported. Since the introduction of genome-wide association studies （GWASs）, there have been significant advances in our understanding of genomic variations of NAFLD. Patatin- like phospholipase domain containing family member A3 （PNPLA3, SNP rs738409, encoding I148M）, also termed adiponutrin, has caught most attention. The evidence that PNPLA3 is associated with increased hepatic fat levels and hepatic inflammation has been validated by a series of studies. Epigenetic modification refers to phenotypic changes caused by an adaptive mechanism unrelated to alteration of primary DNA se- quences. Epigenetic regulation mainly includes microR- NAs （miRs）, DNA methylation, histone modifications and ubiquitination, among which miRs are studied most extensively, miRs are small natural single stranded RNA molecules regulating mRNA degradation or translation inhibition, subsequently altering protein expression of target genes. The miR-122, a highly abundant miR ac- counting for nearly 70% of all miRs in the liver, is sig- nificantly under-expressed in NAFLD subjects. Inhibition of miR-122 with an antisense oligonucleotide results in decreased mRNA expression of lipogenJc genes and improvement of liver steatosis. The investigation into epigenetic involvement in NAFLD pathogenesis is just at the beginning and needs to be refined. This review summarizes the roles of genetics and epigenetics in the development of NAFLD. The progress made in this field may provide novel diagnostic biomarkers and therapeu- tic targets for NAFLD management.展开更多
文摘目的探讨维生素D受体(VDR)基因Fox I、Bsm I、Apa I和Tap I位点多态性与梅毒易感性之间是否存在关联。方法应用质谱分析的方法检测106例梅毒患者及134名健康对照者VDR基因Fox I、Bsm I、Apa I和Tap I位点基因型及等位基因分布频率。结果病例组和对照组间VDR基因Fox I、Bsm I、Apa I和Tap I 4个基因位点基因型分布无明显差异(Fox I:P=0.922;Bsm I:P=0.460;Apa I:P=0.287;Tap I:P=0.093);两组间等位基因分布也均无统计学差异(Fox I C vs.T:P=0.742;Bsm I C vs.T:P=0.345;Apa I G vs.T:P=0.113;Tap I A vs.G:P=0.345);两组间在隐性遗传模型和显性模型下比较也未发现有统计学差异(Fox I CC vs.CT+TT:P=0.687;Fox I TT vs.CT+CC:P=0.905;Bsm I CC vs.CT+TT:P=0.336;Apa I TT vs.GT+GG:P=0.438;Apa I GG vs.GT+TT:P=0.123;Tap I AA vs.AG+GG:P=0.204)。结论 VDR基因Fox I、Bsm I、Apa I和Tap I位点多态性与梅毒易感性之间无显著相关。
文摘Objective The detection of RNA single nucleotide polymorphism(SNP)is of great importance due to their association with protein expression related to various diseases and drug responses.At present,splintR ligase-assisted methods are important approaches for RNA direct detection,but its specificity will be limited when the fidelity of ligases is not ideal.The aim of this study was to create a method to improve the specificity of splintR ligase for RNA detection.Methods In this study,a dualcompetitive-padlock-probe(DCPLP)assay without the need for additional enzymes or reactions is proposed to improve specificity of splintR ligase ligation.To verify the method,we employed dual competitive padlock probe-mediated rolling circle amplification(DCPLP-RCA)to genotype the CYP2C9 gene.Results The specificity was well improved through the competition and strand displacement of dual padlock probe,with an 83.26%reduction in nonspecific signal.By detecting synthetic RNA samples,the method demonstrated a dynamic detection range of 10 pmol/L-1 nmol/L.Furthermore,clinical samples were applied to the method to evaluate its performance,and the genotyping results were consistent with those obtained using the qPCR method.Conclusion This study has successfully established a highly specific direct RNA SNP detection method,and provided a novel avenue for accurate identification of various types of RNAs.
基金the Chinese High Tech Programs (863) from the Ministry of Science and Technology (No. 2002BA- 711A08)the National Natural Science Foundation of China (No. 30671155, and 39993420)+1 种基金Grant FMU-RT002 of Program for Innovative Research Team in Science and Technology in Fujian Province Universitythe Science Foundation from the Depart-ment of Education of Fujian Province (No. JA05251, and JB06215).
文摘The authors investigated the possible association of -4522C/T variation of adiponectin gene with coronary heart disease （CHD） and type 2 diabetes mellitus （T2DM）. Genotyping of SNP --4522C/T in 304 patients with CHD, 389 patients with T2DM, and 405 age and sex-matched healthy control subjects was carried out by means of PCR-RFLP approach. No significant difference in the genotype or allele frequencies was found, either between patients with CHD and control subjects, or between patients with T2DM and control subjects. However, in the subgroup analysis, an association of the TAr genotype and T allele with type 2 diabetes combined with obesity （BMI ≥ 25 kg/m2） was found （P = 0.014 and P = 0.034, respectively）. Also the homeostasis model assessment of insulin resistance （HOMA-IR） in T2DM patients with T/T genotype was significantly higher than that in T2DM patients carrying C allele （P = 0.0069）. The authors＇ findings for the first time demonstrated that SNP --4522 in the adiponectin gene was associated with T2DM that combined with obesity and higher insulin resistance index in patients with T2DM. This indicated that the variation might associate with an increased susceptibility to type 2 diabetic obesity and insulin resistance. But -4522C/T polymorphism did not contribute to the susceptibility of CHD.
文摘Previous research on gene expression analysis and association tests have suggested that RELN is a risk gene for schizophrenia in world populations.Based on the reported down-regulation of RELN in schizophrenia patients compared with normal subjects,we speculated that variants in the RELN promoter region may confer risk for schizophrenia.In this study,we investigated the associations of three SNPs in the promoter region of RELN with schizophrenia in a case-control sample from southwestern China（940 cases and 13 69 controls）.The results suggested that none of the SNPs showed significant associations in our sample,indicating the risk variants for schizophrenia in RELN may not be located in the promoter region.We also performed meta-analysis by combining our data with previously reported data on the Chinese population with a total sample size of 2 843 individuals,and the result remained nonsignificant.Collectively,our results suggested variants in the RELN promoter may not harbor risk SNPs associated with schizophrenia in the Chinese population.
文摘Objective: Vacuolating megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a recently described syndrome with autosomal recessive mode of inheritance. Its possible gene was located on chromosomal 22q tel with 3-cM. The purpose of this study was to narrow down the genetical distance on chromosomal 22q tel with MLC. Methods: Thirty-nine MLC patients in 33 families were collected,and the linkage analysis and haplotype analysis of twelve informative families were done, using seven microsatellite markers and four SNP markers. Results: The maximum tow-point LOD score for marker 355c18 was 6.65 at recombination fraction 0.02. The haplotype analysis narrowed down the critical region of MLC to 250 kb on chromosomal 22q tel. Conclusion: One of the causing genes of MLC was located on chromosomal 22q tel with 250 kb. Four candidate genes were considered. The heterogeneity of one informative family indicated possible existence of a second locus for MLC.
基金grant WS98-17 from the Netherlands Digestive Diseases Foundation
文摘AIM:To study the (functional) relevance of single nucleotide polymorphisms (SNPs) in genes encoding matrix metalloproteinases (MMP)-1,-2,-3,-9,tissue inhibitors of metalloproteinases (TIMP)-1,-2 and tumor necrosis factor (TNF)-α in the etiopathogenesis of inflammatory bowel diseases (IBD),that may enhance susceptibility and/or disease severity. METHODS:Genomic DNA from 134 Crohn's disease (CD),111 ulcerative colitis (UC) patients and 248 control subjects was isolated from resected intestinal tissue or blood. Allelic composition at SNP loci was determined by PCR-RFLP or tetra primer ARMS PCR. RESULTS:The TIMP-1 genotype TT in women and T in men at SNP +372 T/C was found to increase CD susceptibility (39% vs 23.8%,P=0.018 and 67.9% vs 51.6%,P=0.055,respectively),while women with this genotype were less prone to development of fistulae during follow-up (41.4% vs 68.3%,P=0.025). Male IBD or CD patients carrying the TIMP-1 +372 T-allele expressed lower levels of TIMP-1 in surgically resected macroscopically inflamed tissue (0.065 < P < 0.01). The 5T5T genotype at MMP-3 SNP -1613 5T/6T increased the chance of stenotic complications in CD during follow-up (91.2% vs 71.8%,P = 0.022) but seemed to protect against colonic involvement of this disease at first endoscopic/radiologic examination (35.3% vs 59.5%,P=0.017). CONCLUSION:Allelic composition at the examinedSNPs in genes coding for TIMP-1 and MMP-3 affect CD susceptibility and/or phenotype,i.e.,fistulizing disease,stricture pathogenesis and first disease localisation. These findings reinforce the important role of these proteins in IBD.
基金Supported by Grants PICT 2008-1521 and PICT 2010 0441,from National Agency for Science and TechnologyUBACYT CM04,from Universidad de Buenos AiresSookoian S and Pirola CJ belong to National Council of Scientific and Technical Research
文摘Genome-wide and candidate gene association studies have identified several variants that predispose indi- viduals to developing nonalcoholic fatty liver disease （NAFLD）. However, the gene that has been consis- tently involved in the genetic susceptibility of NAFLD in humans is patatin-like phospholipase domain contain- ing 3 （PNPLA3, also known as adiponutrin）. A nonsyn- onymous single nucleotide polymorphism in PNPLA3 （rs738409 C/G, a coding variant that encodes an amino acid substitution I148M） is significantly associated with fatty liver and histological disease severity, not only in adults but also in children. Nevertheless, how PNPLA3 influences the biology of fatty liver disease is still an open question. A recent article describes new aspects about PNPLA3 gene/protein function and suggests that the I148M variant promotes hepatic lipid synthesis due to a gain of function. We revise here the published data about the role of the I148M variant in lipogen- esis/lipolysis, and suggest putative areas of future research. For instance we explored in silico whether the rs738409 C or G alleles have the ability to modify miRNA binding sites and miRNA gene regulation, and we found that prediction of PNPLA3 target miRNAs shows two miRNAs potentially interacting in the 3＇ UTR region （hsa-miR-769-3p and hsa-miR-516a-3p）. In addition, interesting unanswered questions remain to be explored. For example, PNPLA3 lies between two CCCTC-binding factor-bound sites that could be tested for insulator activity, and an intronic histone 3 lysine 4 trimethylation peak predicts an enhancer element, cor- roborated by the DNase I hypersensitivity site peak. Finally, an interaction between PNPLA3 and glycerol- 3-phosphate acyltransferase 2 is suggested by data miming.
基金Supported by The Grants from Guangzhou Municipal Bureau of Health,China,No.2008-Zdi-01 and 2009-ZDi-03
文摘Nonalcoholic fatty liver disease （NAFLD） is common worldwide. The importance of genetic and epigen- eric changes in etiology and pathogenesis of NAFLD has been increasingly recognized. However, the ex- act mechanism is largely unknown. A large number of single nucleotide polymorphisms （SNPs） related to NAFLD has been documented by candidate gene studies （CGSs）. Among these genes, peroxisome pro- liferatoractivated receptor-γ, adiponectin, leptin and tumor necrosis factor-α were frequently reported. Since the introduction of genome-wide association studies （GWASs）, there have been significant advances in our understanding of genomic variations of NAFLD. Patatin- like phospholipase domain containing family member A3 （PNPLA3, SNP rs738409, encoding I148M）, also termed adiponutrin, has caught most attention. The evidence that PNPLA3 is associated with increased hepatic fat levels and hepatic inflammation has been validated by a series of studies. Epigenetic modification refers to phenotypic changes caused by an adaptive mechanism unrelated to alteration of primary DNA se- quences. Epigenetic regulation mainly includes microR- NAs （miRs）, DNA methylation, histone modifications and ubiquitination, among which miRs are studied most extensively, miRs are small natural single stranded RNA molecules regulating mRNA degradation or translation inhibition, subsequently altering protein expression of target genes. The miR-122, a highly abundant miR ac- counting for nearly 70% of all miRs in the liver, is sig- nificantly under-expressed in NAFLD subjects. Inhibition of miR-122 with an antisense oligonucleotide results in decreased mRNA expression of lipogenJc genes and improvement of liver steatosis. The investigation into epigenetic involvement in NAFLD pathogenesis is just at the beginning and needs to be refined. This review summarizes the roles of genetics and epigenetics in the development of NAFLD. The progress made in this field may provide novel diagnostic biomarkers and therapeu- tic targets for NAFLD management.
