AIM To evaluate the association of 12 tag single nucleotide polymorphisms(tag SNPs) in three onco-long non-coding RNA(lnc RNA) genes(HOTTIP,CCAT2,MALAT1) with the risk and prognosis of hepatocellular cancer(HCC). METH...AIM To evaluate the association of 12 tag single nucleotide polymorphisms(tag SNPs) in three onco-long non-coding RNA(lnc RNA) genes(HOTTIP,CCAT2,MALAT1) with the risk and prognosis of hepatocellular cancer(HCC). METHODS Twelve tag SNPs covering the three onco-lnc RNAs were genotyped by the KASP method in a total of 1338 samples,including 521 HCC patients and frequencymatched 817 controls. The samples were obtained from an unrelated Chinese population at the First Hospital ofChina Medical University from 2012-2015. The expression quantitative trait loci(e QTL) analyses were conducted to explore further the potential function of the promising SNPs. RESULTS Three SNPs in HOTTIP,one promoter SNP in MALAT1,and one haplotype of HOTTIP were associated with HCC risk. The HOTTIP rs17501292,rs2067087,and rs17427960 SNPs were increased to 1.55-,1.20-,and 1.18-fold HCC risk under allelic models(P = 0.012,0.017 and 0.049,respectively). MALAT1 rs4102217 SNP was increased to a 1.32-fold HCC risk under dominant models(P = 0.028). In addition,the two-way interaction of HOTTIP rs17501292-MALAT1 rs619586 polymorphisms showed a decreased effect on HCC risk(P interaction = 0.028,OR = 0.30) and epistasis with each other. HOTTIP rs3807598 variant genotype showed significantly longer survival time in HBV negative subgroup(P = 0.049,HR = 0.12),and MALAT1 rs591291 showed significantly better prognosis in female and HBV negative subgroups(P = 0.022,HR = 0.37; P = 0.042,HR = 0.25,respectively). In the study,no significant effect was observed in e QTL analysis. CONCLUSION Specific lnc RNA(HOTTIP and MALAT1) SNPs have potential to be biomarkers for HCC risk and prognosis.展开更多
OBJECTIVE SNPs in lnc RNAs may alter the expression or secondary structure of lnc RNAs and then impact their functions.Whether lnc RNA SNPs affect the prognosis of acute myeloid leukemia(AML)remains unknown.To search ...OBJECTIVE SNPs in lnc RNAs may alter the expression or secondary structure of lnc RNAs and then impact their functions.Whether lnc RNA SNPs affect the prognosis of acute myeloid leukemia(AML)remains unknown.To search the association between lnc RNA SNPs and AML outcomes,thirty tag SNPs in GAS5,H19,MALAT1,WT1-as and SRA were genotyped in313 AML patients.METHODS Survival analysis was performed in both AML patients recruited presently and GEO samples.The expression of GAS5 and TP63 was analyzed by real-time quantitative PCR.Dual-luciferase reporter gene assay was used to confirm the interactions between GAS5 rs55829688 and TP63.RESULTS Survival analysis indicated that rs55829688(T>C),located in GAS5 promoter,was significantly associated with the prognosis of AML.The average overall survival(OS)for patients with the rs55829688 CC genotype was significantly shorter than those carrying the rs55829688 T allele(P=0.018).Patients with rs55829688 CC genotype showed higher GAS5 expression in PBMCs than carriers of rs55829688T allele(P=0.025).Rs55829688 CC homozygotes also harbored a longer platelets recovery than those with rs55829688 T allele(P=0.040).In vitro study showed that GAS5 promoter harboring the rs55829688 C al ele showed marginal y increased reporter gene activity(P=0.054),and the promoter activity was increased by TP63 in a dose-dependent manner(P=0.001).Moreover,GAS5 expression was associated with AML OS in the GEO GSE12417 dataset,and GAS5 higher expression predict shorter OS(P=0.011).CONCLUSION Rs55829688 polymorphism could increase GAS5 expression by interacting with TP63 and was associated with worse OS in Chinese AML patients.展开更多
目的探讨基于SNaPshot技术的精液特异性编码区单核苷酸多态性(coding region single nucleo⁃tide polymorphism,cSNP)遗传标记检测在精液(斑)溯源及混合体液(斑)鉴定中的可行性。方法制备16例精液斑和11例精液-静脉血混合斑样本,提取其...目的探讨基于SNaPshot技术的精液特异性编码区单核苷酸多态性(coding region single nucleo⁃tide polymorphism,cSNP)遗传标记检测在精液(斑)溯源及混合体液(斑)鉴定中的可行性。方法制备16例精液斑和11例精液-静脉血混合斑样本,提取其基因组DNA(genomic DNA,gDNA)和总RNA,并将总RNA逆转录为互补DNA(complementary DNA,cDNA)。在已验证的精液特异性mRNA编码基因上筛选cSNP遗传标记。基于SNaPshot技术构建cSNP复合检测体系并通过CE对样本进行基因分型。结果成功构建了包含5个精液特异性cSNP的复合检测体系。在16例精液样本中,除了位于TGM4基因上的cSNP在cDNA的检测结果中出现等位基因丢失外,其余cSNP的gDNA和cDNA分型结果高度一致。检测精液-静脉血混合斑时,检出的cSNP分型结果均与精液提供者的基因型一致,未受到静脉血提供者基因型的干扰。结论应用SNaPshot技术检测精液特异性cSNP的方法可以应用于法医学精液(斑)的基因分型,并为混合体液(斑)中精液来源个体的判定提供信息。展开更多
The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of c...The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.展开更多
The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs...The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping.We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip.These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis,cell cycles,signal transduction,oncogene,tumor suppressor genes and so on.All of the cSNPs can lead to amino acid substitutions except TP73(rs1801174).The PCR products amplified from 31 hepatocellular carcinoma(HCC)specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips.The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence,indicating that the cSNP chip had a high sensitivity.The statistic data of the SNP(MT,homozygous and HT,heterozygous)in the HCC patients with different phenotypes(HBV+/-,differentiation stage,family history positive or negative,tumor size)indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV.The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients.The numbers of MT and HT were not different between positived and negative family history groups and between tumor size>3 cm and≤3 cm groups.The study results provided useful information for understanding the molecular mechanisms of HCC development.展开更多
基金the Natural Science Foundation of Liaoning Province in China,No.20170541001
文摘AIM To evaluate the association of 12 tag single nucleotide polymorphisms(tag SNPs) in three onco-long non-coding RNA(lnc RNA) genes(HOTTIP,CCAT2,MALAT1) with the risk and prognosis of hepatocellular cancer(HCC). METHODS Twelve tag SNPs covering the three onco-lnc RNAs were genotyped by the KASP method in a total of 1338 samples,including 521 HCC patients and frequencymatched 817 controls. The samples were obtained from an unrelated Chinese population at the First Hospital ofChina Medical University from 2012-2015. The expression quantitative trait loci(e QTL) analyses were conducted to explore further the potential function of the promising SNPs. RESULTS Three SNPs in HOTTIP,one promoter SNP in MALAT1,and one haplotype of HOTTIP were associated with HCC risk. The HOTTIP rs17501292,rs2067087,and rs17427960 SNPs were increased to 1.55-,1.20-,and 1.18-fold HCC risk under allelic models(P = 0.012,0.017 and 0.049,respectively). MALAT1 rs4102217 SNP was increased to a 1.32-fold HCC risk under dominant models(P = 0.028). In addition,the two-way interaction of HOTTIP rs17501292-MALAT1 rs619586 polymorphisms showed a decreased effect on HCC risk(P interaction = 0.028,OR = 0.30) and epistasis with each other. HOTTIP rs3807598 variant genotype showed significantly longer survival time in HBV negative subgroup(P = 0.049,HR = 0.12),and MALAT1 rs591291 showed significantly better prognosis in female and HBV negative subgroups(P = 0.022,HR = 0.37; P = 0.042,HR = 0.25,respectively). In the study,no significant effect was observed in e QTL analysis. CONCLUSION Specific lnc RNA(HOTTIP and MALAT1) SNPs have potential to be biomarkers for HCC risk and prognosis.
基金The project supported by National Natural Science Foundation of China(81422052,81403017)Special Topic of the Major Subject of National Science and Technology(2012ZX09509-339107)+1 种基金Hunan Provincial Natural Science Foundation of China(13JJ1010)by Funds for Hunan Education Department Program(12K006)
文摘OBJECTIVE SNPs in lnc RNAs may alter the expression or secondary structure of lnc RNAs and then impact their functions.Whether lnc RNA SNPs affect the prognosis of acute myeloid leukemia(AML)remains unknown.To search the association between lnc RNA SNPs and AML outcomes,thirty tag SNPs in GAS5,H19,MALAT1,WT1-as and SRA were genotyped in313 AML patients.METHODS Survival analysis was performed in both AML patients recruited presently and GEO samples.The expression of GAS5 and TP63 was analyzed by real-time quantitative PCR.Dual-luciferase reporter gene assay was used to confirm the interactions between GAS5 rs55829688 and TP63.RESULTS Survival analysis indicated that rs55829688(T>C),located in GAS5 promoter,was significantly associated with the prognosis of AML.The average overall survival(OS)for patients with the rs55829688 CC genotype was significantly shorter than those carrying the rs55829688 T allele(P=0.018).Patients with rs55829688 CC genotype showed higher GAS5 expression in PBMCs than carriers of rs55829688T allele(P=0.025).Rs55829688 CC homozygotes also harbored a longer platelets recovery than those with rs55829688 T allele(P=0.040).In vitro study showed that GAS5 promoter harboring the rs55829688 C al ele showed marginal y increased reporter gene activity(P=0.054),and the promoter activity was increased by TP63 in a dose-dependent manner(P=0.001).Moreover,GAS5 expression was associated with AML OS in the GEO GSE12417 dataset,and GAS5 higher expression predict shorter OS(P=0.011).CONCLUSION Rs55829688 polymorphism could increase GAS5 expression by interacting with TP63 and was associated with worse OS in Chinese AML patients.
文摘目的探讨基于SNaPshot技术的精液特异性编码区单核苷酸多态性(coding region single nucleo⁃tide polymorphism,cSNP)遗传标记检测在精液(斑)溯源及混合体液(斑)鉴定中的可行性。方法制备16例精液斑和11例精液-静脉血混合斑样本,提取其基因组DNA(genomic DNA,gDNA)和总RNA,并将总RNA逆转录为互补DNA(complementary DNA,cDNA)。在已验证的精液特异性mRNA编码基因上筛选cSNP遗传标记。基于SNaPshot技术构建cSNP复合检测体系并通过CE对样本进行基因分型。结果成功构建了包含5个精液特异性cSNP的复合检测体系。在16例精液样本中,除了位于TGM4基因上的cSNP在cDNA的检测结果中出现等位基因丢失外,其余cSNP的gDNA和cDNA分型结果高度一致。检测精液-静脉血混合斑时,检出的cSNP分型结果均与精液提供者的基因型一致,未受到静脉血提供者基因型的干扰。结论应用SNaPshot技术检测精液特异性cSNP的方法可以应用于法医学精液(斑)的基因分型,并为混合体液(斑)中精液来源个体的判定提供信息。
文摘The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.
文摘The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping.We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip.These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis,cell cycles,signal transduction,oncogene,tumor suppressor genes and so on.All of the cSNPs can lead to amino acid substitutions except TP73(rs1801174).The PCR products amplified from 31 hepatocellular carcinoma(HCC)specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips.The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence,indicating that the cSNP chip had a high sensitivity.The statistic data of the SNP(MT,homozygous and HT,heterozygous)in the HCC patients with different phenotypes(HBV+/-,differentiation stage,family history positive or negative,tumor size)indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV.The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients.The numbers of MT and HT were not different between positived and negative family history groups and between tumor size>3 cm and≤3 cm groups.The study results provided useful information for understanding the molecular mechanisms of HCC development.
