scholarly journals Polymorphisms in lncRNA PTENP1 and the Risk of Gastric Cancer in a Chinese Population

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Yugang Ge ◽  
Yu He ◽  
Mingkun Jiang ◽  
Dakui Luo ◽  
Xiangkun Huan ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Chinese Population ◽  
Noncoding Rna ◽  
Additive Model ◽  
Nucleotide Polymorphisms ◽  
Bioinformatics Analyses ◽  
Phosphatase And Tensin Homolog ◽  
Normal Tissues ◽  
Tensin Homolog ◽  
Taqman Technology

Long noncoding RNA (lncRNA) phosphatase and tensin homolog pseudogene 1 (PTENP1) is significantly downregulated in gastric cancer (GC), playing critical roles in GC progression. However, the association between PTENP1 genetic variants and GC risk has not yet been reported. Using TaqMan technology, three lncRNA PTENP1 tag single nucleotide polymorphisms (tagSNPs) (rs7853346 C>G, rs865005 C>T, and rs10971638 G>A) were genotyped in 768 GC patients and 768 cancer-free controls in a Chinese population. We found that subjects with rs7853346 G allele had a remarkably decreased risk of GC, compared with those carrying C allele (P=0.011 in an additive model, P=0.033 after Bonferroni’s correction). The further stratified analyses showed that the link between variant genotypes of rs7853346 and decreased GC risk was more obvious in older subjects (≥60 years), nonsmokers, nondrinkers, and subjects without family history of GC. We also found that relative PTENP1 mRNA expression levels were higher in rs7853346 CG/GG genotype carriers than those with common genotype in both GC and normal tissues (P<0.05). Besides, bioinformatics analyses revealed that rs7853346 may change the local folding structure and alter the target microRNAs (miRNAs) of PTENP1. In conclusion, our results suggested that lncRNA PTENP1 polymorphism rs7853346 may predict GC susceptibility.

scholarly journals LINC00673 rs11655237 Polymorphism Is Associated With Increased Risk of Cervical Cancer in a Chinese Population

2018 ◽  
Vol 25 (1) ◽  
pp. 107327481880394 ◽  
Author(s):  
Yanhua Wang ◽  
Tianyou Luo
Keyword(s):  
Cervical Cancer ◽  
Chinese Population ◽  
Noncoding Rna ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Normal Tissues ◽  
Genome Wide ◽  
Increased Risk ◽  
Cancer Tissues

Cervical cancer is the fourth most commonly diagnosed cancer and the fourth leading cause of cancer deaths in women worldwide. Few single-nucleotide polymorphisms associated with risk of cervical cancer have been identified, yet genetic predisposition contributes significantly to this malignancy. Long noncoding RNA LINC00673 has been widely explored for its role in the development and prognosis of many tumors, and 2 genome-wide association studies identified that LINC00673 rs11655237 was associated with susceptibility to pancreatic cancer. In the current study, using a case–control study design, we found rs11655237 significantly increased susceptibility of cervical cancer in a Chinese population (odds ratio = 1.27; 95% confidence interval = 1.08-1.50; P = .005). Expression of LINC00673 was significantly higher in adjacent normal tissues than in paired cancer tissues ( P < .01) and significantly lower in the cancer or paired adjacent normal tissues of patients with cervical cancer having rs11655237 allele A than in those having rs11655237 allele G ( P < .001). Our results indicate that LINC00673 rs11655237 is associated with increased risk of cervical cancer, possibly by downregulating LINC00673 expression in cervical tissues.

scholarly journals Single Nucleotide Polymorphisms in HOTAIR Are Related to Breast Cancer Risk and Prognosis in the Northeastern Chinese Population

2021 ◽  
Vol 11 ◽  
Author(s):  
Zheng Lv ◽  
Changgui Kou ◽  
Naifei Chen ◽  
Lin Jia ◽  
Xu Sun ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Chinese Population ◽  
Noncoding Rna ◽  
Disease Free Survival ◽  
Population Based ◽  
Clinicopathological Characteristics ◽  
Nucleotide Polymorphisms ◽  
Binary Logistic Regression Model ◽  
Single Nucleotide

BackgroundThe long noncoding RNA HOX transcript antisense RNA (HOTAIR) is highly expressed in breast cancer (BC) tissues and is associated with the recurrence and metastasis of BC. Until now, the results of studies on associations between several functional single nucleotide polymorphisms(SNPs) (rs920778, rs1899663, and rs4759314) in HOTAIR with BC susceptibility carried out in different regions of China are still inconsistent. There is no study on correlation between HOTAIR SNPs and prognosis of Chinese population. Therefore, we investigated the relationship between HOTAIR SNPs and susceptibility to and prognosis of BC.MethodWe conducted a population-based case-control study involving 828 BC cases and 905 healthy controls. Peripheral blood DNA was used for genotyping. The association between HOTAIR genotypes and BC risk were estimated by odds ratios (ORs) computed using the binary logistic regression model. The relationships between HOTAIR SNPs and clinicopathological features were tested by Pearson’s chi-square test or Fisher’s exact test. Survival was analyzed using the Kaplan-Meier method.ResultsThe functional rs920778 genetic variant increased BC risk in the codominant model. Individuals with the rs920778 GG genotype had an OR of 2.426 (95% confidence interval [CI] = 1.491–3.947, P &lt; 0.001) for developing BC compared to individuals with the AA genotype. Individuals with the AG genotype had an OR of 1.296 (95% CI = 1.040–1.614, P = 0.021) for developing BC compared to individuals with the AA genotype. Individuals with the rs4759314 GA genotype had a lower BC risk than individuals with the rs4759314 AA/GG genotype (OR = 0.566, 95% CI = 0.398–0.803, P = 0.001). The rs1899663 genotype had no correlation with BC susceptibility. Haplotypes composed of rs920778–rs1899663 and rs920778–rs1899663–rs4759314 could increase BC risk (all P &lt; 0.001). There were no statistically significant associations between HOTAIR SNPs and clinicopathological characteristics. The rs920778 GG/AG genotypes were associated with worse disease-free survival (DFS) (p = 0.012), and the rs4759314 GA genotype was associated with worse DFS and overall survival (OS) (p = 0.011).ConclusionHOTAIR SNPs(rs920778 and rs4759314) are significantly related to BC susceptibility and prognosis in the northeastern Chinese population, indicating the significance in the occurrence and development of BC.

scholarly journals Polymorphisms in RAS/RAF/MEK/ERK Pathway Are Associated with Gastric Cancer

Genes ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 20 ◽  
Author(s):  
Patricio Gonzalez-Hormazabal ◽  
Maher Musleh ◽  
Marco Bustamante ◽  
Juan Stambuk ◽  
Raul Pisano ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Additive Model ◽  
P Value ◽  
Erk Pathway ◽  
Nucleotide Polymorphisms ◽  
Functional Effect ◽  
Cellular Functions ◽  
Single Nucleotide ◽  
Gastric Cancer Patients ◽  
Control Study

The RAS/RAF/MEK/ERK pathway regulates certain cellular functions, including cell proliferation, differentiation, survival, and apoptosis. Dysregulation of this pathway leads to the occurrence and progression of cancers mainly by somatic mutations. This study aimed to assess if polymorphisms of the RAS/RAF/MEK/ERK pathway are associated with gastric cancer. A case-control study of 242 gastric cancer patients and 242 controls was performed to assess the association of 27 single nucleotide polymorphisms (SNPs) in the RAS/RAF/MEK/ERK pathway genes with gastric cancer. Analyses performed under the additive model (allele) showed four significantly associated SNPs: RAF1 rs3729931 (Odds ratio (OR) = 1.54, 95%, confidence interval (CI): 1.20–1.98, p-value = 7.95 × 10−4), HRAS rs45604736 (OR = 1.60, 95% CI: 1.16–2.22, p-value = 4.68 × 10−3), MAPK1 rs2283792 (OR = 1.45, 95% CI: 1.12–1.87, p-value = 4.91 × 10−3), and MAPK1 rs9610417 (OR = 0.60, 95% CI: 0.42–0.87, p-value = 6.64 × 10−3). Functional annotation suggested that those variants or their proxy variants may have a functional effect. In conclusion, this study suggests that RAF1 rs3729931, HRAS rs45604736, MAPK1 rs2283792, and MAPK1 rs9610417 are associated with gastric cancer.

scholarly journals The Haplotype of the TGFβ1 Gene Associated with Cerebral Infarction in Chinese

2012 ◽  
Vol 39 (5) ◽  
pp. 626-631 ◽  
Author(s):  
Hong-miao Tao ◽  
Guo-zhong Chen ◽  
Gan-ping Cheng ◽  
Xiao-yun Shan
Keyword(s):  
Cerebral Infarction ◽  
Chinese Population ◽  
Transforming Growth Factor ◽  
Additive Model ◽  
Chinese Patients ◽  
Amplification Refractory Mutation System ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Individual Snps ◽  
Increased Risk

Background:Transforming growth factor beta1 (TGFβ1) is a multifunctional cytokine involved in inflammation and pathogenesis of atherosclerosis. The aim of the present study was to investigate the relationship between human TGFβ1 gene +869T>C (rs1800470), -509C>T (rs1800469) single nucleotide polymorphisms (SNPs) and haplotypes and cerebral infarction (CI) in a Chinese population.Methods:The genetic association study was performed in 450 Chinese patients (306 male and 144 female) with CI and 450 control subjects (326 male and 124 female). TGFβ1 gene +869T>C and -509C>T polymorphisms were identified with amplification refractory mutation system polymerase chain reaction and DNA sequencing method.Results:The individual SNPs analysis showed the +869T and -509C in an additive model (+869T vs +869C; -509 C vs T), +869TT genotype in a recessive model (TT vs TC+CC) and 509CC genotype in a dominant model (CC+ CT vs TT) were identified to be related to CI (P<0.05). +869T>C and -509C>T SNPs were in strong linkage disequilibrium (d'=0.87, R2=0.75). Haplotype analysis showed that +869C/-509T haplotype was associated with a significant decreased risk of CI (OR= 0.86, 95%CI, 0.70-0.92; P=0.007). Furthermore,+869T/-509C haplotype was associated with a significant increased risk of CI (OR=1.31, 95%CI, 1.10-2.03; P=0.019).Conclusions:The results of this study indicate that polymorphisms and the haplotypes in the TGFβ1 gene might be genetic markers for CI in the Chinese population.

scholarly journals The MALAT1 gene polymorphism and its relationship with the onset of congenital heart disease in Chinese

2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Qian Li ◽  
Wenying Zhu ◽  
Bei Zhang ◽  
Yiping Wu ◽  
Sen Yan ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
Chinese Population ◽  
Congenital Heart ◽  
Additive Model ◽  
Luciferase Assay ◽  
Nucleotide Polymorphisms ◽  
Tag Snps ◽  
Gender And Age ◽  
Functional Investigation

Many long non-coding RNAs (lncRNAs), including lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), are involved in various cardiac diseases. We evaluated the effects of tag single nucleotide polymorphisms (tag-SNPs) on MALAT1 gene in a Chinese population of children with congenital heart disease (CHD). In the present study, 713 CHD patients and 730 gender- and age-matched children without CHD were genotyped for MALAT1 tag-SNPs rs11227209, rs619586, and rs3200401. Further investigation of SNP’s function was performed by luciferase assay. Statistical analyses, including uni- and multivariate logistic regression were performed to quantitate the association between these tag SNPs and CHD. We discovered that MALAT1 rs619586 GG allele was significantly associated with lower risk of CHD (odds ratio (OR) = 0.77, 95% confidence interval (CI) = 0.59–0.92, P=0.014) in additive model. Functional investigation indicated that G allele of rs619586 could trigger higher expression of MALAT1. We demonstrated that the functional MALAT1 polymorphism rs619586 A>G was significantly associated with CHD susceptibility in Chinese population, potentially via regulating MALAT1 expression.

scholarly journals The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene

2017 ◽  
Vol 114 (37) ◽  
pp. 9942-9947 ◽  
Author(s):  
Nicholas Lister ◽  
Galina Shevchenko ◽  
James L. Walshe ◽  
Jessica Groen ◽  
Per Johnsson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Noncoding Rna ◽  
Dna Methyltransferase ◽  
Regulation Of Gene Expression ◽  
Control Of Gene Expression ◽  
Phosphatase And Tensin Homolog ◽  
Tensin Homolog ◽  
Sequence Components ◽  
Antisense Lncrnas

RNA has been found to interact with chromatin and modulate gene transcription. In human cells, little is known about how long noncoding RNAs (lncRNAs) interact with target loci in the context of chromatin. We find here, using the phosphatase and tensin homolog (PTEN) pseudogene as a model system, that antisense lncRNAs interact first with a 5′ UTR-containing promoter-spanning transcript, which is then followed by the recruitment of DNA methyltransferase 3a (DNMT3a), ultimately resulting in the transcriptional and epigenetic control of gene expression. Moreover, we find that the lncRNA and promoter-spanning transcript interaction are based on a combination of structural and sequence components of the antisense lncRNA. These observations suggest, on the basis of this one example, that evolutionary pressures may be placed on RNA structure more so than sequence conservation. Collectively, the observations presented here suggest a much more complex and vibrant RNA regulatory world may be operative in the regulation of gene expression.

scholarly journals Association Analysis between SNPs in LATS1 and LATS2 and Non-Cardia Gastric Cancer

2020 ◽  
Author(s):  
Licong Ma ◽  
Xuyang Tian ◽  
Fang Gao ◽  
Wenjie Dong ◽  
Tong Dang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Protective Factor ◽  
Serological Test ◽  
Additive Model ◽  
Nucleotide Polymorphisms ◽  
Large Tumor ◽  
Additive Inheritance ◽  
And Gender ◽  
H Pylori ◽  
Control Association

Abstract Background: Many studies have found that large tumor suppressor kinase 1 (LATS1) and LATS2 play important roles in many diseases, but studies have been rare on the relationship between these genes and non-cardia gastric cancer (GC). We performed a case-control association study to investigate the associations between single nucleotide polymorphisms (SNPs) in LATS1 and LATS2 genes and Helicobacter pylori (H. pylori) infection as well as the risk of non-cardia GC. Methods: First, H. pylori infection was determined by the serological test using enzyme-linked immunoassay. Then genotyping of SNPs was performed for 808 samples by the Taqman method. Finally, unconditional logistic regression was used to calculate the odds ratios (ORs) and 95% confidence intervals (CIs), adjusted for age and gender, for the association of each SNP with the infection of H. pylori, the risk of non-cardia gastric cancer, as well as the expression of LATS1 and LATS2 proteins in non-cardia GC tissues, using the codominant, dominant, recessive, overdominant, and additive inheritance models, respectively. Results: The statistical results showed that LATS2 rs9552315 was associated with H. pylori infection, and the CC+CT genotype could reduce the risk of H. pylori infection (odds ratio [OR]: 0.549, 95% confidence interval [CI]: 0.339–0.881, P<0.05) compared with the TT genotype in a dominant model. LATS1 rs9393175 was associated with the risk of non-cardia GC, and the AG genotype reduced the risk of non-cardia GC (OR: 0.702, 95% CI: 0.516–0.952, P<0.05) compared with the GG+AA genotype in an overdominant model. LATS2 rs9509492 was associated with the risk of GC in an additive model. No associations were found between five SNPs and expression of LATS1 and LATS2 proteins in non-cardia GC tissue. Conclusions: LATS2 rs9552315 CT genotype may be a protective factor against infection of H. pylori. LATS1 rs9393175 AG genotype and LATS2 rs9509492 GG genotype may be protective factors for non-cardia GC.

scholarly journals Downregulated Expression of hsa_circ_0005556 in Gastric Cancer and Its Clinical Significance

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Liangwei Yang ◽  
Yu Yu ◽  
Xiuchong Yu ◽  
Jiaming Zhou ◽  
Zhiping Zhang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Roc Curve ◽  
Noncoding Rna ◽  
Operating Characteristic ◽  
Diagnostic Value ◽  
Circular Rnas ◽  
Normal Tissues ◽  
Potential Biomarker ◽  
Polymerase Chain

Background. Gastric cancer (GC) has a poor prognosis due to the lack of ideal tumor markers. Circular RNAs (circRNAs) are a novel type of noncoding RNA related to the occurrence of GC. Among our research, we investigated the role of hsa_circ_0005556 in GC. Materials and Methods. The expression of hsa_circ_0005556 of 100 paired GC tissues and adjacent normal tissues was detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A receiver operating characteristic (ROC) curve was established to evaluate the diagnostic value of hsa_circ_0005556. The correlation between the expression of hsa_circ_0005556 and corresponding clinicopathological characteristic was explored. Results. hsa_circ_0005556 was significantly downregulated in GC tissues contrasted with adjacent normal tissues (n=100, p<0.001). The areas under the ROC curve (AUC) of hsa_circ_0005556 were up to 0.773, while 64% sensitivity and 82% specificity, respectively. Moreover, its expression levels were significantly associated with differentiation (p=0.001), TNM stage (p=0.013), and lymphatic metastasis (p=0.039). GC patients of high hsa_circ_0005556 levels had a longer overall survival (OS) than those of the low group (p=0.047). Conclusion. hsa_circ_0005556 is a potential biomarker for GC, which may guide judgment of the indication of endoscopic treatment for early gastric cancer (EGC).

scholarly journals Downregulated Expression of linc-ROR in Gastric Cancer and Its Potential Diagnostic and Prognosis Value

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Xiuchong Yu ◽  
Haixiang Ding ◽  
Yijiu Shi ◽  
Liangwei Yang ◽  
Jiaming Zhou ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Noncoding Rna ◽  
Area Under The Curve ◽  
Diagnostic Value ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Polymerase Chain ◽  
Long Intergenic Noncoding Rna ◽  
Clinical Potential ◽  
The Relationship

Background. Gastric cancer (GC) is one of the global mortality diseases and has a poor prognosis due to the lack of ideal tumor biomarkers. Numerous studies have shown that long noncoding RNAs (lncRNAs) can affect the occurrence and development of cancer through a variety of signaling pathways. The abnormal expression and specificity of lncRNAs in tumors make them potential biomarkers of cancers. Nevertheless, the diagnostic roles of lncRNAs in GC have been poorly understood. So this study focuses on the clinical diagnostic value of lncRNAs in GC. Materials and Methods. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to investigate the expression of the linc-ROR (long intergenic noncoding RNA, regulator of reprogramming) in 105 paired GC tissues and adjacent normal tissues. Receiver operating characteristic (ROC) curve and area under the curve (AUC) were established to assess the diagnostic value of linc-ROR. The relationship between expression of linc-ROR and clinicopathological factors of patients with GC was further explored. Kaplan-Meier analysis was performed to evaluate the prognostic value of linc-ROR expression. Results. The linc-ROR expression level was significantly decreased in GC tissues compared with its adjacent nontumor tissues ( n = 105 , P < 0.001 ). We also discovered that linc-ROR was evidently downregulated in 68.6% (72/105) of GC tissues. The AUC’s value of linc-ROR was up to 0.6495, with sensitivity and specificity of 0.7524 and 0.5143, respectively. Intriguingly, the linc-ROR expression levels were obviously associated with tumor differentiation ( P = 0.004 ). Notably, the overall survival rate of GC patients with high expression of linc-ROR was significantly higher than those with low expression. Conclusion. Our data revealed that linc-ROR has clinical potential as a biomarker for the diagnosis of GC and assessment of its prognosis.

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