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LncRNA-PCAT1 rs2632159 polymorphism could be a biomarker for colorectal cancer susceptibility.

ABSTRACT: Background: Single-nucleotide polymorphisms (SNPs) in lncRNAs could be biomarkers for susceptibility to colorectal cancer (CRC), but the association of PCAT1 polymorphisms and CRC susceptibility is yet to be studied. Methods: Five tagSNPs covering the PCAT1 gene were detected through Kompetitive Allele-Specific PCR among 436 CRC patients and 510 controls. An expression quantitative trait locus (eQTL) bioinformatic analysis was then performed. Results: In the present study, PCAT1 rs2632159 polymorphism increased CRC risk by 1.37-fold and 2.19-fold in the dominant and recessive models, respectively (P=0.040 and 0.041). When the CRC cases were divided into colon cancer and rectal cancer, we found that this polymorphism affected colon cancer risk under the dominant model (P=0.022, OR = 1.51) and affected rectal cancer susceptibility under the recessive model (P=0.009, OR = 3.03). A more pronounced effect was observed in the male subgroup in that PCAT1 rs2632159 SNP increased rectal cancer risk by 3.97-fold (P=0.017). When PCAT1 rs2632159 was present, epistatic effects were observed with rs1902432 and rs785005 (P=0.011 and 0.008, respectively). eQTL analysis showed that rs2632159 could influence binding with the transcription factors EBF, LUN-1, and TCF12. Conclusion: PCAT1 rs2632159 SNP could be a biomarker for CRC risk. And the rs1902432 SNP might only have potential to be a biomarker for colon cancer risk.

SUBMITTER: Yang ML

PROVIDER: S-EPMC6629943 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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lncRNA-PCAT1 rs2632159 polymorphism could be a biomarker for colorectal cancer susceptibility.

Yang Ming-Li ML Huang Zhe Z Wu Li-Na LN Wu Rong R Ding Han-Xi HX Wang Ben-Gang BG

Bioscience reports 20190712 7

Background: Single-nucleotide polymorphisms (SNPs) in lncRNAs could be biomarkers for susceptibility to colorectal cancer (CRC), but the association of PCAT1 polymorphisms and CRC susceptibility is yet to be studied. Methods: Five tagSNPs covering the PCAT1 gene were detected through Kompetitive Allele-Specific PCR among 436 CRC patients and 510 controls. An expression quantitative trait locus (eQTL) bioinformatic analysis was then performed. Results: In the pr ...[more]

PMID: 31253700

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Project description:Objective: To study the relationship between long-chain non-coding RNA small nucleolar RNA host gene 16 (lncRNA SNHG16) polymorphisms and its interaction with environmental factors and susceptibility to colorectal cancer (CRC).Methods: Sanger sequencing was used to analyze genotypes of lncRNA SNHG16 gene rs7353, rs8038, and rs15278 sites. Multifactor dimensionality reduction was used to analyze interactions between lncRNA SNHG16 gene rs7353, rs8038, rs15278 sites, and environmental factors. Haploview 4.1 software was used to analyze linkage disequilibrium of lncRNA SNHG16 gene rs7353, rs8038, and rs15278 sites. Quantitative real-time polymerase chain reaction was used to analyze plasma lncRNA SNHG16 levels of CRC patients and control subjects.Results: Variation of the lncRNA SNHG16 gene rs7353 site A>G variation was associated with decreased CRC susceptibility (Odds ratio [OR]?=?0.50, 95% confidence interval [CI]: 0.40-0.62, P?<?.01). The rs8038 site G>A and rs15278 site A>G variation were associated with increased CRC susceptibility (OR?=?1.87, 95% CI: 1.47-2.36, P?<?.01). The rs15278 site G>A variation was associated with increased CRC susceptibility (OR?=?2.24, 95% CI: 1.61-3.11, P?<?.01). Interaction combinations featuring age, rs7353, rs8038, and rs15278 single nucleotide polymorphism are 13.53 times more susceptible to CRC than other interactions (95% CI: 9.43-19.41, P?<?.01). The rs15278, rs8038, and rs7353 site AGA haplotypes were significantly associated with a decreased CRC risk (OR?=?0.65, 95% CI: 0.48-0.88, P?=?.01), AAG haplotypes were significantly associated with an increased CRC risk (OR?=?2.00, 95% CI: 1.27-3.17, P?<?.01). High lncRNA SNHG16 expression was associated with tumor progression in CRC patients (??=?8.85, P?=?.03). The rs7353 site A>G variation caused a significant decrease in plasma lncRNA SNHG16 level (P?<?.01), while the rs8038 site G>A variation and rs15278 site A>G variation resulted in increased plasma lncRNA SNHG16 levels.Conclusion: Polymorphisms of lncRNA SNHG16 gene rs7353, rs8038, rs15278 loci and their interaction with age are significantly associated with CRC susceptibility.

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LncRNA-PCAT1 rs2632159 polymorphism could be a biomarker for colorectal cancer susceptibility.

Publications

lncRNA-<i>PCAT1</i> rs2632159 polymorphism could be a biomarker for colorectal cancer susceptibility.

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