Risk of eighteen genome-wide association study-identified genetic variants for colorectal cancer and colorectal adenoma in Han Chinese

Common and novel haplotype structures between different types of cancer

BACKGROUND

Background: Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with cancer risk. GWAS data are important for cancer prevention and understanding the underlying mechanisms of cancer.

AIMS

This study aimed to investigate the genetic association between different types of cancer using GWAS data and a bioinformatics approach.

METHODS AND RESULTS

The significant GWAS variants associated with more than one cancer type were identified. Common linkage disequilibrium (LD) variants between different types of cancer were identified by 1000 genomes phase 3 LD data. Haplotype blocks were identified by analyzing 1000 Genomes phase 3 genotyping data in the GWAS populations. Subsequent analyses included functional SNP analyses and TCGA gene expression. The results associated with significant GWAS variants (P<5E-8) showed the following haplotype associations in European population: GT rs4808075-rs8170 haplotype on BABAM1 with breast and ovarian cancers, GC rs16857609-rs11693806 haplotype on DIRC3 with breast and thyroid cancers, GCG rs380286-rs401681-rs31487 haplotype on CLPTM1L with skin and lung cancers, GGG rs4430796-rs11651052-rs11263763 haplotype on HNF1B with prostate and endometrial cancers, and GT rs10505477-rs6983267 haplotype on CASC8 associated with colorectal and prostate cancers. All these genes had significantly different expressions in tumor tissues (P<1E-3). In addition, the rs11693806 variant is located in the hsa-miR-873-5p binding site and has an enhancing effect on the hsa-miR-873-5p:DIRC3 interaction.

CONCLUSION

These novel haplotype structures and miRNA:lncRNA interactions are important for understanding the common genetic link between cancers. These results can potentially be used in genetic panels.

Correlation between Genomic Variants and Worldwide Epidemiology of Prostate Cancer

Prostate cancer (PCa) incidence and mortality vary across territories and populations. This can be explained by the genetic factor of this disease. This article aims to correlate the epidemiological data, worldwide incidence, and mortality of PCa with single-nucleotide polymorphisms (SNPs) associated with the susceptibility and severity of this neoplasm in different populations. Eighty-four genetic variants associated with prostate cancer susceptibility were selected from the literature through genome association studies (GWAS). Allele frequencies were obtained from the 1000 Genomes Project, and epidemiological data were obtained from Surveillance, Epidemiology, and End Results (SEER). The PCa incidence, mortality rates, and allele frequencies of variants were evaluated by Pearson’s correlation. Our study demonstrated that 12 SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs6983267, rs11649743, rs2075110, rs114798100, rs855723, and rs2075109) were correlated with epidemiological data in different ethnic groups. Ten SNPs (rs2961144, rs1048169, rs7000448, rs4430796, rs2066827, rs12500426, rs11649743, rs2075110, rs114798100, and rs2075109) were positively correlated with the mortality rate. Seven SNPs (rs1048169, rs2961144, rs7000448, rs4430796, rs2066827, rs12500426, and rs114798100) were positively correlated with incidence. Positive correlations of incidence and mortality rates were more frequent in the African population. The genetic variants investigated here are likely to predispose to PCa and could play a role in its progression and aggressiveness. This genetic study demonstrated here is promising for implementing personalized strategies to screen for prostate cancer in diverse populations.

Prostate Cancer Susceptibility Loci Identified in GATA2 and ZMIZ1 in Chinese Population

Background

Common genetic risk variants for prostate cancer (PCa) have been identified at approximately 170 loci using genome-wide association studies (GWAS), most of which were identified in European populations. Recently, GWAS were applied to a large Japanese cohort and identified 12 novel susceptibility loci associated with PCa risk. In this study, we aim to investigate PCa susceptibility loci in the Chinese population. The study data will be used to promote PCa risk control in China.

Methods

A total of 235 PCa patients and 252 control subjects (all unrelated) were enrolled in this case-control PCa study. Nine single nucleotide polymorphisms (SNPs) were genotyped in GATA2 (rs73862213, rs2335052, and rs10934857), ZMIZ1 (rs704017, rs77911174, and rs3740259), and SUN2 (rs78397383, rs5750680, and rs138705) genes. The associations between the candidate SNPs and PCa were analyzed using multiple-factor logistic regression and haplotype analysis.

Results

The allele frequency distributions of rs73862213 and rs2335052 in the GATA2 gene and rs704017 and rs77911174 in the ZMIZ1 gene were found to be significantly different between PCa cases and controls. Haplotype analysis revealed that the G-C-A haplotype of the GATA2 gene (order of SNPs: rs73862213-rs2335052-rs10934857) and the G-G-G haplotype of the ZMIZ1 gene (order of SNPs: rs704017-rs77911174-rs3740259) were associated with increased PCa risk. None of the SUN2 haplotypes were associated with PCa.

Conclusions

Our study data indicates that the minor alleles of rs73862213 and rs2335052 in the GATA2 gene and rs704017 and rs77911174 in the ZMIZ1 gene were associated with increased PCa risk. These findings greatly extended our knowledge of the etiology of PCa.

Association between lncRNA CASC8 polymorphisms and the risk of cancer: a meta-analysis

Objective

To explore the relationship between single-nucleotide polymorphisms (SNPs) in one of the long noncoding RNA (lncRNA), cancer susceptibility candidate 8 (CASC8) gene and the risk of cancer.

Materials and methods

A meta-analysis was conducted to summarize the relationship between common SNPs (rs10505477 and rs7837328) in the lncRNA CASC8 gene and the risk of cancer. The relevant references were retrieved from several authoritative databases. Rigorous inclusion and exclusion criteria were adopted to ensure the credibility of the results. The fixed effects or random effects model was used to calculate the OR and 95% CI. We tested for publication bias.

Results

Fifteen articles containing 20 datasets (24,504 cases and 22,969 controls) were finally included in the meta-analysis. Compared to the individuals carrying the rs10505477 TT genotype, those with the TC or CC genotype had a decreased risk of cancer (TC vs TT: OR 0.876, 95% CI 0.832–0.923, P<0.001; CC vs TT: OR 0.748, 95% CI 0.703–0.795, P<0.001). Allele C of rs10505477 might be a protective factor for decreasing susceptibility to cancer (OR 0.866, 95% CI 0.840–0.893, P<0.001). As for rs7837328, the GA and AA genotypes were associated with increased risks of cancer as compared to the GG genotype (ORs 1.209 and 1.336; 95% CIs 1.127–1.298 and 1.202–1.484, respectively); its A allele could significantly increase the risk of cancer compared with the G allele (OR 1.169, 95% CI 1.114–1.227, P<0.001).

Conclusion

The rs10505477 and rs7837328 polymorphisms might be associated with risk of cancer.

Cumulative evidence for relationships between multiple variants in 8q24 and colorectal cancer incidence

Genome-wide association studies (GWAS) have identified multiple independent cancer susceptibility loci at chromosome 8q24.We conducted a comprehensive research synopsis and meta-analysis to evaluate associations between 6 variants in 8q24 and risk of colorectal cancer using data from 31 eligible articles totaling 41,942 cases and 49,968 controls.Of the 6 variants located in 8q24, 3 were significantly associated with risk of colorectal cancer. In particular, both homozygous TT and heterozygous CT genotypes of rs10505477, as well as the GG and TG genotypes of rs6983267, were associated with risk of colorectal cancer.Our study provides summary evidence that common variants in the 8q24 are associated with risk of colorectal cancer in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the exact role of the variants in the 8q24 involved in the etiology of colorectal cancer.

Genetic Risk Score Is Associated With Prevalence of Advanced Neoplasms in a Colorectal Cancer Screening Population

BACKGROUND & AIMS

The presence of specific single nucleotide polymorphisms (SNPs) can be used to calculate an individual's risk for colorectal cancer (CRC), called a genetic risk score (GRS). We investigated whether GRS can identify individuals with clinically relevant neoplasms in a screening colonoscopy population.

METHODS

We derived a GRS based on 48 SNPs associated with CRC, identified in a comprehensive literature search. We obtained genetic data from 1043 participants (50-79 years old) in a screening colonoscopy study in Germany, recruited from 2005 through 2013 (294 with advanced neoplasms, 249 with non-advanced adenoma (NAAs), and 500 without neoplasms). Each participant was assigned a GRS by aggregating their risk alleles (0, 1, or 2). Risk of advanced neoplasms and NAA according to GRS was calculated by multiple logistic regression. Risk advancement periods were calculated. We replicated our findings using data from a subset of the Tennessee Colorectal Polyp Study.

RESULTS

An increased GRS was associated with higher prevalence of advanced neoplasms, but not NAAs. Participants in the middle and upper tertiles of GRS had a 2.2-fold and 2.7-fold increase in risk, respectively, of advanced neoplasms compared to those in the lower tertile. Adjusted odds ratios (ORs) were 1.09 (95% confidence interval [CI], 0.76-1.57) for NAA in the middle tertile and 1.05 (95% CI, 0.70-1.55) for NAA in the upper tertile. The ORs were largest for proximal advanced neoplasms for participants in the middle tertile (OR, 3.55; 95% CI 1.85-6.82) and the upper tertile (OR, 3.61; 95% CI 1.84-7.10). The risk advancement period for medium vs low GRS was 13.4 years (95% CI 4.8-22.0) and for high vs low GRS was 17.5 years (95% CI, 7.8-27.3).

CONCLUSIONS

In a genetic analysis of participants in a CRC screening study in Germany, an increased GRS (based on CRC-associated SNPs) was associated with increased prevalence of advanced neoplasms. These findings might be used in defining risk-adapted screening ages.

SMAD7 rs4939827 variant contributes to colorectal cancer risk in Chinese population

A genome-wide association study identified a common genetic variant rs4939827 at 18q21 in SMAD7 to be related with colorectal cancer (CRC) risk with OR=1.2 and P =7.80E-28. Until recently, several meta-analysis studies have been conducted, and reported significant association between rs4939827 and CRC risk. However none of these studies evaluated the potential association between rs4939827 and CRC risk in Chinese population. In this study, we evaluated this association by a meta-analysis using 12077 samples including 5816 CRC cases and 6261 controls. In the end, we identified the T allele of rs4939827 to be significantly related with an increase CRC risk (P=2.22E-05, OR=1.14, 95% CI 1.07-1.21) in Chinese population.

Role of glucose metabolism related gene GLUT1 in the occurrence and prognosis of colorectal cancer

Colorectal cancer (CRC) ranks the third most commonly diagnosed cancer in males and the second in females worldwide. However, the functional and causal SNPs for CRC remain to be mined. Glucose transporter 1 (GLUT1), a pivotal rate-limiting element in the transport of glucose in malignancy cells, has been identified to be associated with many cancers. Here, we aim to explore the role of GLUT1 in the occurrence and prognosis of colorectal cancer in a Chinese population. We found that GLUT1 expression levels in CRC tumor tissues were significantly higher than those in the corresponding adjacent normal tissues, and Cox multivariate analysis demonstrated that the GLUT1 expression was an independent prognostic factor for CRC (HR = 2.11, 95% CI = 1.33–3.34, P=0.001). For a functional polymorphism of GLUT1 (rs710218), we found that individuals with TT genotype (OR = 1.68, 95% CI = 1.02-2.75, P = 0.041) or AT genotype (OR = 1.47, 95% CI = 1.09-1.99, P = 0.012) of rs710218 had a significantly increased risk of CRC compared to those with AA homozygote. These findings strongly suggest that glucose metabolism related gene GLUT1, and its functional SNP, rs710218 might contribute to CRC susceptibility and prognosis, and the exact biological mechanism awaits further research.