Bone morphogenetic protein-4 polymorphism and colorectal cancer risk: a meta analysis

In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 (BMP4) Promoter Methylation across All Methylation Clusters in Colorectal Cancer

The cytosine-phosphate-guanine (CpG) island methylator phenotype (CIMP) represents one of the pathways involved in the development of colorectal cancer, characterized by genome-wide hypermethylation. To identify samples exhibiting hypermethylation, we used unsupervised hierarchical clustering on genome-wide methylation data. This clustering analysis revealed the presence of four distinct subtypes within the tumor samples, namely, CIMP-H, CIMP-L, cluster 3, and cluster 4. These subtypes demonstrated varying levels of methylation, categorized as high, intermediate, and very low. To gain further insights, we mapped significant probes from all clusters to Ensembl Regulatory build 89, with a specific focus on those located within promoter regions or bound regions. By intersecting the methylated promoter and bound regions across all methylation subtypes, we identified a total of 253 genes exhibiting aberrant methylation patterns in the promoter regions across all four subtypes of colorectal cancer. Among these genes, our comprehensive genome-wide analysis highlights bone morphogenic protein 4 (BMP4) as the most prominent candidate. This significant finding was derived through the utilization of various bioinformatics tools, emphasizing the potential role of BMP4 in colorectal cancer development and progression.

The common variant rs4444235 near BMP4 confers genetic susceptibility of colorectal cancer: an updated meta-analysis based on a comprehensive statistical strategy

OBJECTIVE

We performed an updated meta-analysis, using a comprehensive strategy of a logistic regression and a model-free approach, to evaluate more precisely the role of the rs4444235 variant near the Bone morphogenetic protein-4 (BMP4) gene in susceptibility to colorectal cancer (CRC).

METHODS

A total of 19 studies with 28770 cases and 28234 controls were included. Metagen system with logistic regression was applied to choose the most plausible genetic model for rs4444235. Generalized odds ratio (ORG) metric was used to provide a global test of relationship between rs4444235 and CRC risk.

RESULTS

Metagen analysis suggested the rs4444235 fitted best to an additive model. In assessment of the additive model, heterogeneity was observed (P = 0.059, I2 = 36.1), and pooled per-allele OR was 1.08 (95% CI = 1.05-1.11). Based on the model-free approach, pooled ORG was 1.09 (95% CI = 1.05-1.14) under a random-effect model. Stratified analyses suggested heterogeneity could be in part explained by population ethnicity, study design, sources of controls, and sample size. Sensitivity analysis further supported the robust stability of the current results, by showing similar pooled estimates before and after sequential removal of each study.

CONCLUSIONS

This meta-analysis provides a robust estimate of the positive association between the rs4444235 and CRC risk and further emphasizes the importance of the rs4444235 in CRC risk prediction.

Genome-wide association and sequencing studies on colorectal cancer

Colorectal cancer is a leading cause of morbidity and mortality worldwide. Understanding its genetic mechanisms is key to improving risk prediction, prognostication and treatment. Results from genome-wide association studies have engendered a growing list of colorectal cancer susceptibility genes whereas the application of genome-wide mutational analysis has enabled the depiction of mutational landscape of colorectal cancer at high resolution. The development of novel technologies, such as metagenomic and single-cell sequencing, is expected to have positive impact on future genetic studies. However, challenges remain to address the changing epidemiology of colorectal cancer, issues on genetic testing, and clinical utilization of genomic data.

Vascular endothelial growth factor (VEGF) gene polymorphisms and colorectal cancer: a meta-analysis of epidemiologic studies

BACKGROUND

Studies investigating the association between vascular endothelial growth factor (VEGF) polymorphisms and colorectal cancer (CRC) risk report conflicting results. To clarify the effect of four VEGF (-460T/C, -634G/C, +936C/T, and -2578C/A) gene polymorphisms on the risk of developing CRC, we carried out a meta-analysis using published data to obtain more precise estimates of risk.

METHODS

Electronic searches of PubMed and EMBASE were conducted to select studies for this meta-analysis. The principal outcome measure was the odds ratio (OR) with 95% confidence interval (CI) for the risk of CRC associated with four VEGF (-460T/C, -634G/C, +936C/T, and -2578C/A) gene polymorphisms.

RESULTS

We identified 12 epidemiologic studies, which included 2770 CRC cases and 2568 controls. The combined results based on all studies showed that CRC cases had a significantly higher frequency of VEGF -634GG (OR=1.24, 95% CI=1.06, 1.44) and -2578AA (OR=1.37, 95% CI=1.12, 1.66) genotype and a lower frequency of -634CG (OR=0.82, 95% CI=0.71, 0.95) than controls. When stratifying for race, we found that patients with CRC had a significantly higher frequency of -460TC (OR=1.54, 95% CI=1.22, 1.94), -460CC (OR=2.00, 95% CI=1.50, 2.67), and -2578AA (OR=1.38, 95% CI=1.12, 1.69) and a lower frequency of -2578AA (OR=0.78, 95% CI=0.65, 0.93) genotypes of VEGF than controls, among Caucasians. We also found that patients with CRC had a significantly higher frequency of -634GG (OR=1.61, 95% CI=1.20, 2.15) and a lower frequency of -634CG (OR=0.60, 95% CI=0.46, 0.79) genotypes of VEGF than controls, among Asians.

CONCLUSIONS

Our meta-analysis suggests that the VEGF -460T/C, -634G/C, and -2578C/A gene polymorphisms are associated with a risk of CRC.