Validation of microRNA pathway polymorphisms in esophageal adenocarcinoma survival

Genetic variant in miR-17-92 cluster binding sites is associated with esophageal squamous cell carcinoma risk in Chinese population

BACKGROUND

Single nucleotide polymorphisms (SNPs) located in microRNA (miRNA) binding sites can affect the interactions between miRNAs and target genes, which is related to cancer susceptibility and tumorigenesis. However, the association between SNPs located in miR-17-92 cluster binding sites and ESCC risk remains unclear. Therefore, we aimed to explore the relationship between polymorphisms in miR-17-92 cluster binding sites and ESCC susceptibility.

METHODS

Six SNPs in the binding sites of miR-17-92 cluster were selected using bioinformatics databases, and their association with ESCC risk was investigated in a case-control study (including 488 cases and 512 controls) based on the population from high incidence areas of ESCC in China. We evaluated the SNP-SNP and SNP-smoking interactions using generalized multifactor dimensionality reduction (GMDR). Moreover, the expression of the miR-17-92 cluster and its target genes was determined in ESCC and adjacent normal tissues by quantitative real-time polymerase chain reaction (qRT-PCR). The dual-luciferase reporter assay was conducted to verify the effect of SNPs on the binding affinity between miRNAs and target genes.

RESULTS

We found that the SNP rs1804506 C > T had a significant association with the decreased ESCC risk. The SNP rs1804506 T allele was associated with a significantly decreased risk of ESCC in the additive model (OR = 0.817, 95% CI = 0.681-0.981, P = 0.030). The rs1804506 T allele had more striking effects on reducing ESCC risk in older individuals, female or non-smoker subgroups. We also found a significant interaction effect between rs1366600 and smoking by GMDR methods (P = 0.011). Additionally, the expression levels of miR-19a-3p and TGFBR3 were significantly downregulated in ESCC tissues compared with normal tissues, and the carriers of rs1804506 TT genotype had lower expression level of TGFBR3 than those of rs1804506 CC/CT genotype. Following dual-luciferase reporter assay showed that the rs1804506 T allele reduced the binding of miR-19a-3p and TGFBR3 3'-UTR.

CONCLUSIONS

Our findings suggest that the rs1804506 polymorphism in miR-17-92 cluster binding sites contributes to the susceptibility of ESCC, which might provide new clues and scientific evidence for the etiology and biomarkers for the prevention and treatment of ESCC.

Genetic Variation in DEAD-Box Helicase 20 as a Putative Marker of Recurrence in Propensity-Matched Colon Cancer Patients

Variants of the DEAD-Box Helicase 20 (DDX20), one of the microRNAs (miRNAs) machinery genes, can modulate miRNA/target gene expressions and, hence, influence cancer susceptibility and prognosis. Here, we aimed to unravel the association of DDX20 rs197412 T/C variant with colon cancer risk and/or prognosis in paired samples of 122 colon cancer and non-cancer tissue specimens by TaqMan allelic discrimination analysis. Structural/functional bioinformatic analyses were carried out, followed by a meta-analysis. We found that the T allele was more frequent in cancer tissues compared to control tissues (60.2% vs. 35.7%, p < 0.001). Furthermore, the T variant was highly frequent in primary tumors with evidence of recurrence (73% vs. 47.5%, p < 0.001). Genetic association models, adjusted by age and sex, revealed that the T allele was associated with a higher risk of developing colon cancer under heterozygote (T/C vs. C/C: OR = 2.35, 95%CI = 1.25−4.44, p < 0.001), homozygote (T/T vs. C/C: OR = 7.6, 95%CI = 3.5−16.8, p < 0.001), dominant (T/C-T/T vs. C/C: OR = 3.4, 95%CI = 1.87−8.5, p < 0.001), and recessive (T/T vs. C/C-T/C: OR = 4.42, 95%CI = 2.29−8.54, p = 0.001) models. Kaplan−Meier survival curves showed the shift in the C > T allele to be associated with poor disease-free survival. After adjusting covariates using a multivariate cox regression model, patients harboring C > T somatic mutation were 3.5 times more likely to develop a recurrence (p < 0.001). A meta-analysis of nine studies (including ours) showed a higher risk of CRC (81%) in subjects harboring the T/T genotype than in T/C + C/C genotypes, supporting the potential clinical utility of the specified study variant as a biomarker for risk stratification in CRC cases. However, results were not significant in non-colorectal cancers. In conclusion, the DDX20 rs197412 variant is associated with increased colon cancer risk and a higher likelihood of recurrence in the study population.

Screening the key genes of prognostic value in the microenvironment for head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the sixth common malignancy worldwide. The tumor microenvironment is highly related to tumor initiation, progression, and prognosis. This study aims to screen the tumor microenvironment related key genes of prognostic value for HNSCC.The gene expression and clinical data for HNSCC were downloaded from the cancer genome atlas (TCGA). The immune/stromal/ESTIMATE scores were downloaded from the website of the MD Anderson Cancer Center. Correlation of patient gender and tumor grade with immune/stromal/ESTIMATE score was tested. Patients were divided into low and high immune/stromal/ESTIMATE score subgroups. Survival analysis was performed to evaluate the prognostic value of the immune/stromal/ESTIMATE score. Tumor microenvironment related differentially expressed genes were determined and applied for functional enrichment analysis and protein-protein interaction network was predicted. The prediction value of the common differentially expressed genes on patient survival was tested.Four hundred eighty samples with complete clinical, expression data, and immune/stromal/ESTIMATE scores were enrolled for analysis. Immune/stromal/ESTIMATE score was higher in female patients than males. A total of 44 common differentially expressed genes were screened in high and low immune/stromal/ESTIMATE score subgroups. Of the 44 genes, 7 genes (ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6) were found to be closely related to patient survival. Enrichment analysis showed that the differentially expressed genes mainly enriched in the protein-coupled receptor signaling pathway, extracellular region, G-protein coupled receptor activity, salivary secretion, and regulation of lipolysis in adipocytes. Protein-protein interaction analysis revealed that POSTN and OGN were crucial microenvironments related genes.Tumor microenvironment related genes ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6 are valuable predictors for HNSCC patient survival. POSTN and OGN are crucial in modulating the microenvironment and tumor biology for HNSCC.

Precision medicine for gastrointestinal cancer: Recent progress and future perspective

Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.

GOLGA7 rs11337, a Polymorphism at the MicroRNA Binding Site, Is Associated with Glioma Prognosis

MicroRNAs bind to the 3' untranslated regions of mRNAs, affecting translation, tumorigenesis, and apoptosis. This study evaluated the role of TYMS (rs1059394, C > T, and rs2847153, G > A), RYR3 (rs1044129, G > A), KIAA0423 (rs1053667, T > C), and GOLGA7 (rs11337, G > T) polymorphisms for assessment of glioma risk and prognosis among the Chinese Han population. Five single-nucleotide polymorphisms were assessed in 605 glioma patients and 1,300 controls. We found a significant correlation between rs1059394 and glioma susceptibility in the homozygote and dominant genetic models (TT versus CC, odds ratio [OR] = 0.71, 95% confidence interval [CI] = 0.52-0.97, p = 0.03; CT+TT versus CC, OR = 0.74, 95% CI = 0.55-0.99, p = 0.04). The results of the Kaplan-Meier and log rank tests revealed that the rs11337 GG genotype correlated with better overall survival of glioma patients (p = 0.017) than the GT genotype. Multivariate Cox regression analysis results also showed that the rs11337 GT genotype correlated with worse overall survival (p = 0.017, hazard ratio [HR] = 1.25, 95% CI = 1.04-1.5) than the GG genotype. These results suggest that GOLGA7 (rs11337) polymorphism may play a role in the prognosis of glioma patients and that TYMS (rs1059394) is associated with glioma risk.

MiRNA Polymorphisms and Cancer Prognosis: A Systematic Review and Meta-Analysis

Background: Accumulating studies have focused on the relationship between miRNAs polymorphisms and cancer prognosis. However, the results are conflicting and unconvincing. This systematic review and meta-analysis was conducted to explore the relationship between miRNAs polymorphisms and cancer prognosis, aiming to seek for markers with cancer prognostic function.

Methods: Hazard ratio of overall survival, disease-free survival (DFS) and recurrence-free survival were calculated to evaluate the association between miRNAs polymorphisms and cancer prognosis by using Stata software 11.0.

Results: We systematically reviewed the association of 17 miRNAs SNPs with cancer prognosis including 24,721 samples. It was shown that 6 miRNAs SNPs (miR-608 rs4919510, miR-492 rs2289030, miR-378 rs1076064, miR-499 rs4919510, miR-149 rs2292832, miR-196a2 rs11614913) were associated with better cancer overall survival (OS) while let-7i rs10877887 was associated with poor OS; the homozygous and heterozygote genotype of miR-423 were related to poor cancer relapse-free survival (RFS) when compared with the wild genotype; miR-146 rs2910164 was linked to favorable cancer DFS while miR-196a2 rs11614913 was associated with poor DFS.

Conclusions: In summary, let-7i rs10877887, miR-608 rs4919510, miR-492 rs2289030, miR-378 rs1076064, miR-423 rs6505162, miR-499 rs4919510, miR-149 rs2292832, miR-146 rs2910164, and miR-196a2 rs11614913 might serve as potential biomarkers for cancer prognosis.

Involving the microRNA Targetome in Esophageal-Cancer Development and Behavior

Esophageal cancer (EC) is the eighth most common and sixth leading cause of cancer-related mortality in the world. Despite breakthroughs in EC diagnosis and treatment, patients with complete pathologic response after being submitted to chemoradiotherapy are still submitted to surgery, despite its high morbidity. Single-nucleotide polymorphisms (SNPs) in miRNA, miRNA-binding sites, and in its biogenesis pathway genes can alter miRNA expression patterns, thereby influencing cancer risk and prognosis. In this review, we systematized the information available regarding the impact of these miR-SNPs in EC development and prognosis. We found 34 miR-SNPs that were associated with EC risk. Despite the promising applicability of these miR-SNPs as disease biomarkers, they still lack validation in non-Asian populations. Moreover, there should be more pathway-based approaches to evaluate the cumulative effect of multiple unfavorable genotypes and, consequently, identify miR-SNPs signatures capable of predicting EC therapy response and prognosis.

Comprehensive Assessment of the Relationship Between MicroRNA-124 and the Prognostic Significance of Cancer

BACKGROUND

Numerous studies have demonstrated the presence of microRNA-124 abnormalities involving gene expression, methylation, and single nucleotide polymorphism (SNP) in multiple and diverse cancers, but the prognostic value of these abnormalities in cancer remains inconclusive.

OBJECTIVE

The aim of this study is to determine the prognostic value of miR-124 in cancer.

METHODS

We scrutinized the electronic databases and estimate the association between miR-124 expression, methylation and single nucleotide polymorphisms (SNPs), and prognosis in cancers. The pooled hazard ratios with 95% confidence intervals (CIs) for overall survival (OS), and disease-free survival/recurrence-free survival (RFS)/progression-free survival (PFS) were calculated to estimate the effects of miR-124 expression, methylation, and SNPs on cancer prognosis. The Quality in Prognosis Studies and Newcastle-Ottawa Scale were utilized to assess the quality of included studies.

RESULTS

A total of 20 studies involving 3,574 participants were analyzed in evidence synthesis. Our findings showed that the low expression of miR-124 was significantly associated with poor OS (HR = 2.37, 95% CI: 1.91-2.94, P = 0.00; HR = 3.10, 95% CI: 2.04-4.70, P = 0.00) and PFS/RFS (HR = 2.21, 95% CI: 1.50-3.26, P = 0.00; HR = 2.12, 95% CI: 1.20-3.74, P = 0.00). The hyper-methylation of miR-124 was associated with poor OS (HR = 2.09, 95% CI: 1.48-2.95, P = 0.00) and PFS (HR = 3.70, 95% CI: 1.72-7.97, P = 0.00) (Table 3). The patients carrying with Allele C of miR-124 rs5315649 had a worse OS (HR = 1.50, 95% CI: 1.09-2.07, P = 0.00) and PFS (HR = 1.67, 95% CI: 1.20-2.33, P = 0.00) than the carriers with Allele G.

CONCLUSION

The low expression and hyper-methylation of miR-124 was strongly associated with poor prognosis, and genetic variations of miR-124 rs531564 affected prognosis in cancer patients.

Validation of microRNA pathway polymorphisms in esophageal adenocarcinoma survival

Polymorphisms in miRNA and miRNA pathway genes have been previously associated with cancer risk and outcome, but have not been studied in esophageal adenocarcinoma outcomes. Here, we evaluate candidate miRNA pathway polymorphisms in esophageal adenocarcinoma prognosis and attempt to validate them in an independent cohort of esophageal adenocarcinoma patients. Among 231 esophageal adenocarcinoma patients of all stages/treatment plans, 38 candidate genetic polymorphisms (17 biogenesis, 9 miRNA targets, 5 pri-miRNA, 7 pre-miRNA) were genotyped and analyzed. Cox proportional hazard models adjusted for sociodemographic and clinicopathological covariates helped assess the association of genetic polymorphisms with overall survival (OS) and progression-free survival (PFS). Significantly associated polymorphisms were then evaluated in an independent cohort of 137 esophageal adenocarcinoma patients. Among the 231 discovery cohort patients, 86% were male, median diagnosis age was 64 years, 34% were metastatic at diagnosis, and median OS and PFS were 20 and 12 months, respectively. GEMIN3 rs197412 (aHR = 1.37, 95%CI: [1.04-1.80]; P = 0.02), hsa-mir-124-1 rs531564 (aHR = 0.60, 95% CI: [0.53-0.90]; P = 0.05), and KIAA0423 rs1053667 (aHR = 0.51, 95% CI: [0.28-0.96]; P = 0.04) were found associated with OS. Furthermore, GEMIN3 rs197412 (aHR = 1.33, 95% CI: [1.03-1.74]; P = 0.03) and KRT81 rs3660 (aHR = 1.29, 95% CI: [1.01-1.64]; P = 0.04) were found associated with PFS. Although none of these polymorphisms were significant in the second cohort, hsa-mir-124-1 rs531564 and KIAA0423 rs1053667 had trends in the same direction; when both cohorts were combined together, GEMIN3 rs197412, hsa-mir-124-1 rs531564, and KIAA0423 rs1053667 remained significantly associated with OS. We demonstrate the association of multiple miRNA pathway polymorphisms with esophageal adenocarcinoma prognosis in a discovery cohort of patients, which did not validate in a separate cohort but had consistent associations in the pooled cohort. Larger studies are required to confirm/validate the prognostic value of these polymorphisms in esophageal adenocarcinoma.