Associations between promoter polymorphism -106A/G of interleukin-11 receptor alpha and papillary thyroid cancer in Korean population

Genetic signature of differentiated thyroid carcinoma susceptibility: a machine learning approach

To identify a peculiar genetic combination predisposing to differentiated thyroid carcinoma (DTC), we selected a set of single nucleotide polymorphisms (SNPs) associated with DTC risk, considering polygenic risk score (PRS), Bayesian statistics and a machine learning (ML) classifier to describe cases and controls in three different datasets. Dataset 1 (649 DTC, 431 controls) has been previously genotyped in a genome-wide association study (GWAS) on Italian DTC. Dataset 2 (234 DTC, 101 controls) and dataset 3 (404 DTC, 392 controls) were genotyped. Associations of 171 SNPs reported to predispose to DTC in candidate studies were extracted from the GWAS of dataset 1, followed by replication of SNPs associated with DTC risk (P < 0.05) in dataset 2. The reliability of the identified SNPs was confirmed by PRS and Bayesian statistics after merging the three datasets. SNPs were used to describe the case/control state of individuals by ML classifier. Starting from 171 SNPs associated with DTC, 15 were positive in both datasets 1 and 2. Using these markers, PRS revealed that individuals in the fifth quintile had a seven-fold increased risk of DTC than those in the first. Bayesian inference confirmed that the selected 15 SNPs differentiate cases from controls. Results were corroborated by ML, finding a maximum AUC of about 0.7. A restricted selection of only 15 DTC-associated SNPs is able to describe the inner genetic structure of Italian individuals, and ML allows a fair prediction of case or control status based solely on the individual genetic background.

A Comprehensive Meta-analysis of Case-Control Association Studies to Evaluate Polymorphisms Associated with the Risk of Differentiated Thyroid Carcinoma

BACKGROUND

Linkage analyses and association studies suggested that inherited genetic variations play a role in the development of differentiated thyroid carcinoma (DTC).

METHODS

We combined the results from a genome-wide association study (GWAS) performed by our group and from published studies on DTC. With a first approach, we evaluated whether a SNP published as associated with the risk of DTC could replicate in our GWAS (using FDR as adjustment for multiple comparisons). With the second approach, meta-analyses were performed between literature and GWAS when both sources suggested an association, increasing the statistical power of the analysis.

RESULTS

rs1799814 (CYP1A1), rs1121980 (FTO), and 3 SNPs within 9q22 (rs965513, rs7048394, and rs894673) replicated the associations described in the literature. In addition, the meta-analyses between literature and GWAS revealed 10 more SNPs within 9q22, six within FTO, two within SOD1, and single variations within HUS1, WDR3, UGT2B7, ALOX12, TICAM1, ATG16L1, HDAC4, PIK3CA, SULF1, IL11RA, VEGFA, and 1p31.3, 2q35, 8p12, and 14q13.

CONCLUSION

This analysis confirmed several published risk loci that could be involved in DTC predisposition.

IMPACT

These findings provide evidence for the role of germline variants in DTC etiology and are consistent with a polygenic model of the disease. Cancer Epidemiol Biomarkers Prev; 25(4); 700-13. ©2016 AACR.

Association Study of FOS-Like Antigen-2 Promoter Polymorphisms With Papillary Thyroid Cancer in Korean Population

Objectives

FOS-like antigen-2 (FOSL-2), a member of the FOS gene family, encode leucine zipper proteins that can heterodimerize with proteins of Jun family. Thus, activating protein (AP)-1 transcription factor is formed, has a crucial role in proliferation, differentiation and apoptosis of normal tissue as well as oncogenic transformation and progression. We performed an association study of single nucleotide polymorphisms (SNPs) in the FOSL-2 with papillary thyroid cancer (PTC). We also estimated the relationships between the SNPs and the clinicopathologic characteristics of PTC.

Methods

One promoter SNPs (rs925255) of FOSL-2 gene were genotyped with direct sequencing method in 94 PTC and 213 controls. PTC patients were dichotomized and compared with respect to clinical parameters of PTC. Genetic data were analyzed using Helixtree, SNPAnalyzer, SNPStats. Multivariate logistic regression analysis was fulfilled to evaluate the genetic effect with adjustment for age and sex.

Results

SNP (rs925255) in FOSL-2 showed a significant association (codominant 1 model [G/G vs. A/G]: odds ratio [OR], 0.531, 95% confidence interval [CI], 0.293 to 0.96, P=0.036; dominant model: OR, 0.50, 95% CI, 0.28 to 0.89, P=0.015) with PTC. The frequency of allele G in rs925255 was also significantly associated with PTC (OR, 0.59; 95% CI, 0.34 to 0.91; P=0.02). But we fail to prove significant association between this polymorphism (rs925255) and clinico-pathological parameters.

Conclusion

Our findings suggest that the rs925255 SNP and its allele G show significant association with the PTC in Korean population.

Interleukin 22 polymorphisms and papillary thyroid cancer

BACKGROUND

IL22RA1 (Interleukin 22 receptor-alpha 1), a member of the class II cytokine receptor family, mediates diverse biologic activities and appears to be important in pathogen defense, wound healing, and tissue reorganization. Polymorphisms in genes encoding inflammatory cytokines are associated with increased cancer risk.

AIM

The aim of this study was to evaluate the association between the single nucleotide polymorphisms (SNP) in the IL22 and IL22RA1 and papillary thyroid cancer (PTC), and to assess the relationship between the SNP in the IL22 and IL22RA1 and the clinical parameters of PTC.

MATERIAL AND METHODS

Study enrolled experimental group of 94 PTC patients and 213 controls. PTC patients were grouped and compared for clinical PTC parameters. One promoter SNP of IL22, -429C/T (rs2227485), and one SNP of IL22RA1, Arg518Gly (rs3795299) were analyzed using direct sequencing. Genetic data were analyzed using Helixtree, SNPAnalyzer Pro, SNPStats, and Haploview.

RESULTS

A SNP in IL22 (rs2227485) was significantly associated with PTC (codominant2 model [C/C vs T/T], odds ratio (OR) 2.39, 95% confidence interval (CI) 1.21-4.71, p=0.012; dominant model, OR 1.89, 95% CI 1.08-3.31, p=0.022). The allele T frequency of rs2227485 in IL22 was also associated with PTC (OR 1.59, 95% CI 1.13-2.25, p=0.009). According to clinical parameters, rs2227485 of IL22 was associated with number of cancers (dominant model, OR 3.03, 95% CI 1.02-9.01, p=0.035). By haplotype analysis, TG was associated with PTC (codominant model, OR 1.52, 95% CI 1.07-2.16, p=0.019; dominant model, OR 1.91, 95% CI 1.13- 3.24, p=0.015). Genotype and allele analysis of rs3795299 in IL22RA1 showed no significant differences between PTC patients and controls.

CONCLUSION

The rs2227485 SNP in IL22 might be associated with the risk and the multifocality of PTC.

Interleukin-1 beta polymorphisms are associated with lymph node metastasis in Korean patients with papillary thyroid carcinoma

In this study, we investigated whether single nucleotide polymorphisms (SNPs) of the interleukin-1 beta (IL-1B) were associated with papillary thyroid carcinoma (PTC). We also assessed the relationships between IL-1B SNPs and the clinicopathologic characteristics of PTC patients. Ninety-three PTC patients and 324 controls were recruited. The patients with PTC were dichotomized and compared with respect to the clinicopathologic characteristics of PTC. Seven SNPs in the IL-1B gene were selected and genotyped using direct sequencing. Four SNPs (rs1143627, rs3136558, rs1143633, and rs1143643) in the IL-1B gene were significantly associated with PTC (p < 0.05). In clinicopathologic features, 3 SNPs (rs1143630, rs1143633, and rs1143643) showed a strong relationship with lymph node metastasis of PTC. The genotype and allele frequencies of rs1143630 and rs1143643 remained significantly associated with lymph node metastasis after Bonferroni correction for multiple testing. In haplotype analysis, two linkage disequilibrium blocks (block 1 consisted of rs1143627, rs3917356, and rs1143630; block 2 consisted of rs1143633 and rs1143643) also revealed significant associations with lymph node metastasis. Our results suggest that IL-1B polymorphisms may be associated with the risk of PTC in the Korean population. Especially, IL-1B polymorphisms might be a predictive factor for lymph node metastasis of PTC patients.

A Polymorphism (rs1801018, Thr7Thr) of BCL2 is Associated with Papillary Thyroid Cancer in Korean Population

Objectives

Among the apoptosis signals, B-cell CLL/lymphoma 2 (BCL2) is a well-known regulator of apoptosis with anti-apoptotic properties. We investigated here whether single nucleotide polymorphisms (SNPs) of the BCL2 were associated with host susceptibility of papillary thyroid cancer (PTC) occurrence and clinicopathologic parameters.

Methods

Ninety-two PTC patients and 222 control subjects were recruited. One promoter SNP (rs2279115, -938A/C) and one synonymous SNP (rs1801018, Thr7Thr) in the BCL2 gene were selected and genotyped using direct sequencing. Multiple logistic regression models were performed to evaluate odds ratios, 95% confidence intervals, and P-values.

Results

rs1801018 of the BCL2 gene was not associated with the development of PTC. In the clinicopathologic features, rs1801018 SNP was associated with the number and location. The G allele frequency of rs1801018 in PTC patients with multifocality (13.3%) was about four-fold higher than that in PTC patients with unifocality (3.4%). The G allele frequency of rs1801018 in PTC patients with both lobes (15.4%) was increased by about five-fold, compared to PTC patients with one lobe (3.2%).

Conclusion

The results suggest that synonymous SNP rs1801018 and the G allele of the BCL2 gene may be associated with the multifocality and bilaterality of PTC in Korean population.