Single Nucleotide Polymorphisms Rs2910164 Research Articles

Prognostic Stratification of Acute Myeloid Leukemia and Mylodysplastic Syndrome Patients on the Basis of Genetic Variations

Acute Myeloid Leukemia (AML) is a heterogeneous disorder characterized by the accumulation of acquired genetic alterations in hematopoietic progenitor cells that alter normal mechanisms of self-renewal, and differentiation. Once a rapidly and life fatal disease, the prognosis of AML has improved in the past decades. Recurrent cytogenetic and molecular genetic abnormalities are proven to be of diagnostic and therapeutic value. All cases of AML cannot be explained by the low resolution cytogenetic techniques or biased molecular genetic approaches. Recent advancements in high resolution genomic techniques has allowed detection of additional submicroscopic abnormalities in the AML genome. This study set out to determine the copy number alterations (CNAs) in bone marrow and oral epithelial samples from 08 AML cases by whole genome Single Nucleotide Polymorphism (SNP) genotyping using Illumina OmniExpress-12 v1-1 Bead Chips containing 700,000 SNPs. Additionally, using a targeted approach with TaqMan real-time quantitative polymerase reaction (RT-qPCR), we tested for previously reported SNP (rs11554137) in a group of 47 AML patients.The group of patients comprised of AML-M1 (n=1), M2 (n=5), M4 (n=1) and M5 (n=1), SNP genotyping data analysis identified 13 acquired CNAs in 05 out 08 AML patients. Deletions were more common than amplifications. These CNAs were distributed across all FAB subtypes except AML-M3.AML-M4 subtypes were found to have more CNAs compared to other subtypes. Notably, in three AML-M2 cases4q24 microdeletion was identified. This region spans TET2 gene which is has been shown to cause microdeletions and copy-neutral loss of heterozygosity (LOH) in a patient with diverse myeloid malignancies. Oral epithelial cells from the same patients were negative for the CNAs. Moreover, the 47 patients tested for known SNPs, 4 patients (8.5%) were found positive for rs11554137. SNP (rs11554137) has been reported to be of prognostic importance for overall survival (OS).The results from this study shows CNAs in regions implicated in myeloid malignancies. The use of high-resolution genomic array identified significant number of CNAs and SNPs which were not previously documented in AML patients in Pakistani population. Further studies dissecting out their role in AML pathogenesis are required. DisclosuresNo relevant conflicts of interest to declare.

FREQUENCY OF THE MDR1 GENE POLYMORPHISM RS1045642 (C3435T) IN HCV-HIV CO-INFECTED PATIENTS.

Due to the high prevalence of co-infection by hepatitis C virus (HCV) and human immunodeficiency virus (HIV) and the severity of these infections, the understanding of the biological mechanisms involved in these processes, including viral behavior and host genetic profile, is of great importance for patient treatment and for public health policies.Some single nucleotide polymorphisms (SNPs) in the human genome, such as the SNP rs1045642 (C3435T) in the MDR1 gene, have been reported to be associated to the sustained virological response (SVR) to HCV treatment in HCV-HIV co-infected patients. The present study analyzes the MDR1 gene C3435T polymorphism in HCV-HIV co-infected patients. A total of 99 HCV-HIV patients were included in the study. The DNA was extracted from blood samples, and the SNP rs1045642 was assessed by Real Time PCR (qPCR). Risk factors for acquiring the virus and the SVR after HCV treatment with pegylated interferon-alpha and ribavirin were also analyzed. Among the patients, 54 (54.5%) were male and 45 (45.5%) were female. The average age was 46.1±9.8 years. The SVR after HCV treatment was 40%. The frequencies of MDR1 genotypes CC, CT and TT were 28.3%, 47.5% and 24.2%, respectively. Allele frequencies were 52% for the C allele and 48% for the T allele. No association was found for SNP rs1045642 (C3435T) regarding response to treatment (P=0.308). - In this study, the C3435T polymorphism in the MDR1 gene appears not to be associated with SVR in HCV-HIV co-infected individuals.

Significance of Polymorphism and Expression of miR-146a and NFkB1 Genetic Variants in Patients with Rheumatoid Arthritis.

MicroRNA-146a (miR-146a) has been shown to play an important role in the regulation of inflammatory innate immune responses, and found to be differentially expressed in rheumatoid arthritis (RA). Through NF-κB pathway, this molecule is able to stimulate the release of pro-inflammatory cytokines such as TNF-α, IL-1β, and IL-17. It has been also suggested that single-nucleotide polymorphisms (SNPs) in miRNA sequences may alter miRNA expression and that miR-146a rs2910164 SNP may contribute to RA development. These observations prompted us to analyze the potential associations between the miR-146a-3p (rs2910164, G > C) and NFkB1 (rs28362491, ins/del ATTG) polymorphisms and miR-146a-5p expression in patients’ sera in relation to clinical outcome of the treatment as well as predisposition to RA. Genotyping was performed in 111 patients and 130 healthy individuals while 16 controls and 13 RA patients (before and after three months of therapy with TNF-α inhibitors (TNFi)) were studied for the circulating miR-146a-5p serum expression level. Patients carrying the NFkB1 ins/ins genotype were characterized by worse response to TNFi treatment (p = 0.023). In patients, before TNFi therapy, expression levels of miR-146a-5p were less (0.422 ± 0.171) as compared to those detected after three months of treatment (1.809 ± 0.658, p = 0.033) and observed for healthy controls (5.302 ± 2.112, p = 0.048). Moreover, patients with higher circulating miR-146a-5p levels after three months of TNFi administration were more frequently carrying the rs2910164-C allele (p = 0.032). These results support the hypothesis that miR-146a might be involved in pathogenesis of RA and imply that miR-146a-3p polymorphism may be associated with miR-146a-5p levels in serum after anti-TNF-α treatment.

Association of vitamin-D-related genetic variations and treatment response to pegylated interferon in patients with chronic hepatitis B.

Vitamin D, a potent immune-modulator, has been linked to the pathogenesis of chronic hepatitis B (CHB). This study was aimed at investigating the association between single nucleotide polymorphisms (SNPs) in vitamin-D-related genes and treatment response to pegylated interferon (PEG-IFN) in patients with CHB. A total of 275 Thai patients (122 hepatitis B e antigen [HBeAg]-positive and 153 HBeAg-negative CHB) treated with 48-week PEG-IFN were recruited. Virological response (VR) at 48 weeks post-treatment was defined as HBeAg seroconversion plus HBV DNA <2,000 IU/ml for HBeAg-positive CHB and HBV DNA <2,000 IU/ml for HBeAg-negative CHB. The SNPs VDR (rs2228570), DBP (rs7041) and CYP27B1 (rs4646536) were analysed. The distribution of TT, CT and CC genotypes of rs4646536 in this cohort was 21.8%, 46.2% and 32.0%, respectively. There was no difference in its distribution according to HBeAg status. In HBeAg-positive CHB, patients with TT genotype, compared with non-TT genotype, achieved higher VR (53.3% versus 31.5%; P=0.032) and hepatitis B surface antigen (HBsAg) clearance (20.0% versus 5.4%; P=0.016). In HBeAg-negative CHB, the corresponding figures were 60.0% versus 30.9% (P=0.003) and 16.7% versus 5.7% (P=0.045), respectively. Patients with TT genotype had more rapid HBsAg decline than those with non-TT genotype. However, SNPs rs2228570 and rs7041were not associated with VR and HBsAg clearance. Logistic regression analysis demonstrated that SNP rs4646536 and baseline HBsAg level were independent predictors of VR in both HBeAg-positive and HBeAg-negative CHB. Our data suggest that SNP rs4646536 in the CYP27B1 gene is a predictive factor of response to PEG-IFN therapy in Thai patients with CHB.

Association of Long Non-Coding RNA HOTAIR Polymorphisms with Cervical Cancer Risk in a Chinese Population.

Long non-coding RNAs (lncRNAs), HOTAIR has been reported to be upregulated in cervical cancer development and progression. However, SNPs (single nucleotide polymorphisms) in the lncRNAs and their associations with cervical cancer susceptibility have not been reported. In the current study, we hypothesized that SNPs within the lncRNA HOTAIR may influence the risk of cervical cancer. We performed a case-control study including 510 cervical cancer patients (cases) and 713 cancer-free individuals (controls) to investigate the association between three haplotype-tagging SNPs (rs920778, rs1899663 and rs4759314) in the lncRNA HOTAIR and the risk of cervical cancer. We found a strong association between the SNP rs920778 in the intronic enhancer of the HOTAIR and cervical cancer (P<10−4). Moreover, the cervical cancer patients with homozygous TT genotype were significantly associated with tumor-node-metastasis (TNM) stage. In vitro assays with allele-specific reporter constructs indicated that the reporter constructs bearing rs920778T allele conferred elevated reporter gene transcriptional activity when compared to the reporter constructs containing rs920778C allele. Furthermore, HOTAIR expression was higher in cervical cancer tissues than that in corresponding normal tissues, and the high expression was associated with the risk-associated allele T. In summary, our studies provide strong functional evidence that functional SNP rs920778 regulates HOTAIR expression, and may ultimately influence the predisposition for cervical cancer.

The rs6983267 SNP and long non-coding RNA CARLo-5 are associated with endometrial carcinoma.

The single nucleotide polymorphism (SNP) rs6983267 and cancer-associated region long non-coding RNA (CARLo-5) are associated with various human cancers. This study aimed to investigate the expression of CARLo-5 in endometrial carcinoma (EC) and its relationship with clinicopathological features and patient survival. The association of the rs6983267 SNP with EC risk and its involvement in the regulation of CARLo-5 expression in EC were investigated. The rs6983267 SNP was genotyped by polymerase chain reaction (PCR) and ligase detection reaction in 543 EC patients and 584 controls. The expression of CARLo-5 in 108 EC tissues and 66 normal endometrial tissues (NETs) was determined using quantitative real-time PCR. The genotype and allele distributions of the rs6983267 SNP differed significantly between patients and controls. There was a significant correlation between the rs6983267 genotypes and lymph node metastasis of EC patients (P = 0.026). CARLo-5 expression was significantly higher in EC tissues than in NETs (P < 0.001) and significantly associated with FIGO stage (P = 0.029) and lymph node metastasis (P = 0.030). Patients with high CARLo-5 expression had significantly shorter overall survival than those with low CARLo-5 expression (P = 0.003). The rs6983267 genotype was significantly correlated with CARLo-5 expression (P < 0.05). In conclusion, CARLo-5 was identified as a pro-oncogenic lncRNA that may play an important role in EC progression and represent a prognostic marker for EC. The expression of CARLo-5 was significantly correlated with the rs6983267 genotype associated with increased susceptibility to EC. Environ. Mol. Mutagen. 57:508-515, 2016. © 2016 Wiley Periodicals, Inc.

Effects of common polymorphisms in miR-146a and miR-196a2 on lung cancer susceptibility: a meta-analysis.

MicroRNAs (miRNAs) may play an important role in organ development, cell differentiation, apoptosis, proliferation, cell growth regulation and act as tumor suppressor genes or proto-oncogenes. Single nucleotide polymorphisms (SNPs) in miRNAs are considered to be genetic factors to influence the susceptibility to lung cancer (LC). Rs2910164 in miR-146a and rs11614913 in miR-196a2 are shown to be associated with increased/decreased LC risk. The aim of this meta-analysis was to systematically summarize the possible association. The relevant articles were retrieved from several important databases. Studies were selected using specific inclusion and exclusion criteria. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of association between miRNA polymorphism and susceptibility to LC. All analyses were performed using the Stata software. Seven studies were included in this meta-analysis. There were 3,225 cases and 3,268 controls for SNP rs2910164 and 2,794 cases and 2,840 controls for SNP rs11614913. The significant associations between SNP rs2910164 and LC risk were observed (CC vs. GG: OR =1.30, 95% CI: 1.13-1.50; CC + GC vs. GG: OR =1.15, 95% CI: 1.02-1.29; CC vs. GC + GG: OR =1.27, 95% CI: 1.13-1.42; C vs. G: OR =1.15, 95% CI: 1.08-1.24). SNP rs11614913 was found to be associated with LC risk in most genetic models (TC vs. TT: OR =1.16, 95% CI: 1.02-1.32; CC vs. TT: OR =1.24, 95% CI: 1.06-1.44; CC + TC vs. TT: OR =1.19, 95% CI: 1.06-1.34; C vs. T: OR =1.11, 95% CI: 1.03-1.20). In the subgroup analysis by ethnicity, genotyping method and control characteristics, significantly affected LC risks were also suggested. The rs2910164 in miR-146a and the rs11614913 in miR-196a2 are likely to be associated with LC risks.

Association of the MicroRNA-146a SNP rs2910164 with Ischemic Stroke Incidence and Prognosis in a Chinese Population.

We conducted a case-control study investigating the association between the single-nucleotide polymorphism rs2910164 in microRNA (miR)-146a and the risk and prognosis of stroke. We recruited a total of 1139 ischemic stroke patients and 1585 sex- and age-matched control subjects. After a median follow-up period of 4.5 years, 1071 of these ischemic stroke patients were then recruited for a prospective study. Our study revealed that rs2910164 was not associated with ischemic stroke incidence (odds ratio = 1.00; 95% confidence interval (CI) = 0.80–1.24; p = 0.985) by multivariate logistic regression. Meta-analysis of our case-control study and three others on Asian populations also suggested that there was no relationship between rs2910164 and ischemic stroke incidence. The significance of differences in long-term outcomes was examined by the log-rank test of the respective comparison groups. The prospective study showed that rs2910164 led to a 1.56-fold increased risk of stroke recurrence (hazard ratio (HR) = 1.56; 95% CI = 1.10–2.20; p = 0.013) and a 2.13-fold increased risk of death caused by cardiovascular disease or stroke (Csdeath) (HR = 2.13; 95% CI = 1.31–3.46; p = 0.002). The independent association of rs2910164 with stroke prognosis was evaluated using Cox regression models. Therefore, rs2910164 appears to be a strong predictor of stroke prognosis but not of stroke incidence in Asian populations.

Association between the three functional miR-146a single-nucleotide polymorphisms, rs2910164, rs57095329, and rs2431697, and autoimmune disease susceptibility: A meta-analysis

Studies suggest associations between the miR-146a single nucleotide polymorphisms (SNPs) and susceptibility to autoimmune diseases. However, the results are inconsistent and inconclusive. Therefore, the aim of this study was to arrive at a conclusion about the association between the three functional miR-146a SNPs and autoimmune disease risk. Studies were identified through PubMed/MEDLINE searches for studies published up to January 2016 using as keywords rs2910164, rs57095329, rs2431697, and miR-146a polymorphisms. Thirty studies were included in the meta-analysis. The SNP rs2910164 G > C was found to be associated with increased risk of multiple sclerosis (CC + CG versus GG, OR = 1.25, 95% CI: 1.01–1.55), with decreased risks of psoriasis (C versus G, OR = 0.81, 95% CI: 0.69–0.96; CC versus GC + GG, OR = 0.73, 95% CI: 0.56–0.94), Behcet’s disease (CC versus GC + GG, OR = 0.60, 95% CI: 0.50–0.73), asthma (C versus G, OR = 0.80, 95% CI: 0.69–0.93; CC versus GC + GG, OR = 0.65, 95% CI: 0.48–0.86), and uveitis (CC + CG versus GG, OR = 0.61, 95% CI: 0.49–0.77). The SNP rs2431697 C > T was found to be associated with an increased risk of SLE (T versus C, OR = 1.26, 95% CI: 1.15–1.38; TC + TT versus CC, OR = 1.28, 95% CI: 1.03–1.58; TT versus TC + CC, OR = 1.40, 95% CI: 1.21–1.62). The SNP rs57095329 A > G was found to be associated with an increased risk of SLE (G versus C, OR = 1.25, 95% CI: 1.17–1.35). The miR-146a SNPs rs2910164, rs57095329, rs2431697 are associated with susceptibility to certain autoimmune diseases. However, for other autoimmune diseases, they may be protective or insignificant.

Genetic variant of miR-146a rs2910164 C>G and gastric cancer susceptibility.

The single nucleotide polymorphism (SNP) rs2910164 G>C within miR-146a has been reported that is associated with the increased risk of gastric cancer (GCa). However, the results are inconclusive, espicially among Asian populations, which probably due to small sample size in each single study. To validate this association and get a more precise estimation, we conducted a large GCa study including 1,125 cases and 1,196 controls in an eastern Chinese population. Our results showed that this SNP was not associated with GCa risk in either of the three genetic models [co-dominant model: CG vs. CC, odds ratio (OR) = 0.99, 95% confidence interval (95%CI): 0.83-1.19; GG vs. CC, OR = 1.03, 95%CI: 0.81-1.32; dominant model: (CG+GG) vs. CC, OR = 1.00, 95%CI = 0.84-1.19; recessive model: GG vs. (CG+CC), OR = 1.04, 95%CI = 0.83-1.29]. Stratified analysis by age, gender, smoking status, drinking status, or tumor location confirmed this non-significant association. In summary, these results suggest that the miR-146a SNP rs2910164 may not be a risk factor for GCa in this Chinese population. Larger and well-designed, preferably prospective studies are needed to further confirm our findings.

A single-nucleotide polymorphism in the MicroRNA-146a gene is associated with diabetic nephropathy and sight-threatening diabetic retinopathy in Caucasian patients.

This study aimed to investigate whether the single-nucleotide polymorphism (SNP) rs2910164 residing within microRNA-146a (miR-146a) is associated with diabetic microvascular complications diabetic nephropathy (DN), proliferative diabetic retinopathy (PDR) or diabetic macular oedema (DME) in either Caucasian patients with type 1 (T1DM) or type 2 (T2DM) diabetes mellitus. Caucasian patients with T1DM (n=733) or T2DM (n=2215) were recruited from ophthalmology, renal and endocrine clinics in Australia and the UK. Patients with T2DM were required to have diabetes mellitus (DM) for at least 5years and be on treatment with oral hypoglycaemic drugs or insulin. In total, 890 participants had DN (168 with T1DM and 722 with T2DM), 731 had PDR (251 with T1DM and 480 with T2DM) and 1026 had DME (170 with T1DM and 856 with T2DM). Participants were genotyped for SNP rs2910164 in miR-146a. Analyses investigating association were adjusted for relevant clinical covariates including age, sex, DM duration, HbA1c and hypertension. A significant association was found between the C allele of rs2910164 and DN in the T1DM group (OR 1.93; CI 1.23-3.03; P=0.004), but no association found in the T2DM group (OR 1.05; CI 0.83-1.32; P=0.691). In the subset of T2DM patients, the C allele was specifically associated with DME (OR 1.25; CI 1.03-1.53; P=0.025). No association with DME was found in the T1DM group (OR 0.87; CI 0.54-1.42); P=0.583), or with PDR for either type of DM. Rs2910164 is significantly associated with microvascular complications DN in patients with T1DM and DME in patients with T2DM.

Distribution of polymorphic variants of the GSTP1 gene involved in biotransformation of xenobiotics in Tundra Nenets and Nganasans in comparison to Russians

The first study on the frequencies of polymorphic variants of the GSTP1 gene encoding glutathione-S-transferase P1 in Tundra Nenets and Nganasan populations was performed. The subject of the study was the single nucleotide polymorphisms rs1695 (Ile105Val substitution in the protein sequence) and rs1138272 (Ala114Val substitution) that had previously been shown to be associated with cancer and other multifactorial diseases. The data for Tundra Nenets of the Yamalo-Nenets autonomous okrug, Nganasans of the Taimyr Peninsula, and Russian residents of the Northern Siberia were compared. The frequencies of the mutant 105Val and 114Val variants were 10.8% and 0.8% in Nganasans, 23.7% and 4.8% in Nenets, and 35.8% and 9.1% in Russian population samples, respectively. The differences within all pairs of populations were significant for each allele. These differences may characterize the population-level susceptibility to cancer and other multifactorial diseases.

Abstract P3-07-40: Pharmacogenetic study of exemestane and everolimus in metastatic breast cancer patients progressing on prior non-steroidal aromatase inhibitors

Abstract Background: Activation of the mTOR pathway has been observed in patients (pts) with metastatic breast cancer (MBC) progressing on endocrine therapy. BOLERO-2 trial demonstrated a significant increase in progression free survival (PFS) obtained with everolimus (EVE) and exemestane (EXE) versus EXE alone in pts refractory to a prior non-steroidal aromatase inhibitors (NSAI). However, there is large interindividual variability in toxicity and efficacy profiles of EXE-EVE treatment. Single Nucleotide Polymorphisms (SNPs) have been proposed to explain some of these differences. The objective of this study was to perform a pharmacogenetic analysis to identify SNPs associated with EVE toxicity and activity. Methods: This is a prospective unicentric clinical trial for postmenopausal pts with hormone receptor-positive, HER2 negative, MBC progressing on prior NSAI, treated with EXE-EVE. Blood samples were obtained from all pts, and 12 SNPs in key genes involved in EXE pharmacokinetics (ABCB1, CYP2C8, CYP3A4, CYP3A5) and pharmacodynamics (AKT1, AKT2, FGFR4, PHLPP2, PIK3R1, RAPTOR) were genotyped. EVE pharmacokinetics data was available for a subset of 37 pts. The association between the SNPs and EVE pharmacokinetic parameters were analyzed using U-Mann-Whitney test. A selection of clinically relevant toxicities (non-infectious pneumonitis (NIP), mucositis, hyperglycemia and hematological) was analyzed using binary logistic regression. Cox regression was used to analyze the association of SNPs with time to treatment modifications (reduction or interruption) due to toxicity, PFS and OS. Results: 90 patients with median age of 62 yrs were included. At data cut off, a total of 77 pts had discontinued treatment. Major reasons for discontinuation were: disease progression (80%), adverse events (17%) and death (2%). Number of prior chemotherapy lines: 0; 50%, 1;18%, 2;10%, ≥3; 22%. 76% of pts experienced at least one adverse event related to EVE. CYP3A4 rs35599367 (CYP3A4*22 allele) heterozygous pts had higher EVE concentration in blood compared to wild type pts (P=0.019), in agreement with previous data. Regarding EVE toxicities, ABCB1 SNP rs1045642 showed a higher risk of mucositis (HR=2.3, 95%CI=1.1-4.8, P=0.031; multivariable analysis), and PIK3R1 rs10515074 variant was inversely associated with hyperglycemia (HR=0.24, 95%CI=0.1-0.8, P=0.016; multivariable analysis). RAPTOR rs9906827 protected for NIP (HR=0.38, 95%CI=0.2-0.9, P=0.024; multivariable analysis). When analyzing the time to treatment modification due to any toxicity, we observed a trend for FGFR4 rs351855 and RAPTOR rs9906827 (HR=0.59, 95%CI=0.3-1.0, P=0.06 and HR=0.71, 95%CI=0.5-1.1, P=0.12; respectively, in multivariable analysis). Regarding activity, RAPTOR rs9906827 was also associated with longer PFS (dominant model HR=0.48, 95%CI=0.3-0.8, P=0.006; multivariable analysis). No SNP was significantly associated with OS. Conclusions: We found altered EVE pharmacokinetics for CYP3A4*22 carriers and protection for NIP and longer PFS for RAPTOR rs9906827. This study supports prospective trials for genetic testing prior to EXE-EVE therapy to stratify patients according to toxicity and efficacy risk profiles. Citation Format: Pascual-Martínez T, Apellániz-Ruiz M, Pernaut C, Cueto-Felgueroso C, Villalba P, Alvarez C, Manso L, Rodriguez-Antona C, Ciruelos EM. Pharmacogenetic study of exemestane and everolimus in metastatic breast cancer patients progressing on prior non-steroidal aromatase inhibitors. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-40.

Evaluation of a newly discovered breast cancer susceptibility locus at 6q25.1 in Iranian Azari-Turkish women.

Aim of the studyA recent breast cancer genome-wide association study (GWAS) identified single-nucleotide polymorphism (SNP) rs2046210 on 6q25.1 showing a strong association with breast cancer risk. Numerous association studies have been conducted to investigate the relationship between this polymorphism and breast cancer risk in various populations. There have been conflicting reports about the association of this locus with breast cancer risk in different ethnic groups. For the first time, this study has investigated the association of rs2046210 SNP with breast cancer risk in Iranian Azari-Turkish women in North West Iran.Material and methodsIn this study 192 breast cancer subjects and 186 healthy controls were genotyped using Taqman SNP genotyping assays for different SNP rs2046210 alleles.ResultsNo significant association between rs2046210 SNP alleles and the risk of breast cancer was detected in Iranian Azari-Turkish women.ConclusionsThe data suggests that rs2046210SNP does not play a role in the aetiology of breast cancer in the Iranian Azari-Turkish population, and it indicates possible genetic differences for breast cancer between different population ancestries. Our result is an important contribution to the literature about genetic susceptibility for breast cancer in Asian populations. Additional studies are required to confirm our findings.

MicroRNA variants and colorectal cancer risk: a meta-analysis.

Colorectal cancer (CRC) is a multi-factorial disease, and genetic background may contribute to its etiology. Single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) may be used as specific markers of predisposition for CRC diagnosis and prevention. In this review, we summarize and discuss recent publications evaluating the roles of miRNA SNPs in CRC. A meta-analysis was also carried out to assess the association between the five most frequently studied miRNA SNPs and CRC risk. No relationship was established between this disease and the three SNPs rs11614913, rs2910164, and rs3746444 in miR-196a-2, miR-146a, and miR-499, respectively. However, polymorphisms of miR-149 (rs2292832; CT vs TT: odds ratio [OR] = 0.816, 95% confidence interval [CI] = 0.691-0.963; CC+CT vs TT: OR = 0.834, 95%CI = 0.715-0.972) and pre-miR-27a (rs895819; GG vs AA: OR = 1.534, 95%CI = 1.148-2.049; GG+AG vs AA: OR = 1.324, 95%CI = 1.066-1.645) were found to be associated with CRC in our analysis. In conclusion, the SNPs rs2292832 in miR-149 and rs895819 in pre-miR-27a were associated with CRC susceptibility, whereas rs11614913, rs2910164, and rs3746444 in miR-196a-2, miR-146a, and miR-499, respectively, were not. Further studies should be carried out to validate these findings.

Combining Telomerase Reverse Transcriptase Genetic Variant rs2736100 with Epidemiologic Factors in the Prediction of Lung Cancer Susceptibility.

Genetic variants from a considerable number of susceptibility loci have been identified in association with cancer risk, but their interaction with epidemiologic factors in lung cancer remains to be defined. We sought to establish a forecasting model for identifying individuals with high-risk of lung cancer by combing gene single-nucleotide polymorphisms with epidemiologic factors. Genotyping and clinical data from 500 lung cancer cases and 500 controls were used for developing the logistic regression model. We found that lung cancer was associated with telomerase reverse transcriptase (TERT) rs2736100 single-nucleotide polymorphism. The TERT rs2736100 model was still significantly associated with lung cancer risk when combined with environmental and lifestyle factors, including lower education, lower BMI, COPD history, heavy cigarettes smoking, heavy cooking emission, and dietary factors (over-consumption of meat and deficiency in fish/shrimp, vegetables, dairy products, and soybean products). These data suggest that combining TERT SNP and epidemiologic factors may be a useful approach to discriminate high and low-risk individuals for lung cancer.

Effects of GSTP1 and GPX1 Polymorphisms on the Risk of Preeclampsia in Chinese Han Women

Background/Aims: Increasing evidence shows that oxidative stress plays an important part in the pathophysiological mechanisms of preeclampsia (PE). Polymorphic variants of oxidative stress-related candidate genes GST1 and GPX1 can affect the antioxidant activities of their encoded enzymes. Therefore, this study aimed to explore the associational analysis between GSTP1 and GPX1 single nucleotide polymorphisms (SNPs) and susceptibility to PE in Chinese Han women. Methods: DNA from 1130 PE patients and 1226 healthy individuals was genotyped for SNPs rs1695 in GSTP1 and rs1050450 in GPX1 using a predesigned TaqMan SNP genotyping assay. The χ2 test compared differences in genetic distributions between the two groups in a case-control study. Results: No significant differences in allelic or genotypic frequencies of GSTP1 rs1695 or GPX1 rs1050450 were detected between cases and controls (GSTP1 rs1695: χ2=1.122, p=0.571 by genotype, χ2=0.138, p=0.710, odds ratio=1.027, 95% confidence interval 0.892-1.183 by allele; GPX1 rs1050450: χ2=0.036, p=0.982 by genotype, χ2=0.002, p=0.960, odds ratio=1.005, 95% confidence interval 0.822-1.229 by allele). Moreover, no significant differences in genetic distribution were found between early/late-onset PE or mild/severe PE and control subgroups. Conclusion: Our results suggest that GSTP1 rs1695 and GPX1 rs1050450 SNPs have no effects on the risk of PE in the Chinese Han population. However, these results should be confirmed by replication in different populations.

Associations of Polymorphisms in MTHFR Gene with the Risk of Age-Related Cataract in Chinese Han Population: A Genotype-Phenotype Analysis.

Homocysteine (Hcy) is a potential risk factor for age-related cataract (ARC). Methylenetetrahydrofolate reductase (MTHFR) is the key enzyme for Hcy metabolism, and variants of MTHFR may affect MTHFR enzyme activity. This study mainly evaluated the associations between variants in MTHFR gene, plasma MTHFR enzyme activity, total Hcy (tHcy) levels and ARC risk in Chinese population. Four single nucleotide polymorphisms (SNPs) in MTHFR gene were genotyped using the high-resolution melting (HRM) method in 502 ARC patients (mean age, 70.2 [SD, 9.0], 46.0% male) and 890 healthy controls (mean age, 67.1 [SD, 11.1], 47.6% male). The plasma MTHFR activity, folic acid (FA), vitamins B12 and B6 levels were detected by enzyme-linked immunosorbent assays (ELISA). The plasma tHcy levels were measured by an automated enzymatic assay. After the Bonferroni correction, the minor allele T of SNP rs1801133 showed a significant association with an increased risk of overall ARC (OR = 1.26, P = 0.003). Consistent association was also found between SNP rs1801133 and cortical ARC risk (OR = 1.44, P = 0.003). Haplotype analyses revealed an adverse effect of the haplotype "C-A-T-C" (alleles in order of SNPs rs3737967, rs1801131, rs1801133 and rs9651118) on ARC risk (OR = 1.55, P = 0.003). Moreover, in a joint analysis of SNPs rs9651118 and rs1801133, subjects with two unfavorable genotypes had a 1.76-fold increased risk of ARC compared with the reference group, and a statistically significant dose-response trend (Ptrend = 0.001) was also observed. Further, in healthy controls and patients with cortical ARC, the allele T of SNP rs1801133 and the increasing number of unfavorable genotypes were significantly correlated with decreased MTHFR activity as well as increased tHcy levels. However, there was no significant association between FA, vitamins B12, B6 levels and MTHFR variants. Our data indicated that variants in MTHFR gene might individually and jointly influence susceptibility to ARC by affecting MTHFR enzyme activity and tHcy levels.

Evaluation of potential regulatory function of breast cancer risk locus at 6q25.1.

In a genome-wide association study conducted among Chinese women, we identified the single nucleotide polymorphism (SNP) rs2046210 at 6q25.1 for breast cancer risk. To explore a potential regulatory role for this risk locus, we measured expression levels of nine genes at the locus in breast cancer tissue and adjacent normal tissue samples obtained from 67 patients recruited in the Shanghai Breast Cancer Study. We found that rs2046210 had a statistically significant association with the expression levels of the AKAP12 and ESR1 genes in adjacent normal breast tissues. Women who carry the AA/AG risk genotypes had higher expressions of these two genes compared to those who carry G/G genotypes (P = 0.02 and 0.04 for the AKAP12 and ESR1, respectively). However, no significant differences of SNP rs2046210 with gene expression levels were found in tumor tissues. In The Cancer Genome Atlas samples, the AA/AG risk genotypes of SNP rs2046210 were associated with a significantly higher expression level of the AKAP12 gene and a lower level of the ESR1 gene in tumor tissue. Functional analysis using ENCODE data revealed that SNP rs7763637, which is in strong linkage disequilibrium with SNP rs2046210, is likely a potential functional variant, regulating the AKAP12 gene. Taken together, these results from our study suggest that the association between the 6q25.1 locus and breast cancer risk may be mediated through SNPs that regulate expressions of the AKAP12 gene.

Recipient Dendritic Cells Are Regulated By MiR-146a during Acute GvHD

Acute Graft-versus-host disease (GvHD) is a major immunological complication following allogeneic hematopoietic cell transplantation (allo-HCT) occurring in 30-40% of patients. Although immunosuppression with corticosteroids serves as standard first-line therapy in acute GvHD, sustained responses are achieved in less than 50% of patients. Therefore, the identification of risk factors and a better understanding of the molecular mechanisms underlying the disease are indispensable to develop novel therapeutic strategies. MicroRNAs control various key biological processes, including innate and adaptive immune responses. In particular, microRNA-146a (miR-146a) is emerging as a central regulator of innate immune cell signaling.Here we found that a G/C single nucleotide polymorphism (SNP) within the pre-miR-146a gene, which reduces the amount of miR-146a produced from the C allele, was strongly associated with the risk to develop severe acute GvHD. Patients with the rs2910164 CC genotype had a significantly higher risk to develop acute GvHD grade III-IV than all other allo-HCT recipients (P =0.002) as well as an overall increased histopathological GvHD severity. In order to functionally dissect the role of miR-146a in recipient cells during GvHD, we used gene targeted (miR-146a-/-) mice and a major histocompatibility complex (MHC)-mismatched experimental model for acute GvHD. MiR-146a deficiency of the recipient mice resulted in increased GvHD severity, elevated serum levels of pro-inflammatory cytokines and accelerated mortality compared to wild type (WT) recipients after allo-HCT. Chimeric mice with a lack of miR-146a specifically in the hematopoietic system showed an even more distinct disease exacerbation, whereas miR-146a deficiency only in non-hematopoietic recipient cells did not affect GvHD severity. Moreover, co-transplantation of recipient type miR-146a-/-dendritic cells (DCs) elicited a more aggressive course of GvHD, while overexpression of miR-146a in DCs using a specific miR-146a mimic ameliorated disease. Phenotypically, miR-146a-/- DCs displayed a more activated phenotype with increased MHC class II, CD80 and CD86 surface expression levels after endotoxin stimulation when compared to WT DCs. Global gene expression analysis revealed upregulation of the JAK-STAT signaling pathway in miR-146a-/- DCs, which we confirmed at the protein and phosphoprotein level using Western blot and flow cytometry. Importantly, inhibition of JAK-STAT signaling in DCs using the JAK1/2 inhibitor ruxolitinib prevented miR-146a-/- DC-induced GvHD exacerbation.In conclusion, our findings indicate that miR-146a acts as a central regulator of recipient type DCs during GvHD, by dampening cytokine receptor signaling via the JAK-STAT pathway. We detected the SNP rs2910164 as a marker to identify patients at high risk for GvHD before allo-HCT, facilitating the opportunity to apply pre-emptive interventions. DisclosuresNo relevant conflicts of interest to declare.