IL28B gene polymorphisms and Th1/Th2 cytokine levels might be associated with HTLV-associated arthropathy

The present study is the first investigation of the association between single nucleotide polymorphisms (SNPs – rs8099917, rs12979860 and rs8103142) of the IL28B gene and the development of human T-lymphotropic virus (HTLV)-associated arthropathy (HAA). Individuals with HAA exhibited low interleukin (IL) 6 (p < 0.05) and high IL-10 (p < 0.05) levels compared with asymptomatic patients. TNF-α/CD4⁺ T cell count, TNF-α/CD8⁺ T cell count and IFN-γ/proviral load positively correlated in asymptomatic patients. The allelic and genotypic frequencies did not differ between patients with HAA and asymptomatic patients. Seven haplotypes were detected in the investigated population, with haplotype CCT (p < 0.05) being the most frequent among the HTLV-infected individuals, while haplotype TTG (p < 0.05) was detected in the group with HAA only. Compared with asymptomatic patients, individuals with HAA and genotype TT (rs8099917) exhibited larger numbers of CD8⁺ T cells (p < 0.05) and higher proviral load levels (p < 0.05). Those patients with HAA and genotypes CC (rs12979860) and TT (rs8103142) exhibited high TNF-β (p < 0.05) and IFN-γ (p < 0.05) levels. Those patients with HAA and genotype CT/TT (rs12979860) exhibited high IL-10 levels (p < 0.05). These results suggest that haplotypes CCT and TTG might be associated with susceptibility to HTLV infection and progression to HAA, respectively. Genotype TT (rs8099917) might be a risk factor for elevation of the proviral load and CD8⁺ T cell count. In addition, genotypes CC (rs12979860) and TT (rs8103142) seem to be associated with increased TNF-β and IFN-γ levels.     

TNRC9 基因rs12443621A/G 多态性与中国女性乳腺癌易感性及临床病 理关系的研究

目的:研究TNRC9/LOC643714 基因 rs12443621A/G 多态性与乳腺癌易感性及临床病理之间的关系.方法:DNA 试剂盒提取321 例乳腺癌患者和340 例正常女性静脉血全基因组DNA,PCR扩增目的基因片段,提取扩增样本进行DNA 测序检测分析rs12443621 多态性.应用 SPSS17.0 软件对实验结果进行统计学分析.结果:应用 SPSS17.0软件对TNRC9/LOC643714 基因rs12443621A/G多态性AA、AG、GG 进行卡方检验分析,结果显示三种基因型分布在病例组及对照组中无统计学意义(X<'2>=1.43,P>0.05),与乳腺癌易感性无关,与乳腺癌病理分型、ER、PR、HER-2状态以及淋巴结是否转移无相关性(X<'2>=2.90,P>0.05;X<'2>=2.25,P>0.05;X<'2>=1.671,P>0.05;X<'2>=1.34,P>0.05;X<'2>=3.24,P>0.05).结论:TNRC9 基因rs12443621A/G 多态性与乳腺癌易感性及临床病理特征无关.不能作为独立的基因标志物对乳腺癌进行早期检测和诊断.

Abstract：

Objective: To investigate the relationship between the rs12443621 polymorphisms of TNRC9/LOC643714 and breast cancer risk and clinico-pathological characteristics in Chinese women. Methods: Genomic DNA was extracted from peripheral blood. The Single Nucleotide Polymorphisms of the TNRC9/LOC643714 rs12443621,from breast cancer of 321 cases and 340 controls were detected by polymerase chain reaction (PCR) and direct DNA sequencing.Results:The genotypes of rs12443621 can not increase the risk for breast cancer(X2=1.43,P>0.05).There was no relationship between the genotypes and pathological category,lymph node metastases, ER status or PR staus or Her-2 status (x2=2.90,P>0.05; X2=2.25,P>0.05;X2=1.671,P>0.05; X2=1.34,P>0.05; X2=3.24,P>0.05). Conelusion:There was no relationship between three genotypes of rs12443621A/G and individual susceptibitity or clinic pathological characteristics of breast cancer.     

Association of genetic variants rs641153 (CFB), rs2230199 (C3), and rs1410996 (CFH) with age-related macular degeneration in a Brazilian population

This study aimed to investigate the association among genetic variants of the complement pathway CFB R32Q (rs641153), C3 R102G (rs2230199), and CFH (rs1410996) with age-related macular degeneration (AMD) in a sample of the Brazilian population. In a case-control study, 484 AMD patients were classified according to the clinical age-related maculopathy grading system (CARMS) and compared to 479 unrelated controls. The genetic variants rs1410996 of complement H (CFH), rs641153 of complement factor B (CFB), and rs2230199 of complement 3 (C3) were evaluated through polymerase chain reaction (PCR) and direct sequencing. The associations between single nucleotide polymorphisms (SNPs) and AMD, adjusted by age, were assessed by using logistic regression models. A statistically significant association was observed between AMD risk and rs2230199 variant with an OR of 2.01 (P  = 0.0002) for CG individuals compared to CC individuals. Regarding the comparison of advanced AMD versus the control group, the OR was 2.12 (P = 0.0036) for GG versus AA genotypes for rs1410996 variant. Similarly, the OR for rs2230199 polymorphism was 2.3034 (P  = 5.47^e-05) when comparing CG individuals to CC carriers. In contrast, the rs641153 variant showed a significant protective effect against advanced AMD for GA versus GG genotype (OR = 0.4406; P  = 0.0019). When comparing wet AMD versus controls, a significant association was detected for rs1410996 variant (OR = 2.16; P  = 0.0039) comparing carriers of the homozygous GG versus AA genotype, as well as in the comparisons of GG (OR = 3.0713; P  = 0.0046) and CG genotypes (OR = 2.2249; P  = 0.0002) versus CC genotype for rs2230199 variant, respectively. The rs641153 variant granted a significant protective effect against wet AMD for GA versus GG genotypes (OR = 0.4601; P  = 0.0044). Our study confirmed the risk association between rs2230199 and rs1410996 variants and AMD, and the protective role against AMD for rs641153 variant.     

Association study of rs10768683 and rs968857 polymorphisms with transfusion-dependent thalassemia (TDT) in a southern Iranian population

Previous studies reported that detection of polymorphisms inherited through paternal model could be potential markers for the Non-Invasive Prenatal Diagnosis (NIPD) of β-thalassemia. The aim of the current study was to find out the associations of rs10768683 and rs968857 with transfusion-dependent thalassemia (TDT) in a southern Iranian population. A total of 175 subjects were investigated, divided into patients with TDT as case group (n?=?75) and healthy people as control group (n?=?100). Genomic DNAs were extracted from peripheral blood using salting out procedure. Genotyping rs10768683 and rs968857 was carried out by ARMS-PCR, then statistical analyses were assessed using SPSS, and Medcalc ver. 18 software. Data showed that rs10768683 was statistically significant in co-dominant model of inheritance (P?=?0.025, OR?=?2.11 [1.08-4.15]) and genotype frequencies of CG among controls and cases were 0.68 and 0.80, respectively. However, according to genotype frequencies, there was no association between rs968857 and TDT among cases and healthy controls in any models of inheritance. In conclusion, the present study showed the association of rs10768683 with major β-thalassemia through ARMS-PCR technique.     

Association of caspase 8 promoter variants and haplotypes with the risk of breast cancer and its molecular profile in an Iranian population: A case-control study

Caspase 8 (CASP8) gene plays a key role in the regulation of apoptotic cell death. Expression variation in this gene has been associated with the risk of breast cancer. The aim of this study was to investigate the association of rs3834129 and rs3769821, as functional variants, and their haplotypes with molecular profile as well as the risk of breast cancer in an Iranian population. A case-control study was conducted on 812 participants including 293 breast cancer patients and 519 healthy controls. Genotyping was performed by polymerase chain reaction–based methods. Statistical analysis was performed using SPSS Ver16. The association between polymorphisms and haplotypes with the risk of breast cancer was estimated by calculating odds ratios (OR) and chi-square (χ²) tests. In comparison with ins allele (I) of rs3834129, carriers of del allele (D) showed a lower risk of breast cancer (OR, 0.65; 95% confidence interval [CI], 0.49-0.87; P = 0.004). The multivariate logistic regression model indicated DD genotype as an independent factor for a decreased risk of breast cancer in our population (OR, 0.18; 95% CI, 0.06-0.58; P = 0.004). Also, the C allele of rs3769821 was associated with a 43% increased risk of breast cancer (P = 0.005); however, after adjustment for confounding factors, no association with rs3769821 and breast cancer was observed. In addition, D-T haplotype and diplotype presented protective effects (P < 0.05). Our results indicate that genetic variations in the promoter region of CASP8 gene, especially rs3834129, may serve as a genetic risk factor for breast cancer in an Iranian population.     

炎性肠病易感基因GPR35在肠炎发生发展中的功能研究

炎性肠病在全球范围内发生极其普遍,具有反复发作、难以治愈的特点,也是诱发结直肠癌的高风险因素之一。肠炎的发生与遗传因素密切相关,有报道发现位于GPR35基因座上的多个单核苷酸多态性(single nucleotidepolymorphism,SNP)位点rs4676410、rs3749171和rs3749172与肠炎敏感性高度相关,但是GPR35基因在肠炎的发生发展进程中的功能及相关机制尚没有明确结论。为了研究GPR35在肠炎中的作用,首先通过CRISPR/Cas9技术构建Gpr35敲除小鼠,随后利用DSS诱导的肠炎模型评价Gpr35在肠炎发生中的作用,发现敲除小鼠在体重变化、DAI评分、肠上皮损伤以及炎性细胞浸润等肠炎相关指标显著低于野生型小鼠。为了研究肠炎相关SNP突变对GPR35活性的影响,首先根据rs3749171和rs3749172SNP位点突变信息构建GPR35-T108M和GPR35-S294R两种突变型受体,其次通过多种GPR35下游信号通路活性测试,发现两种突变均能够增强GPR35受体活性。最后通过Westernblotting分析发现相较于野生型小鼠,Gpr35敲除小鼠肠上皮Erk1/2磷酸化水平增加,表明Gpr35敲除后可能通过上调Erk1/2信号通路的方式抑制肠炎的发生发展。综上所述,本研究发现人类肠炎易感的rs3749171和rs3749172位点可能通过激活GPR35及下游信号通路的方式促进肠炎的发生发展,为炎性肠病的治疗提供了潜在的药物作用靶点。     

Another functional frame‐shift polymorphism of DEFB126 (rs11467497) associated with male infertility

DEFB126 rs140685149 mutation was shown to cause sperm dysfunction and subfertility. Indel rs11467497 is another 4‐nucleotide frame‐shift mutation (151bp upstream of rs140685149) that leads to the premature termination of translation and the expression of peptide truncated at the carboxyl terminus. In the present study, we performed a comprehensive association study to check the contribution of rs140685149 and rs11467497 to male infertility. Our results confirmed the previous findings that there was no association between rs140685149 and sperm motility. In contrast, we found a significant association of another indel rs11467497 with male infertility. Moreover, rs11467497 was shown to be associated with higher number of round cells in the infertile males with low sperm motility. Surprisingly, the two mutations commonly existed in the sperm donors (n = 672), suggesting a potential application of the two indels in the screening for eligible sperm donors. Western blotting assays showed the sperms with rs140685149 2‐nt deletion tended to have unstable DEFB126 protein in contrast of no DEFB126 protein expressed in the sperms with rs11467497 4‐nt deletion, suggesting a more severe consequence caused by rs11467497 mutation. In conclusion, our study presented a significant contribution of another functional frame‐shift polymorphism of DEFB126 (rs11467497) to male infertility.     

PVT1 (rs13281615) and miR-146a (rs2910164) polymorphisms affect the prognosis of colon cancer by regulating COX2 expression and cell apoptosis

In this study, we aimed to investigate the potential correlation between rs13281615/rs2910164 polymorphisms and the prognosis of colon cancer (CC). Taqman was utilized to genotype the rs13281615/rs2910164 polymorphisms in recruited subjects. Kaplan–Meier survival curves were calculated to study the prognostic values of different genotypes of rs13281615/rs2910164 polymorphisms. Real-time polymerase chain reaction, enzyme-linked immunosorbent assay, immunohistochemistry, and terminal deoxynucleotidyl transferase dUTP nick-end labeling assays were conducted to establish a potential signaling pathway underlying the role of rs13281615/rs2910164 polymorphisms, whereas bioinformatics analysis and luciferase reporter assays were performed to identify plasmacytoma variant translocation 1 (PVT1) and cyclooxygenase-2 (COX2) as targets of microRNA-146a (miR-146a). No significant difference was observed in respect to clinical characteristics among subjects with different genotypes. However, patients genotyped as GG/CC + GC showed the lowest chance of survival, whereas patients of GA + AA/GG genotype showed the highest chance of survival. Moreover, the relative expressions of PVT1, prostaglandin E2 (PGE2), and COX2 were the lowest and the relative expression of miR-146a was the highest in GA + AA/GG subjects, validating the roles of PVT1, miR-146a, and COX2 in CC. In addition, both PVT1 and COX2 were identified as virtual targets of miR-146a, and the luciferase activities of cells cotransfected with wild-type PVT1/COX2 and miR-146a mimics were significantly reduced. Moreover, the presence of PVT1 decreased the level of miR-146a whereas increasing the messenger RNA and protein levels of COX2, thus establishing a PVT1/miR-146a/COX2 signaling pathway underlying the pathogenesis of CC. The presence of rs13281615 G > A polymorphism on PVT1 and the rs2910164 C > G polymorphism on miR-146a contributes to a favorable prognosis in CC patients via modulating the activity of the PVT1/miR-146a/COX2 signaling pathway.     

FTO基因rs9939609 A/T多态与多囊卵巢综合征易感性的研究

目的:探讨FTO基因rs9939609 A/T单核苷酸多态性位点与多囊卵巢综合征易感性及其临床生化特征的相关性。方法:选择102例多囊卵巢综合征患者和96例健康女性作为研究对象并收集其病例临床信息,采用突变敏感性分子开关方法检测各受试者FTO基因rs9939609A/T多态,比较多囊卵巢综合征组与对照组基因型与基因频率的差异,分析基因型与临床生化特征的相关性。结果:rs9939609A/T多态位点共检测到TT、AT、AA三种基因型,其在多囊卵巢综合征组与对照组的频率分别为77.5%、21.5%、1.0%,77.1%12.5%10.4%,两者之间存在显著性差异(P=0.006);等位基因T、A的频率在多囊卵巢综合征组(88.2%、11.8%)与对照组(83.3%、16.7%)之间的分布不具有显著性差异;多囊卵巢综合征组与对照组中,TT与AT+AA两基因型群体的临床和生化特征比较均未发现显著性差异。结论:FTO基因rs9939609 A/T多态位点与PCOS易感性存在相关性。     

CYP1A1 rs1048943 and rs4646903 polymorphisms associated with laryngeal cancer susceptibility among Asian populations: a meta‐analysis

Many studies have investigated the association between CYP1A1 rs1048943 and rs4646903 polymorphisms and laryngeal cancer risk, but their results have been inconsistent. The PubMed and CNKI were searched for case–control studies published up to 01 July 2015. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated. In this meta‐analysis, we assessed 10 published studies involving comprising 748 laryngeal cancer cases and 1558 controls of the association between CYP1A1 rs1048943 and rs4646903 polymorphisms and laryngeal cancer risk. For CYP1A1 rs1048943 of the homozygote G/G and G allele carriers (A/G + G/G) versus A/A, the pooled ORs were 1.77 (95% CI = 1.28–2.81, P = 0.007 for heterogeneity) and 1.86 (95% CI = 1.45–2.40, P = 0.000 for heterogeneity). For CYP1A1 rs4646903 of the homozygote G/G and G allele carriers (A/G + G/G) versus A/A, the pooled ORs were 1.53 (95% CI = 1.31–2.21, P = 0.012 for heterogeneity) and 1.33(95% CI = 1.04–1.71, P = 0.029 for heterogeneity). In the stratified analysis by ethnicity, the significantly risks were found among Asians for both the G allele carriers and homozygote G/G. However, no significant associations were found in Caucasian population all genetic models. These results from the meta‐analysis suggest that CYP1A1 rs1048943 and rs4646903 polymorphisms contribute to risk of laryngeal cancer among Asian populations.     

Frequent Mutation of rs13281615 and Its Association with PVT1 Expression and Cell Proliferation in Breast Cancer

The q24 band of chromosome 8 （8q24） is frequently amplified in human cancers including breast cancer, and several SNPs （single nucleotide polymorphisms） at 8q24, including rs13281615, have been identified for their association with cancer risks. These SNPs are in a ＂gene desert＂ region, and their functions in cancer development remain to be illustrated, although several of the SNPs appear to influence the genes in the ＂desert＂ in a long-range manner, including the v-myc avian myelocytomatosis viral oncogene homolog （MYC） and the non- protein coding plasmacytoma variant translocation 1 （PVT1）, both of which have been implicated in human cancers. In the current study, we examined rs13281615 for its potential role in breast cancer using normal and cancer tissues from 121 Chinese women with breast cancer. In addition to confirming the association of the GG genotype of rs 13281615 with breast cancer risk, we found that germline GG genotype was significantly associated with estrogen receptor （ER） positivity, higher tumor grade and higher proliferation index. We also found frequent somatic mutations （22/121 or 18.2%） of this SNP in breast cancer. Interestingly, the majority of the mutations （17/22 or 77%） involved a G→ A change, resulting in a decrease in the number of cancers with the GG risk genotype and subsequent loss of GG association with higher tumor grade and proliferation index in cancers. Furthermore, PVT1 expression was increased in cancers, and the increase was associated with the GG genotype of rs13281615. These results suggest that the GG genotype of SNP rs13281615 plays a role in breast cancer likely by influencing PVT1 expression, and that during oncogenesis, ＂protective＂ mutations could occur.     

A LncRNA gene polymorphism (rs1814343) is associated with the risk of coronary artery lesions in southern Chinese Kawasaki disease patients

Background

Kawasaki disease (KD) is a multisystemic angiitis, and its most disastrous complication is coronary artery lesions (CALs). Recently, the role of long non-coding RNAs (lncRNAs) in KD has been reported. rs1814343 is a lncRNA, but the relationship between the lncRNA rs1814343 polymorphism and KD risk remains elusive.

Methods

We enrolled 1625 Kawasaki disease patients (583 patients with CAL and 1042 without CAL) and 1000 healthy controls from a southern Chinese population. We genotyped the rs1814343 C > T polymorphism in KD and control patients using the TaqMan method. The odds ratio (OR) and 95% confidence interval (CI) were used to estimate the strength of the association.

Results

There was no significant association between the lncRNA rs1814343 C > T polymorphism and KD susceptibility. However, we stratified patients in this study by CAL and sex. First, compared with the control groups, we found that the rs1814343 genotype increased risk for KD patients with CAL (TT vs. CC + CT: OR = 1.36, 95% CI = 1.08–1.71, p = 0.009). Moreover, when KD patients were stratified by CAL, the TT genotypes of this lncRNA polymorphism contributed to a relatively higher occurrence of KD with CAL than that was found in the CC/CT genotype patients (TT vs. CC + CT: OR = 1.35, 95% CI = 1.07–1.69, p = 0.011). In addition, our research suggested that the TT variant genotype in the lncRNA rs1814343 had an obvious risk of KD with CAL susceptibility in male children.

Conclusion

The lncRNA rs1814343 C > T polymorphism was related to higher susceptibility of KD with CAL.     

The two common polymorphic forms of human NRH-quinone oxidoreductase 2 (NQO2) have different biochemical properties

There are two common forms of NRH-quinone oxidoreductase 2 (NQO2) in the human population resulting from SNP rs1143684. One has phenylalanine at position 47 (NQO2-F47) and the other leucine (NQO2-L47). Using recombinant proteins, we show that these variants have similar steady state kinetic parameters, although NQO2-L47 has a slightly lower specificity constant. NQO2-L47 is less stable towards proteolytic digestion and thermal denaturation than NQO2-F47. Both forms are inhibited by resveratrol, but NQO2-F47 shows negative cooperativity with this inhibitor. Thus these data demonstrate, for the first time, clear biochemical differences between the variants which help explain previous biomedical and epidemiological findings.     

Exploring a possible association between the occurrence of the SERPINE1-675 4G/5G (rs1799889) polymorphism and the increased risk of esophageal cancer in the Caucasian population

The goal of this research was to analyze the SERPINE1 -675 4G/5G (rs1799889) and MMP9 T-1702A (rs2297864) polymorphisms in esophageal cancer among polish patients, classified as part of the Caucasian population. The analysis of polymorphic gene variants was performed on 35 randomly selected samples excised from patients with esophageal cancer. The tissue specimens were stored as Formalin-Fixed, Paraffin-Embedded (FFPE) blocks. All patients in the sample group were of Caucasian ethnicity. The genotype distribution of MMP9 T-1702A and SERPINE1 -675 polymorphisms was analyzed using the Restriction Fragment Length Polymorphism (RFLP) method. A correlation between the expression of ?675 polymorphic form of SERPINE1 and alcohol abuse has been found. Additionally, a correlation between the ?675 polymorphism and the subtype of EC developed by the patient has been shown. To the best of the authors’ knowledge, this is the first report investigating the SERPINE1 -675 4G/5G (rs1799889) polymorphism as a potential candidate for a prognostic biomarker of esophageal cancer.     

IL28B基因多态性检测的质粒标准品构建

人类白介素28b（IL28b）的SNP位点rs12980275的多态性（AA、AG和GG）与聚乙二醇干扰素、利巴韦林联合治疗的效果具有显著相关性。为了确保rs12980275预测丙型肝炎患者抗病毒治疗效果的价值,需要构建标准品作为rs12980275检测的标准对照。提取人类外周血基因组DNA,以IL28B SNP rs12980275为目的基因片段设计引物,进行PCR扩增;纯化目的片段与pGM-T Vector连接并转化到大肠杆菌中;提取重组质粒DNA,并进行PCR、测序鉴定。结果 IL28B SNP rs12980275目的片段制备成功,获得稳定的重组质粒,保证了目的片段的特异性与序列完整性。成功构建了IL28B基因SNP rs12980275突变检测的AA、AG和GG 3种质粒标准品,可作为预测丙型肝炎患者抗病毒治疗效果rs12980275突变检测的阳性质控物。     

Associations of APOE Gene Variants rs429358 and rs7412 with Parameters of the Blood Lipid Profile and the Risk of Myocardial Infarction and Death in a White Population of Western Siberia

The present study aimed to analyze possible associations of rs7412 and rs429358 of the APOE gene with lipid profile parameters, the risk of myocardial infarction, and death in the mostly white population of Western Siberia (Russia). The study population was selected from a sample surveyed within the framework of the Health, Alcohol and Psychosocial Factors In Eastern Europe (HAPIEE) study (9360 subjects, age 53.8 ± 7.0 years, males/females 50/50). PCR was conducted with fluorescence detection according to the TaqMan principle on a real-time PCR machine. The frequency of a minor allele (C) of rs429358 was 0.13, and the frequency of a minor allele (T) of rs7412 was 0.09. In our study, the woman with the rare ɛ1/ɛ4 genotype had substantial aberrations in blood lipid levels. In Kaplan–Meier curves, statistically significant differences were revealed in the prognosis of survival within the subgroup of females who had a myocardial infarction (p = 0.0006): the prognosis was worse for carriers of the ɛ2/ɛ2 genotype and for ɛ4/ɛ4 carriers. Survival analysis regarding deaths from all causes showed (p = 0.0238) that female carriers of the ɛ2/ɛ4 genotype had a worse prognosis than did carriers of other genotypes. Thus, in the population of Western Siberia (Russia), we confirmed statistically significant associations between rs7412 & rs429358 genotypes and lipid profile parameters.