广东汉族人群TLR2基因的多态性研究

目的:人类Toll样受体2(TLR2)是先天免疫系统中一个重要的病原微生物识别受体。本研究将建立广东汉族人群TLR2基因座位的功能性多态性图谱,为下一步疾病相关性研究打下基础。方法:收集200例健康、无亲缘关系的中国广东汉族人外周血液,随机抽取其中24例样品,对TLR2基因的启动子区、3个外显子以及它们周围的部分内含子序列进行聚合酶链式反应(PCR)扩增和直接测序,找出多态性位点,对剩余176例样品分别用序列特异性引物聚合酶链反应(PCR-SSP)及PCR技术对发现的单核苷酸多态性(SNPs)和插入/缺失(INDEL)多态性位点进行基因分型,分型结果进行Hardy-W e inberg平衡分析、中性进化分析以及连锁不平衡分析。结果:发现5个SNPs位点,其中2个位于启动子区的SNPs是首次发现,位于编码区的3个SNPs位点均为同义突变,频率最高的SNP是rs3804099,其次要等位基因频率为26.3%;在第1外显子区发现1个长度为22bp的INDEL多态位点(-196到-174),其缺失等位基因所占的频率为31.8%。所有多态性位点均符合Hardy-W e inberg平衡。中性检验显示广东汉族人群TLR2基因符合中性进化假说。连锁不平衡分析显示位于调控区的-18945 C/T和-18883 C/G 2位点之间完全连锁,而位于编码区的rs3804099和rs3804100两位点之间紧密连锁。结论:本研究首次建立了汉族正常人群TLR2基因座位的功能性多态性图谱,并研究了其分布频率,发现了一些种族特异性的多态性位点,为今后开展汉族人基因多态性与疾病相关性研究以及人群进化研究提供了重要资料。     

广东汉族正常人群TLR4基因单核苷酸多态性研究(英)

目的：人类Toll样受体4（TLR4）是先天免疫系统中一个重要的病原微生物识别受体。本研究将建立中国汉族正常人群TLR4基因座位的单核苷酸多态性图谱。方法：收集191例健康、无亲缘关系的中国广东汉族人外周血液,通过对TLR4基因的启动子区、3个外显子区以及它们周围的内含子区进行PCR扩增和测序,得到汉族正常人群TLR4基因座位单核苷酸多态性图谱及其频率分布特点。结果：共发现8个单核苷酸多态性位点,其中5个是首次发现的新位点。分布频率最高（0.283）的单核苷酸多态性位点是-1607 C/T。常见于高加索人中的2个非同义突变Asp299Gly和Thr399Ile在汉族人中没有被发现。中性检验显示汉族人群TLR4基因符合中性进化模型。结论：本研究建立了汉族正常人群TLR4基因座位的单核苷酸多态性图谱,发现了一些种族特异性的单核苷酸多态性位点,这些工作将为今后开展汉族人基因多态性与疾病相关性研究以及人群进化研究提供一定的帮助。     

广东地区汉族人群TLR1 基因多态性的测序研究

目的: 人类Toll样受体1(TLR1)在先天性免疫中起着重要作用。本文将着重研究广东地区汉族正常人群中TLR1 基因功能区的单核苷酸多态性(SNPs)图谱和频率分布。方法: 随机收集50例健康、无亲缘关系的中国广东地区汉族人外周血液,对TLR1 基因的启动子区、5'和3'非翻译区、4个外显子区的序列进行PCR扩增和直接测序,找出多态性位点及其频率分布规律。在此基础上对多态性位点进行Hardy-Weinberg平衡分析、中性进化分析和连锁不平衡分析。结果: 共发现17个SNPs以及2个插入/缺失多态位点,其中2个是首次发现的新多态性位点。位于编码区的新SNP位点+1 378 A/G为非同义突变位点,能导致460位丝氨酸(Ser)残基替换为甘氨酸(Gly)残基,并且这个氨基酸残基的替换处于TLR1胞外区的LRR结构域中,从而有可能影响蛋白的识别功能。另外,频率最高的SNPs是+743 A/G和+1 518 A/G,其次要等位基因频率均达到48%。所有多态性位点均符合Hardy-Weinberg平衡。中性检验显示广东汉族人群 TLR1 基因不符合中性进化假说,很可能是其调控区受到平衡选择作用的原因。连锁不平衡分析显示多态性位点-6 912 C/TA、-6 876 C/T、-6 399 C/T和-6 375 C/T之间,-6 847 A/G和-6 737 A/T之间,以及-5 984 -/CT、-5 531 A/G和-5 490 C/G之间完全连锁。结论: 本研究首次报道了汉族正常人群TLR1 基因的功能性多态性图谱,发现了一些种族特异性的多态性位点及频率分布规律,为今后开展汉族人基因多态性与疾病相关性研究打下一定的基础。     

TLR4基因多态性在中国人群中的初步研究

目的检测中国人Toll样受体4(Toll—like receptor 4．TLR4)基因调控区和编码区的单核苷酸多态性(single nucleotide polymorphisms，SNPs)．寻找TLR4基因的遗传标记。方法采用直接测序的方法检测基因的5′区、编码区、部分内含子区和3′区，以确定中国人群中TLR4基因SNP的位置和类型，并用聚合酶链反应-限制性片段长度多态性对重庆汉族样本进行了抽样调查。结果在4．98kb的测序范围内，发现5个新的SNP，3个位于5′区．2个位于3′非翻译区。在重庆地区汉族样本中．两个高频分布SNP的等位基因频率分别是0．266和0．404。结论在TLR4基因新发现的两个高频多态性位点在我国人群中比较常见，可以作为关联分析的遗传标记。     

Polymorphisms in the leptin receptor (LEPR)—putative association with obesity and T2DM

Leptin plays an important role in regulating adipose-tissue mass. Leptin controls energy balance and food intake through the leptin receptor in the hypothalamus of the brain, which suggests that some polymorphisms of the leptin receptor gene (LEPR) might contribute to obesity or obesity-related diseases. In an effort to identify genetic polymorphisms in a potential candidate gene for obesity and type 2 diabetes mellitus (T2DM) in the Korean population, we have sequenced the LEPR gene. Thirty-five sequence variants were identified (including 9 novel polymorphisms): 1 single nucleotide polymorphism (SNP) in the promoter region, 1 SNP in the 5 UTR, 8 SNPs in exons (3 non-synonymous SNPs), 23 SNPs in introns, 1 ins/del in the 3 UTR, and 1 SNP in the 3 downstream region. To investigate possible association of LEPR polymorphisms with body mass index (BMI) and the risk of T2DM, we genotyped for 11 polymorphisms in the Korean population (n=1,463). Using statistical analyses, no significant associations between the genetic polymorphisms in the LEPR gene and the risk of T2DM were detected. However, one non-synonymous SNP in exon 3, +5193G>A (Arg109Lys), showed marginal association with BMI (P=0.02) and gene dose-dependent genetic effects were observed. The present study provides information about additional genetic polymorphisms in LEPR and positive associations of those polymorphisms with BMI in the Korean population.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.Kyong Soo Park and Hyoung Doo Shin contributed equally to this work     

Polymorphisms in Toll‐like receptor 3 are associated with asthma‐related phenotypes in the Chinese Han patients

Toll‐like receptor (TLR) 3 mediates antivirus immunity and is involved in asthma exacerbation and development. However, the genetic association between TLR3 and asthma remains unclear. This study aimed to evaluate the effects of polymorphisms within TLR3 on asthma risk and asthma‐related phenotypes in the Chinese Han population. A total number of 462 unrelated adult patients with asthma and 398 healthy volunteers were enrolled in this study. The genotypes of tagging single nucleotide polymorphisms (SNPs) in TLR3 gene were determined using multiplex SNaPshot SNP genotyping assays. Case–control and case‐only studies were used to assess any links with asthma and asthma‐related phenotypes. The results showed that the genetic variants in TLR3 were associated with asthma‐related phenotypes, including eosinophil counts, serum immunoglobulin E levels and lung function. However, there was no obvious association between the TLR3 SNPs and asthma susceptibility or asthma severity. TLR3 polymorphisms may play a considerable role in the pathogenesis of asthma. It will help in better understanding the pathogenesis of asthma and development of more effective strategies for the prevention, prediction and treatment of asthma.     

广西人群miRNA-107基因多态性分布特征及其与血脂的关系

目的探讨miR-107基因单核苷酸多态性(SNP)位点rs2296616 C/T在广西地区健康人群中的分布特点,对比其在不同种族间基因型及等位基因频率分布的差异,并进一步探讨rs2296616 C/T位点单核苷酸多态性(SNP)与血脂水平的相关性。方法采用多重单碱基延伸SNP分型技术(multiplex SNa Pshot)和DNA测序法,检测372例广西健康人rs2296616 C/T位点的多态性,用7600生化仪检测其血脂相关指标,并用统计学方法分别比较rs2296616C/T位点多态性在各种族人群间的分布差异及不同基因型间的血脂水平差异。结果广西人群miR-107基因rs2296616 C/T位点存在TT(91.1%)和CT(8.9%)两种基因型及T(95.6%)和C(4.4%)两种等位基因。该位点的基因型和等位基因型频率在广西人群不同性别间的比较,差异无统计学意义(P>0.05)。其基因型和等位基因频率与人类基因组单体型图(Hap Map)所公布的欧洲人、日本人、非洲人、印第安人和墨西哥人分型数据相比较,差异均有统计学意义(P<0.05),但与北京汉族人群比较,差异无统计学意义(P>0.05)。rs2296616 C/T位点两种基因型人群血脂之间比较,携带TT基因型人群的高密度脂蛋白胆固醇(HDL-C)与CT组比较,差异具有统计学意义(P<0.05)。结论广西人群miR-107基因rs2296616 C/T位点多态性与其他种族人群之间比较存在不同程度的差异;rs2296616 C/T位点多态性与HDL-C水平高低有关。     

Identification of polymorphisms in the human SHP1 gene

 Because mutations in human SHP1 underlie obesity and diabetes, SHP1 is a candidate gene for human lipodystrophy syndromes. To identify possible disease mutations and/or common single-nucleotide polymorphisms (SNPs), we developed primer pairs to amplify the promoter and coding region of SHP1. We used these pairs to sequence SHP1 in lipodystrophy patients who had no mutations in known lipodystrophy genes, and also in normal control subjects. We found no rare SHP1 coding sequence variants that were exclusive to patients with lipodystrophy. However, we found four polymorphisms, namely, an SNP [−394]C>T in the promoter, a micro-deletion polymorphism [−195]delCTGA in the promoter, a missense SNP 541G>C in exon 1 (which changed the amino acid sequence G171A), and an SNP 903C>T in exon 2. The findings suggest that SHP1 mutations are not commonly seen in patients with lipodystrophy who had no mutations in known disease genes. However, the identification of amplification primers and polymorphisms provides tools to further investigate SHP1 for association with other phenotypes. Received: April 1, 2002 / Accepted: April 22, 2002     

Toll‐Like Receptor 2 (P631H) Mutant Impairs Membrane Internalization and is a Dominant Negative Allele

We have sequenced 416 Toll‐like receptor‐2 (TLR2) alleles in 208 subjects in a tuberculosis case–control study in Croatian Caucasian population. We found ten single nucleotide polymorphisms (SNP) among which three were novel (S97S, T138I and L266F). The genotype containing TLR2‐P631H SNP was significantly overrepresented in patients with tuberculosis when compared to contact controls, suggesting a small yet increased risk to disease. The causative agent of tuberculosis is Mycobacterium tuberculosis, which can bind to TLR2 with its lipoprotein coat. The TLR2‐P631H mutant has a dominant negative effect on the wild type TLR2 signalling in transfected HEK293 kidney cells using the NF‐κB‐driven luciferase as a reporter gene with ligands like M. avium extracts, Pam3CysSK4 or FSL‐1 that bind TLR2/TLR1 or TLR2/TLR6 heterodimers, respectively. Studies on internalization from the Regular Madine Darby Canine Kidney cell surface into the early endosomal compartments showed a lower rate of the mutant compared to the wild type. Our data, in combination with a report by others show that the TLR2‐P631H allele could be associated with protection to meningococcal meningitis, suggest that by dominantly inhibiting the response of cells important in the immune response this mutant might confer either protection or susceptibility to meningitis or tuberculosis, respectively.     

变性高效液相色谱法检测中国汉族人SCN1A外显子16T1067A基因多态性

目的 建立检测SCN1A外显子16 T1067A单核苷酸多态性(SNP)的变性高效液相色谱(DHPLC)方法,并检测中国汉族人SCN1A外显子16 T1067A基因多态性.方法 设计针对SCN1A编码区引物,应用DHPLC技术检测其序列多态性,并检测127例中国汉族人SCN1A外显子16 T1067A基凶多态性.结果 127例汉族人中,SCNIA T1067A AA、AG、GG表型频率分别为0.8031、0.1969、0,SCNIA T1067A A、SCN1A T1067A G基因频率分别为0.9016、0.0984.结论 DHPLC简便、快速、准确.适合于大规模的人群调查.SCN1A外显子16 T1067A基因多态性在不同种族间分布存在着明显的差异.     

Catalog of 162 single nucleotide polymorphisms (SNPs) in a 4.7-kb region of the HLA-DP loci in southern Chinese ethnic groups

HLA class-II proteins are cell-surface molecules that present antigens to T cells, and their expressional regulation is crucial to the immune reaction. Sequence variation at the regulatory region can directly affect the gene expression level. We cloned and sequenced a 4.7-kb region containing the regulatory region, exon1, and partial intron1 of both HLA-DPA1 and DPB1 genes in 25 variable sequences from southern Chinese ethnic groups and got a high-density map of 162 single nucleotide polymorphisms (SNPs): seven in 5-flanking regions, four in 5-untranslated regions, and four in the coding regions. By comparing these data with SNPs in dbSNP database in the NCBI, 145 SNPs (89.5%) were novel. In addition, eight genetic variations of insertion-deletion polymorphisms (INDELs) were discovered within the 4.7-kb region. These high-resolution maps can be used as resources of markers for association studies of complex diseases, assessment of individuals predisposition to diseases, and tailoring of therapies, as well as research markers for population genetics and evolution.     

Association of Toll-Like Receptor 4 Polymorphisms with Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is characterized by a chronic low-grade inflammatory state. Toll-like receptor 4 (TLR4) is a critical mediator of innate immunity. Polymorphisms in TLR4 gene have been shown to be associated with impaired inflammatory response. Here, we investigated the association of TLR4 polymorphisms with T2DM. Four TLR4 polymorphisms (+986A/G, +1196C/T, +3725G/C, and +11367G/C) were genotyped in a total number of 822 T2DM patients and 835 healthy controls. Results showed that the +986A/G and +1196C/T polymorphisms did not exist in the Han Chinese population. The prevalence of TLR4 +3725GC and CC genotypes were significantly decreased in T2DM cases than in controls (odds ratio (OR)?=?0.62, 95 % confidence interval (CI)?=?0.50–0.78, p?=?3.48?×?10^?5, and OR?=?0.36, 95 % CI?=?0.22–0.59, p?=?1.55?×?10^?5, respectively). Also, the frequency of TLR4 +3725C allele was significantly lower in T2DM patients (p?=?2.46?×?10^?9). When analyzing the TLR4 +11367G/C polymorphism, the +11367CC genotype revealed lower numbers in patients compared to healthy controls (OR?=?0.46, 95 % CI?=?0.27–0.78, p?=?0.0032). Analysis of the clinical features on the control subjects demonstrated no correlations between these TLR4 polymorphisms and sex, age, body mass index, etc. (p?>?0.05). In conclusion, these data indicate that TLR4 +3725G/C and +11367G/C polymorphisms may be novel protective factors against T2DM in the Chinese population.     

中国人群IL-1R1基因变异及其对跨膜区功能影响的预测

目的　检测中国人白细胞介素 1Ⅰ型受体基因 (interleukin 1receptortypeⅠ ,IL 1)调控区和编码区的单核苷酸多态性 (singlenucleotidepolymorphisms ,SNPs) ,并初步探讨其可能对中国人IL 1R1的功能影响。方法　采用直接测序的方法检测基因的 5′区、编码区、部分内含子区和 3′区 ,以确定中国人群中IL 1R1基因SNP的位置和类型 ,用生物信息学方法对编码区SNP的功能进行了预测。结果　在 964 3bp的测序长度中 ,共发现了 16个SNP ,包括 5′区 4个 ,内含子区 4个 ,编码区 1个 ,3′非编码区 7个。其中一个SNP能引起IL 1R1跨膜区氨基酸的替代 ,生物信息学分析显示它能够引起跨膜区结构的改变。结论IL 1R1基因变异可能对IL 1R1的功能产生影响。     

Genetic Polymorphisms in the Toll‐like Receptor 10, Interleukin (IL)17A and IL17F Genes Differently Affect the Risk for Tuberculosis in Croatian Population

Proinflammatory conditions leading to activation of macrophages via interferon‐γ bear an important role in host defence against intracellular bacteria such as Mycobacterium tuberculosis (Mt). Interleukin‐17 plays a similar role, as it appears to be also an activator of macrophages. Recently, the TLR‐10 was identified as an anti‐inflammatory factor that exerts its action via association with the TLR‐2 chain at the cell surface of macrophages, the latter being an Mt‐binding protein. We have previously found that gene polymorphisms that either inactivate the TLR2 gene product or have a dominant‐negative role are associated with tuberculosis (TB) in Croatian population. We have now extended our survey and found that single nucleotide polymorphism (SNP) in TLR10 (rs11096957) is associated with risk for TB. Homozygotes carrying the A allele are associated with predisposition to disease as analysed by the dominant model of inheritance. In contrast, SNPs in the proinflammatory IL17A and IL17F genes (rs2275913 and rs763780, respectively), found previously to correlate with the disease occurrence in Chinese population, were not significantly associated with tuberculosis in the Croatian population.     

Absence of association between two insertion/deletion coding genetic polymorphisms of TIM-1 gene and asthma in Chinese Han population

TIM-1, a member of T-cell immunoglobulin domain and mucin domain (TIM) gene family, was implicated as an asthma susceptibility gene in previous studies. TIM-1 was expressed on CD4(+) T cells after activation and its expression was sustained preferentially in T-helper type 2 (T(H)2) but not in T(H)1 cells, therefore TIM-1 became a good candidate gene for atopic diseases. Recent studies indicated that two insertion/deletion (ins/del) coding genetic polymorphisms in exon 4 of TIM-1 were associated with asthma susceptibility in some but not in all populations. In order to investigate the relationship between TIM-1 genetic polymorphisms and asthma in Chinese Han population, we performed a case-control study for two insertion/deletion polymorphisms in TIM-1 exon 4 (5383_5397ins/del and 5509_5511delCAA) and a single nucleotide polymorphism (SNP) in intron 8 (IVS 8+9 G/A) between a healthy control group of 309 people and an asthma patient group of 352 people recruited from Chinese Han population. The polymorphisms were genotyped and the allele and genotype frequencies were analysed, but none of the three polymorphisms showed association with asthma susceptibility in single-locus association analyses. Linkage disequilibrium (LD) analyses demonstrated that the two insertion/deletion polymorphisms were in strong LD but the haplotypes constructed from these two polymorphisms showed no significant association with asthma. In conclusion, our findings suggest that 5383_5397ins/del, 5509_5511delCAA and SNP IVS 8+9 G/A polymorphisms are not associated with asthma susceptibility in Chinese Han population.     

中国汉族人群TIRAP基因编码区多态性与结核病易感性的相关性研究

目的 筛选中国汉族人群Toll/白细胞介素1受体结构域衔接蛋白(TIRAP)基因编码区多态性位点,并分析其与结核病易感性的相关性.方法 在小样本中测序筛选TIRAP基因编码区多态性位点,再用连接酶特异检测技术在大样本中进行单核苷酸多态性(SNP)分型,并通过统计学方法分析基因多态性与结核病易感性的相关性.结果 共筛选到4个TIRAP基因编码区多态性位点.G394A位点在结核病病人中的突变频率高于健康人,但是该位点等位基因频率在两组人群中的差异没有统计学意义(P>0.05).G164A位点跟结核病病情有关,复治病人与健康人该位点等位基因差异具有统计学意义(P<0.05),同时肺部形成空洞病人与菌阳病人突变率均比健康人要低.结论 TIRAP 基因编码区多态性可能是中国汉族人群结核病发生发展的危险因素.

Abstract：

Objective To detect specific polymorphisms in Toll-interleukin 1 receptor domain containing adaptor protein(TIRAP) coding region for Chinese Han population, and verify whether they are associated with susceptibility to tuberculosis. Methods Search TIRAP polymorphisms by sequencing in small sample; detect single nucleotide polymorphism(SNP) by ligase detection reaction technique in large sample; analyze whether polymorphisms are related to tuberculosis by statistic methods. Results Four polymorphisms were present in the TIRAP coding region. 394A had higher frequencies in the tuberculosis(TB)group than the control. But allelic and genotypic analysis showed that there were no significant difference in statistic between TB patients and controls(P>0.05). The SNP G164A mutation related with TB patient's condition. Comparing to controls, retreatment patients' allelic frequencies had significant difference in statistic(P<0.05), sputum positive patients and lung cavitation patients had lower 164A frequencies. Conclusion TIRAP coding region polymorphisms may be risk factors for TB occurrence and development in Chinese Han population.     

The promoter polymorphism -232C/G of the PCK1 gene is associated with type 2 diabetes in a UK-resident South Asian population

Background  

The PCK1 gene, encoding cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C), has previously been implicated as a candidate gene for type 2 diabetes (T2D) susceptibility. Rodent models demonstrate that over-expression of Pck1 can result in T2D development and a single nucleotide polymorphism (SNP) in the promoter region of human PCK1 (-232C/G) has exhibited significant association with the disease in several cohorts. Within the UK-resident South Asian population, T2D is 4 to 6 times more common than in indigenous white Caucasians. Despite this, few studies have reported on the genetic susceptibility to T2D in this ethnic group and none of these has investigated the possible effect of PCK1 variants. We therefore aimed to investigate the association between common variants of the PCK1 gene and T2D in a UK-resident South Asian population of Punjabi ancestry, originating predominantly from the Mirpur area of Azad Kashmir, Pakistan.     

No association of toll-like receptor 2 polymorphisms with Alzheimer's disease in Han Chinese

Toll-like receptor 2 (TLR2) represents a reasonable functional and positional candidate gene for Alzheimer's disease (AD) as it is located under the linkage region of AD on chromosome 4q, and is functionally involved in the microglia-mediated inflammatory response and amyloid β (Aβ) clearance. In the current study, 7 single nucleotide polymorphisms (SNPs) that span the TLR2 were selected and their associations with late-onset AD (LOAD) risk were assessed in a case-control sample comprising 785 individuals in a Han Chinese population. No significant differences in the frequency of TLR2 alleles, genotypes, and haplotypes in the AD cases were detected compared with the controls. TLR2 gene might not play a major role in the genetic predisposition to late-onset Alzheimer's disease in this population.