IL-1b基因单核苷酸多态性与腰椎间盘疾病的相关性

为研究汉族人白细胞介素-1b（IL-1b）基因 ^-511T>C 和 ⁺³⁹⁵⁴C>T位点单核苷酸多态性与腰椎间盘疾病的关系, 采用聚合酶链反应技术, 扩增 81 例腰椎间盘疾病患者和 101 例正常对照者中分别包含IL-1b 基因 ^-511T>C 和 ⁺³⁹⁵⁴C>T 位点的片段, 酶切法鉴定 IL-1b基因 ^-511T>C和 ⁺³⁹⁵⁴C>T 位点单核苷酸多态性情况, 比较两组中基因多态性与腰椎间盘疾病的关系。同时, 利用 MRI 检测两组腰椎间盘退变的情况, 并分析其中小于45岁者IL-1b基因多态性与腰椎间盘退变严重程度的关系。结果显示, 腰椎间盘疾病病例组及对照组中均存在IL-1b基因 ^-511T>C 和 ⁺³⁹⁵⁴C>T 位点单核苷酸多态性。IL-1b 基因 ^-511T>C 位点 TT、TC 和 CC基因型, T、C 基因型差别与腰椎间盘疾病有关（P<0.01）, 与腰椎间盘退变严重程度无关(P>0.05), 但IL-1b基因 ⁺³⁹⁵⁴C>T 位点单核苷酸多态性与腰椎间盘退变严重程度及腰椎间盘疾病均无关(P>0.05)。表明在汉族人中, 存在 IL-1b 基因 ^-511T>C 和 ⁺³⁹⁵⁴C>T 位点单核苷酸多态性, 但仅 ^-511T>C 位点单核苷酸多态性与腰椎间盘疾病有关。     

Ethnic variation in the mitochondrial targeting sequence polymorphism of MnSOD.

In contrast to CuZn superoxide dismutase (SOD), only a very limited number of mutations have been described in MnSOD. One interesting example is a polymorphism (Ala-9Val) in the mitochondrial targeting sequence of this radical-scavenging enzyme. We have studied the Ala-9Val polymorphism in various ethnic groups by means of the oligonucleotide ligation assay. There were significant variations in this unique polymorphism between three different language groups: Baltic (Lithuanians), Finnic (Finns and Saamis) and Germanic (Swedes). The Ala frequency in an Asiatic population (Chinese) was significantly lower than in most European populations. This polymorphism may affect the mitochondrial targeting rate of MnSOD which may result in mitochondrial damage with implication in various late-onset neurological diseases.     

Analysis of mitochondrial targeting sequence and coding region polymorphisms of the manganese superoxide dismutase gene in German Parkinson disease patients

Two polymorphisms of the MnSOD gene, Ile58Thr and Ala9Val, have been associated with Parkinson disease (PD). The Ile58Thr amino acid exchange affects the stability at the tetrameric interface of the enzyme and reduces the enzymatic activity of MnSOD while the Ala/Val substitution at position -9 of the mitochondrial targeting sequence (MTS) may lead to misdirected intracellular trafficking. We have analyzed 63 German Caucasian PD patients for possible sequence variation in the MTS as well as in exon 3 of the MnSOD gene. All 63 PD patients analyzed exhibited a T at nucleotide position 5777 in exon 3 of the MnSOD gene corresponding to ATA, or Ile at the peptide level, and no other sequence variants were found. In addition, both alleles of the Ala9Val polymorphism in the MTS of MnSOD were equally distributed between German PD patients and controls excluding this gene variant as a risk factor for PD in Caucasian subjects.     

Nucleotide diversity of the melanocortin 1 receptor gene (MC1R) in the gayal (Bos frontalis)

The melanocortin 1 receptor gene (MC1R) plays a crucial role in determining coat colour of mammals. To investigate the relationship of polymorphism of the MC1R with coat colour in gayal, the coding sequence (CDS), and the 5'- and 3'-untranslated regions (UTR) of the MC1R were sequenced from 63 samples from the gayal and compared with the sequences of the MC1R from other ruminant species. A sequence of 1,136 bp including the whole CDS (954 bp) and parts of the 5'- and 3'-UTR (164 and 18 bp, respectively) of the gayal MC1R was obtained. A total of nine single nucleotide polymorphisms (SNPs) including four SNPs (c.-129T>C, c.-127A>C, c.-106C>T, c.-1G>A) in the 5'-UTR and five SNPs (c.201C>T, c.583C>T, c.663T>C, c.871A>G and c.876T>C) in the CDS were detected, revealing high genetic diversity. Three novel coding SNPs including c.201C>T, c.583C>T and c.876T>C, which have not been reported previously in bovid species, were retrieved. Within five coding SNPs, c.201C>T, c.663T>C and c.876T>C were silent mutations, while c.583C>T and c.871A>G were mis-sense mutations, resulting in changes in the amino acids located in the fifth (p.L195F) and seventh (p.T291A) transmembrane regions, respectively. The alignment of amino acid sequences was found to be very similar to those for other bovid species. It was demonstrated, using the functional effect prediction, that the p.T291A amino acid replacement could have an effect on MC1R protein function but not for the p.L195F substitution. Using phylogenetic analyses it was revealed that the gayal has a close genetic relationship with the yak. However, three classical bovine MC1R loci the E (D), E (+) and e were not retrieved in the gayal, indicating other genes or factors could affect coat colour in this species.     

Mutations in Leptin (LEP) Gene Are Associated with Carcass and Meat Quality Traits in Crossbreed Rabbits

Leptin is a hormone synthesized and secreted primarily in adipose cells that help to regulate energy balance. This study examined the associations of single nucleotide polymorphisms in the rabbit leptin gene with growth traits, slaughter traits and physicochemical parameters of New Zealand White (NZW) and Belgian Giant Grey (BGG) crossbreed rabbits. In total, 320 crossbreed animals were genotyped for polymorphisms within exon 2—g.16081633T>C, intron 1_2—g.16081420C>T, and within UTR—g.16079636C>G for association analysis. Identified polymorphisms within rabbits leptin gene showed significant differences for dissectible fat percentage in carcass and dissectible fat weight in intermediate part (g.16081633T>C). Moreover, meat traits like protein content (g.16081633T>C; g.16079636C>G), intramuscular fat content (g.16081633T>C; g.16079636C>G, g.16081420C>T), dry matter (g.16081420C>T), ash (g.16081420C>T), water (g.16081420C>T), and cohesiveness (g.16081420C>T, g.16079636C>G) were affected by polymorphisms in leptin gene. We conclude that polymorphism in the rabbit leptin gene influences important carcass and meat traits of NZW?×?BGG crossbreeds. Therefore, polymorphisms identified in this study may be used in selection as a meat trait markers.     

Genetic polymorphism of manganese superoxide dismutase (MnSOD) and breast cancer susceptibility

Within mitochondria, manganese superoxide dismutase (MnSOD) provides a major defence against oxidative damage by reactive oxygen species (ROS). An alanine-9valine (Ala-9Val) polymorphism in the mitochondrial targeting sequence of MnSOD has been described and has recently been associated with risk of human breast cancer. Our present case-control study was performed to explore the association between MnSOD genetic polymorphism and individual susceptibility to breast cancer. Ala-9Val polymorphism in the signal sequence of the protein for MnSOD was determined using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in a study population. There was no significant difference in risk for breast cancer development between patients positive and negative for the MnSOD Ala allele with adjusted odds ratio (OR): 0.86 (95% confidence interval (CI(0.43 to 1.72). When MnSOD Ala was combined with either cytochrome P450 1B1 CYP1B1*1 and catechol O-methyltransferase COMT-L (V158M) genotypes, the risk for developing breast cancer was significantly increased in patients with a body mass index (BMI) greater than 24 kg m(-2) (OR: 1.42 (95%CI=1.04-1.93)).     

湖北汉族人群载脂蛋白A5遗传多态性分析

采用聚合酶链反应-限制性片断长度多态性(polymerase chain reaction restriction-fragment length polymorphism, PCR-RFLP)对257例湖北健康汉族人群APOA5 -1131T>C及56C>G基因多态性进行鉴定。结果发现: 湖北汉族人群中ApoA5 -1131T>C存在TT、TC、CC基因型, 3种基因型的频率分别为50.9%、32.9%及16.2%; 56C>G位点存在CC、CG基因型, 257名研究对象中, G等位基因分布频率小于5%; 各基因型频率和等位基因频率在不同种族和地域间分布存在显著性差异。结论: 湖北汉族人群中ApoA5基因-1131T>C位点存在单核苷酸多态性(single nucleotide polymorphism, SNP), 56C>G在该人群中应视为一个突变位点而不是多态性位点     

Association analysis of monocyte chemotactic protein-3 (MCP3) polymorphisms with asthmatic phenotypes

The monocyte chemotactic protein-3 (MCP3), on chromosome 17q11.2-q12, is a secreted chemokine, which attracts macrophages during inflammation and metastasis. In an effort to discover additional polymorphism(s) in genes whose variant(s) have been implicated in asthma, we scrutinized the genetic polymorphisms in MCP3 to evaluate it as a potential candidate gene for asthma host genetic study. By direct DNA sequencing in twenty-four individuals, we identified four sequence variants within the 3 kb full genome including 1,000bp promoter region of MCP3; one in promoter region (-420T>C), three in intron (+136C>G, +563C>T, +984G>A) respectively. The frequencies of those four SNPs were 0.020 (-420T>C), 0.038 (+136C>G), 0.080 (+563C>T), 0.035 (+984G>A), respectively, in Korean population (n = 598). Haplotypes, their frequencies and linkage disequilibrium coefficients (|D'|) between SNP pairs were estimated. The associations with the risk of asthma, skin-test reactivity and total serum IgE levels were analyzed. Using statistical analyses for association of MCP3 polymorphisms with asthma development and asthma-related phenotypes, no significant signals were detected. In conclusion, we identified four genetic polymorphisms in the important MCP3 gene, but no significant associations of MCP3 variants with asthma phenotypes were detected. MCP3 variation/haplotype information identified in this study will provide valuable information for future association studies of other allergic diseases.     

Inter-ethnic variability of three functional polymorphisms affecting the IMPDH2 gene

Human type II inosine monophosphate dehydrogenase (IMPDH2) is a key enzyme in the purine nucleotide biosynthetic pathway and constitutes a pivotal biological target for immunosuppressant and antiviral drugs. Several Single Nucleotide Polymorphisms (SNP) affecting the IMPDH2 gene sequence have been reported with potential functional relevance and could impact drugs response. We aimed to determine the frequency of three of these polymorphisms, namely g.3375C>T (Leu(263)Phe), c.-95T>G and IVS7+10T>C, in Caucasians, Tunisians, Peruvians and Black Africans (Gabonese and Senegalese). The g.3375C>T and c.-95T>G polymorphisms are rare with a Minor Allele Frequency ≤1.0% in our populations, whereas the third variant, IVS7+10T>C, is more frequent and displays large interethnic variations, with an allelic frequency ranging from 14.6% in the French Caucasian population studied to less than 2% in Black African and Peruvian populations. This ethnic-related data might contribute to a better understanding of the variability in clinical outcome and/or dose adjustments of drugs that are IMPDH inhibitors such as mycophenolic acid.     

CDH1 -160C>A gene polymorphism is an ethnicity-dependent risk factor for gastric cancer

The associations between E-cadherin (CDH1) gene polymorphisms and gastric cancer (GC) susceptibility are still controversial. Given this uncertainty, we carried out a meta-analysis of published case-control studies to derive more precise estimations of these relationships. Relevant studies were identified from PubMed and EMBASE up to March 2011. Seventeen studies with 3511 GC cases and 4826 controls were selected. Crude odds ratios (OR) and 95% confidence intervals (CI) were used to investigate the strength of the associations. No associations between CDH1 (+54T>C, -160C>A, -347G>GA, -616G>C, -2076C>T and -3159T>C) gene polymorphisms and GC risk for all genetic models were found. As for CDH1 -160C>A polymorphism, subgroup analyses by country, gender, study design, smoking status, Helicobacter pylori infection, and the Lauren classification of GC did not change the results. When stratified by ethnicity, we found the A allele carriers had a significantly increased risk of GC among Caucasians (AA vs. CA+CC: OR=1.50, 95% CI=1.03-2.19, P=0.03), but not among Asians (AA vs. CA+CC: OR=0.87, 95% CI=0.56-1.37, P=0.56). No publication bias was found in the present study. This meta-analysis suggests that CDH1 -160C>A gene polymorphism may contribute to increased risk of GC among Caucasians.     

Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons

Genotyping by high-resolution melting analysis of small amplicons is homogeneous and simple. However, this approach can be limited by physical and chemical components of the system that contribute to intersample melting variation. It is challenging for this method to distinguish homozygous G::C from C::G or A::T from T::A base-pair neutral variants, which comprise approximately 16% of all human single nucleotide polymorphisms (SNPs). We used internal oligonucleotide calibrators and custom analysis software to improve small amplicon (42-86 bp) genotyping on the LightScanner. Three G/C (PAH c.1155C>G, CHK2 c.1-3850G>C and candidate gene BX647987 c.261+22,290C>G) and three T/A (CPS1 c.3405-29A>T, OTC c.299-8T>A and MSH2 c.1511-9A>T) human single nucleotide variants were analyzed. Calibration improved homozygote genotyping accuracy from 91.7 to 99.7% across 1105 amplicons from 141 samples for five of the six targets. The average T(m) standard deviations of these targets decreased from 0.067 degrees C before calibration to 0.022 degrees C after calibration. We were unable to generate a small amplicon that could discriminate the BX647987 c.261+22,290C>G (rs1869458) SNP, despite reducing standard deviations from 0.086 degrees C to 0.032 degrees C. Two of the sites contained symmetric nearest neighbors adjacent to the SNPs. Unexpectedly, we were able to distinguish these homozygotes by T(m) even though current nearest neighbor models predict that the two homozygous alleles would be identical.     

Significant associations of polymorphisms in the prolactin gene with growth traits in Asian seabass (Lates calcarifer)

Prolactin (encoded by PRL) is a multifunctional hormone involved in osmoregulation, reproduction, growth, development, immunomodulation, endocrine and metabolic regulation. We cloned the full-length cDNA of Asian seabass PRL, searched for polymorphism in the DNA sequence, and conducted association analyses. Twelve SNPs and one 4-bp deletion were identified in PRL. The SNP c.264+127C>G was used for linkage mapping, and this gene was mapped to linkage group 11. The c.264+980_983delTTGT, c.264+127C>G, c.264+138T>G, c.264+269T>C and c.330C>G polymorphisms were genotyped in 521 individuals with growth trait records. Association analyses between single markers and growth traits revealed that the c.264+269T>C SNP was significantly associated with body weight (BW), total length (TL), standard length (SL) and Fulton's condition factor (KTL and KSL), while the other four were not. Analysis of haplotypes showed that there were 10 haplotypes and 22 haplotype combinations in the population. The differences of BW, TL, KTL and KSL among different haplotype combinations were significant.     

Identification of novel cystinuria mutations and polymorphisms in SLC3A1 and SLC7A9 genes: absence of SLC7A10 gene mutations in cystinuric patients

Cystinuria represents 3% of nephrolithiasis in humans with an overall prevalence of 1 in 7,000 neonates. Two genes have been reported to account for the genetic basis of cystinuria, the SLC3A1 and the SLC7A9. Recently, the possible involvement of the SLC7A10 gene in the genetic basis of the disorder was also reported. In the present study, we found a total of 15 mutations in 20 Greek cystinuric patients. Eight mutations are novel, 4 in the SLC3A1: F266S, T351I, R456C, and N516D, and 4 in the SLC7A9: 479-1G>C, Y232C, D233E, and 1399+1G>T. Furthermore, 2 polymorphisms were identified in the SLC3A1 gene and 16 polymorphic variants were also found in the SLC7A9 gene of which the 235+18C>A, 604+10G>A, and 604+24T>C are novel. Finally, no mutation was found in the SLC7A10 gene in all patients. Only, the novel 634+8C>G and the previously reported 913-11C+T polymorphisms were identified in the SLC7A10 gene. In conclusion, a spectrum of SLC3A1 and SLC7A9 mutations are responsible for the genetic basis of cystinuria in Greek patients.     

Renin-angiotensin and kinin-bradykinin genes polymorphism effects on permanent arterial hypertension in children

New methods are required for more objective estimation of the polymorphic genes contribution in multifactorial diseases. We suggest new approach based on the calculation of relative "score" as a sum of relevant genetic polymorphisms studied. Application of suggested approach is evaluated in analysis of the genes REN (19-83G>A), AGT (M235T), ACE (I/D), AGTR1 (1166A>C), AGTR2 (3123C>A), BKR2 (-58T>C and I/D) in children with arterial hypertension. The method proved that polymorphism of renin-angiotensin and kinin-bradikynin gene systems renders essential influence on formation of stably raised arterial pressure in girls.     

Manganese superoxide dismutase gene coding region polymorphisms lack clinical incidence in general population

Two functional polymorphisms within the manganese superoxide dismutase (MnSOD) gene have been reported to lead to increased oxidative stress damage. The MnSOD 58T > C single nucleotide polymorphism (SNP) within exon 3 changes isoleucine to threonine, leading to decreased thermal stability and reduced enzymatic activity in vivo and in vitro. The MnSOD 60C > T polymorphism within exon 3 changes leucine to phenylalanine, rendering the protein sensitive to redox regulation by intracellular thiols. Thus, the goal of this study was to evaluate the 58T > C and 60C > T MnSOD polymorphisms in a large case-control study. Taqman allelic discrimination assays were developed to identify the 58T > C and 60C > T SNPs in exon 3. Two hundred and eight lung cancer cases and 141 controls were evaluated for these two SNPs, and all 349 subjects were of the wild-type homozygous genotype for both 58C and 60T in exon 3. This study suggests that although the 58T > C and 60C > T polymorphisms reduce MnSOD enzymatic activity, these polymorphisms were not identified in the present case-control study population.     

The impact of OGG1, MTH1 and MnSOD gene polymorphisms on 8-hydroxy-2′-deoxyguanosine and cellular superoxide dismutase activity in myocardial ischemia–reperfusion

Ischemia–reperfusion (I/R) injury, by inducing oxidative DNA damage, is one of the leading causes of increased patient morbidity and mortality in coronary artery by-pass grafting (CABG) surgery. 8-Hydroxyguanine (8-OHG) is an important oxidative base lesion. The 8-oxoguanine glycosylase (hOGG1) and hMTH1, which have several polymorphisms, remove 8-OHdG from the nucleotide pool. We investigated whether there are any correlations the biomarkers of oxidative stress (superoxide dismutase; SOD and 8-OHdG in serum) with genotype for two DNA repair genes (OGG1 and MTH1) and an antioxidant enzyme gene (manganese superoxide dismutase; MnSOD). Therefore, we measured DNA damage (8-hydroxy-2-deoxyguanosine; 8-OHdG) and endogenous antioxidant activity (SOD) at five different time points (T1, before anesthesia; T2, after anesthesia; T3, after ischemia; T4, after reperfusion and T5, after surgery). and also, MnSOD and MutT homolog 1 (MTH1) genes polymorphisms were genotyped by polymerase chain reaction–restricted fragment length polymorphism (PCR–RFLP) in patients undergoing coronary artery by-pass grafting (CABG) surgery. No statistically significant differences were detected in the levels of 8-OHdG and SOD in serum in terms of OGG1 Ser326Cys, MTH1 Val83Met and MnSOD Ala16Val genetic polymorphisms. Our results suggest that OGG1, MTH1 and MnSOD gene polymorphisms are not genetic risk factors for I/R injury.     

Relationships between mitochondrial DNA subhaplogroups and intracellular calcium dynamics

Although an association between mitochondrial DNA (mtDNA) subhaplogroups and complex traits has been suggested, few functional analyses have been reported. To identify the mtDNA subhaplogroups that alter intracellular calcium dynamics, we analysed data on intracellular calcium dynamics in 35 transmitochondrial hybrid cells (cybrids). One cybrid showing decreased calcium levels had mtDNA subhaplogroup G3 or G4, characterised by 1413T>C, 2109A>T, 3434A>G, 5460G>A, 7521G>A, 9011C>T, 9670A>G and 15940T>C. The cybrid having higher calcium levels was subhaplogroup D4a, characterised by a non-synonymous polymorphism, 13651A>G. These mtDNA subhaplogroups might have functional effects.     

IL6 and IL1B polymorphisms are associated with fat mass in older men: the MrOS Study Sweden

There is growing evidence that immune functions are linked to the regulation of body fat. Our studies of knockout mice indicate that both endogenous interleukin (IL)-6 and IL-1 can suppress mature-onset obesity. We now investigated whether four common polymorphisms of the IL6 and IL1 systems are associated with the fat mass measured with dual-energy X-ray absorptiometry (DXA) in elderly men (n = 3,014). The study subjects were from the Swedish part of the MrOS multicenter population study and 69-81 years of age. The IL6 -174 G>C (Minor allele frequency (MAF) = 48%) gene promoter polymorphism was associated with the primary outcome total fat mass (P = 0.006) and regional fat masses, but not with lean body mass. The IL1B -31T>C (MAF = 34%) polymorphism was also associated with total fat (P = 0.007) and regional fat masses, but not lean body mass. The IL-1 receptor antagonist (IL-1ra) gene (IL1RN) +2018 T>C (MAF = 27%) polymorphism (in linkage disequilibrium (LD) with a well-studied variable number tandem repeat of 86 base pair (bp)) and IL1B +3953 C>T (MAF = 26%) polymorphism were not associated with total fat mass. In conclusion, the IL-1 and IL-6 systems, shown to suppress mature-onset obesity in experimental animals, contain gene polymorphisms that are associated with fat, but not lean, mass in elderly men.