广东人群PVRL1的多态性与NSCL/P的相关性分析

目的: 探讨脊髓灰质炎病毒受体相关基因( PVRL1 )的多态性与广东人群中非综合征型唇腭裂(NSCL/P,MIM 119530)的相关性。方法: 应用聚合酶链式反应和直接测序的方法对71例广东人群NSCL/P患者和100个健康志愿者的 PVRL1 exon 2和exon 5的多态性进行检测;应用基质辅助激光解吸电离飞行时间(MALDI-TOF)质谱分析的方法对100例广东人群NSCL/P患者和100个健康志愿者的 PVRL1 α亚型的334、391、1 183位点和β亚型的1082位点进行突变检测。结果: PVRL1 的exon 2和exon 5未发现有突变位点;质谱分析没有发现 PVRL1 α亚型的334、391、1 183位点和β亚型的1 082位点相关的S112A、T131A、G361V、V395M突变。结论: PVRL1 的exon 2、exon 5,α亚型334T>A、391A>T、1 183G>A,及β亚型1 082G>T的突变并不参与所研究的广东人群非综合征型唇腭裂的发生。     

2p24.2 (rs7552) is a susceptibility locus for nonsyndromic cleft lip with or without cleft palate in the Brazilian population

The population of Brazil is highly admixed, with each individual showing variable levels of Amerindian, European and African ancestry, which may interfere in the genetic susceptibility of known risk loci to nonsyndromic cleft lip with or without cleft palate (NSCL±P). Here, we investigated 5 reported genome‐wide loci for NSCL±P in an ancestry‐structured case‐control study containing 1697 Brazilian participants (831 NSCL±P and 866 healthy controls). SNPs rs7552 in 2q24.2, rs8049367 in 16p13.3, rs1880646, rs7406226, rs9891446 in 17p13, rs1588366 in 17q23.2 and rs73039426 in 19q13.11 were genotyped using TaqMan allelic discrimination assays and genomic ancestry was estimated using a panel of 40 biallelic short insertion/deletion polymorphic markers informative of the Brazilian population. Logistic regression analysis of the single‐markers revealed rs7552 in 2p24.2 as a susceptibility risk marker for NSCL±P, yielding an odds ratio (OR) of 1.71 (95% confidence interval (CI): 1.31‐2.24, P = 9 × 10^?6) in the homozygous state. Several SNP‐SNP interactions containing rs7552 reached significance after adjustment for multiple tests (both Bonferroni assumption and 1000 permutation test), with the most significant interaction involving the 3‐loci among rs7552, rs9891446 and rs73039426 (P = 6.1 × 10^?9 and p_{1000 permutation} = 0.001). Our study is the first to support the association of rs7552 in 2p24.2 with NSCL±P in the highly admixed Brazilian population.     

MSX1基因微卫星多态性与非综合征性唇腭裂的相关性研究

目的探讨肌肉片段同源盒1基因（muscle segment homeobox1,MSX1）与湖南汉族非综合征性唇腭裂（nonsydromic cleft lip and patate,NSCLP）的相关性。方法以MSX1基因内含子区的（CA）n微卫星作为遗传标记,对湖南汉族129例NSCLP患儿和108名正常儿童采用聚合酶链反应-变性聚丙烯酰胺凝胶基因分型技术进行基因分型,并经测序确定片段长度,应用病例对照研究进行相关性分析。结果湖南汉族人群MSX1基因（CA）n等位基因分布符合Hardy-Weinberg平衡,杂合率及多态信息量均为0.50;CA4等位基因频率在唇裂伴或不伴腭裂组及单纯性腭裂组高于对照组,CA4,4基因型频率在唇裂伴或不伴腭裂组和单纯性腭裂组高于对照组,差异均有统计学意义（均P〈0.05）。结论MSX1基因内（CA）n微卫星是多态性较好的遗传标记;MSX1基因可能与湖南汉族人群NSCLP发病相关。     

西北地区人群JAG2基因多态性与非综合征性唇腭裂的相关性研究

目的探讨JAG2基因多态性与西北地区人群非综合征性唇腭裂(nonsyndromic cleft lip with or without cleft palate,NSCLP)的相关性。方法采用病例-对照研究方法,选取NSCLP患者301例,正常对照304人,采用iMLDR™基因分型技术对JAG2基因的3个单核苷酸多态性(single nucleotide polymorphism,SNP)位点[rs741859(T/C)、rs11621316(A/G)以及rs1057744(C/T)]进行分型,比较其等位基因、基因型及所构建的单倍型在两组人群中的分布差异。结果rs741859位点等位基因C和T在NSCLP组和对照组中的分布差异有统计学意义。rs741859位点CT基因型可将NSCLP的患病风险显著降低至65%(P<0.05),将唇裂伴或不伴腭裂(cleft lip with or without cleft palate,CL/P)的患病风险降低至62%(P<0.05);而rs11621316、rs1057744处于同一连锁不平衡(linkage disequilibrium,LD)区域,连锁程度较高(r2>0.8),其基因型、等位基因在两组中的分布差异无统计学意义(P>0.05)。结论JAG2基因rs741859位点CT基因型可能是中国西北人群NSCLP的保护性基因型。     

蛋氨酸合酶基因A275 6G位点多态性与非综合征型唇腭裂的关联性研究

目的 研究蛋氨酸合酶基因(methionine synthase,MS)A2756G位点多态性与非综合征型唇腭裂(nonsyndromic cleft lip with or without cleft palate,NSCL/P)的关联性.方法 采用PCR-限制性片段长度多态性技术检测97个NSCL/P病例组核心家庭和104个对照家庭的MS基因A2756G位点的多态性;用人群关联研究分析、病例组核心家庭的传递不平衡检测(transmission disequilibrium test,TDT)、单体型的相对危险度分析(haplotype-based haplotype relative risk,HHRR)、家庭为基础的关联研究(family-based association tests,FBAT)等统计分析.结果 子代、父亲、母亲病例组和对照组之间基因型和等位基因的分布差异均无统计学意义(P>0.05);本研究中在子代和母亲组中未检出GG基因型,AG基因型相对于AA基因型的比值比OR和95%CI分别为子代1.78(0.74～4.34)、父亲0.80(0.36～1.79)、母亲1.26(0.54～2.93),G相对于A基因的OR和95%CI分别为子代1.70(0.78～3.73)、父亲0.88(0.49～1.75)、母亲1.23(0.59～2.60),携带有突变基因G并不能增加患NSCL/P的危险.病例组核心家庭分析,TDT分析χ2=0.034,P>0.05;HHRR分析χ2=0.03,P>0.05;FBAT分析Z=0.186,P>0.05.结论 结果未显示出MS基因A2756G位点多态性和NSCL/P发生的相关性,还待进一步研究.     

A novel mutation in the PHF8 gene is associated with X-linked mental retardation with cleft lip/cleft palate

Recently, two truncating mutations in the PHF8 (plant homeodomain finger protein 8) gene have been found to cause X-linked mental retardation associated with cleft lip/cleft palate (CL/P). One of the truncating mutations was found in the original family with Siderius-Hamel CL/P syndrome where only two of the three affected individuals had mental retardation (MR) with CL/P and one individual had mild MR. The second mutation was present in a family with four affected men, three of whom had MR and CL/P, while the fourth individual had mild MR without clefting. Here, we report a novel nonsense mutation (p.K177X) in a male patient who has MR associated with CL/P. The mutation results in a truncated PHF8 protein lacking the Jumonji-like C terminus domain and five nuclear localization signals. Our finding further supports the hypothesis that the PHF8 protein may play an important role in cognitive function and midline formation.     

Rs2262251 in lncRNA RP11‐462G12.2 is associated with nonsyndromic cleft lip with/without cleft palate

Nonsyndromic cleft lip with/without cleft palate (NSCL/P) is one of the most common human congenital defects. Rs2262251 (G>C) in long noncoding RNA (lncRNA) RP11‐462G12.2 is in high linkage disequilibrium with rs8049367, which was identified in our previous genome‐wide association study on NSCL/P, and is a potential causative single‐nucleotide polymorphism (SNP) for NSCL/P. To test these hypotheses, rs2262251 was evaluated in another cohort of 1,314 cases and 1,259 controls. Rs2262251 was associated with NSCL/P risk (p = .003). However, no association was detected for cleft palate only. SNP rs2262251 affected the structure and expression of lncRNA RP11‐462G12.2 in HEK293 and HEPM cells and in lip tissues from patients with NSCL/P. Overexpression of the rs2262251 G allele contributed to reducing the number of cells in the G0/G1 phase, inhibiting cell apoptosis, and promoting cell proliferation in vitro. The rs2262251 C allele regulated the expression of miR‐744‐5p and its target gene IQSEC2, both of which were expressed in human lip tissues, and showed reverse correlation during mouse lip development. Taken together, these findings suggest that rs2262251 is associated with the risk of NSCL/P and participates in a lncRNA–miRNA–mRNA regulatory axis in which miR‐744‐5p and IQSEC2 combine to control NSCL/P development.     

Evidence of the involvement of the DHFR gene in nonsyndromic cleft lip with or without cleft palate

Studies aimed at evidencing genetic causes for neural tube defect (NTD) occurrence have often provided the inspiration for orofacial cleft aetiology investigations. The correlation between the two congenital malformations is provided by the similar incidence timing and the involvement of structures localized in the midline of the embryo. This connection is corroborated by the existence of a number of genes involved in both malformations. In this article, we considered the dihydrofolate reductase (DHFR) gene, previously seen implicated in NTDs, as a candidate for cleft lip with or without cleft palate (CL/P) risk. Four SNPs mapping on the DHFR gene were genotyped for 400 Italian CL/P triads, using TaqMan^® approach. The rs1677693 provided evidence of association, even if at borderline level (P value 0.049). In particular, the variant allele seems to have a protective effect OR = 0.80 (95% C.I. 0.64–0.99). Moreover, the combination of rs1677693(A)-rs1650723(G) alleles showed a significant association OR 0.64 (95% C.I. 0.47–0.86) (P value = 0.006). This represents the first attempt to demonstrate a role for DHFR in CL/P aetiology, howbeit the study of such gene deserves a deepening.     

Association of interleukin-18 gene single-nucleotide polymorphisms with susceptibility to inflammatory bowel disease

Interleukin-18 (IL-18) is believed to be one of the most important cytokines in the pathogenesis of inflammatory bowel disease (IBD). The aim of the study was to clarify the significance of single-nucleotide polymorphisms (SNPs) at the 5'-end of the IL-18 gene in the development of IBD. DNA was obtained from peripheral blood of 99 patients with ulcerative colitis (UC), 79 patients with Crohn's disease (CD), and 102 healthy controls. All participants were Japanese. SNPs at -656G/T, -607C/A, -137G/C, +113T/G, and +127C/T were determined by means of direct sequencing, and a genetic association with IBD was examined. The frequencies of the G allele at +113 and the T allele at +127 were significantly higher in patients with CD and UC compared with controls. The differences in allelic frequencies were more striking in patients with CD than in patients with UC, and at position +127 than at position +113. The haplotype estimation, according to the E-M algorithm, suggested that TACGT is closely associated with IBD, especially with CD. It was concluded that SNPs at the 5'-end of IL-18 gene might be closely related to the etiology of IBD.     

Association of ATP-binding cassette transporter A1 gene polymorphisms with plasma lipid variability and coronary heart disease risk

Objective: Our study aimed to investigate the association of ABCA1 polymorphisms with plasma lipid variability and CHD risk in the Chinese Han population. Methods: 754 CHD patients and 760 controls were included in this case-control study. Three SNPs (rs363717, rs4149339, and rs4149338) in ABCA1 3’UTR and one nonsynonymous SNP (rs2230808) in ABCA1 exon 35 were selected and genotyped. The analysis of genetic data was performed using the SNPstats program and the SPSS17.0 software. Results: Significant associations were observed between SNP rs363717 and CHD risk under different genetic models before or after Bonferroni corrections (codominant model: OR = 0.70, P = 0.003 for AG vs. AA; dominant model: OR = 0.71, P = 0.003 for GG + AG vs. AA). The nonsynonymous SNP rs2230808 was associated with higher total cholesterol levels (P = 0.047). The GCC haplotype (consisting of alleles of SNPs rs363717, rs4149339, and rs4149338) was associated with a decreased risk of CHD (OR = 0.8, P = 0.027). Three ABCA1 SNPs interacted with high triglyceride levels to increase CHD risk (P values of interactions were 0.010 for rs363717, 0.010 for rs4149339, and 0.020 for rs4149338, respectively). Conclusions: Our results suggest that ABCA1 polymorphisms influence plasma lipid variability and CHD risk. ABCA1 polymorphisms could also modify the effects of plasma lipids on CHD risk.     

Association between GOLGB1 tag‐polymorphisms and nonsyndromic cleft palate only in the Brazilian population

Nonsyndromic oral clefts are common congenital birth defects that exhibit variable prevalence around the world, often influenced by population‐dependent genetic predisposition. Few studies have been performed with nonsyndromic cleft palate only (NSCPO), limiting the knowledge of the genetic risk factors related to this type of oral cleft. Genetic variants in golgin subfamily B member 1 (GOLGB1), a gene that is essential for normal murine palatogenesis, were analyzed in this study to establish its potential association with NSCPO risk in the Brazilian population. Five tag‐single nucleotide polymorphisms (SNPs) of GOLGB1 (rs1169, rs7153, rs9968051, rs9819530, and rs6794341), which capture the majority of alleles spanning within gene, were genotyped in a case–control study with 270 patients with NSCPO and 284 unrelated healthy controls. The samples were also genotyped for 40 biallelic polymorphic markers to characterize the genetic ancestry. After adjustment for co‐variants, the GOLGB1 tag‐SNPs and the haplotypes formed by those SNPs were not significantly associated with NSCPO in this Brazilian case–control cohort. Our results suggest that common polymorphisms of GOLGB1 are not associated NSCPO susceptibility in the Brazilian population.     

PAX9 and TGFB3 are linked to susceptibility to nonsyndromic cleft lip with or without cleft palate in the Japanese: population-based and family-based candidate gene analyses

The prevalence of nonsyndromic cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) are believed to be higher in the Japanese than in Americans, Europeans or Africans. The purpose of this study was to investigate, in a Japanese population, relationships between CL/P or CPO and seven candidate genes (TGFB3, DLX3, PAX9, CLPTM1, TBX10, PVRL1, TBX22) that showed positive associations in other populations and are expressed in the oral/lip region in developing mice. We first searched for mutations in these genes among 112 CL/P and 16 CPO patients, and found a heterozygous missense mutation (640A>G, S214G) in exon 3 of PAX9 in two sibs with CL/P and their phenotypically normal mother from a Japanese family. A population-based case-control analysis and a family-based transmission disequilibrium test (TDT), using single nucleotide polymorphisms (SNPs), and two-SNP haplotypes of the genes, between the 112 CL/P cases with their parents and 192 controls indicated a significant association at one SNP site, IVS1+5321, in TGFB3 with a P-value of 0.0016. Population-based haplotyping revealed that the association was most significant for haplotype A/A consisting of IVS1+5321 and IVS1–1572; TDT also gave a P-value of 0.0252 in this haplotype.     

Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate

We investigated the prevalence of mutations in the PHD finger protein 8 (PHF8) gene in X-linked mental retardation (XLMR) and facial cleft starting from the original cohort of 7712 patients operated on since 1 January 1950 for cleft lip/cleft palate in the Cleft Centre at the Helsinki University Hospital. From this nationwide material, 18 patients including one family with two male patients with cleft lip/cleft palate and unknown cause of mental retardation (MR) were sequenced for the coding regions and splice sites of the PHF8 gene. A novel missense mutation c.836C>T of the PHF8 gene was identified in a Finnish family with multiple-affected male patients. The mutation resides in exon 8 and changes phenylalanine to serine (F279S) in the functionally important Jmonji C domain of the protein. The clinical phenotype of the male patients was characterized by mild MR, mild dysmorphic features, unilateral cleft lip and cleft palate in one and bilateral cleft lip and cleft palate in the other sibling. The mutation was not present in 200 anonymous blood donors (approximately 300 X-chromosomes). To our knowledge, F279S is the third mutation of the PHF8 gene identified so far.     

No evidence of association of the MYO9B polymorphisms with celiac disease in the Spanish population

Inconsistent results concerning the association of polymorphisms in the MYO9B gene with celiac disease (CD) have been recently published. This gene encodes a myosin with a guanosine-triphosphatase (GTPase)-activating protein domain for the Rho-family of small G proteins, which are involved in cytoskeleton remodeling and therefore potentially involved in intestinal permeability. Functional and positional reasons led us to investigate the role of MYO9B polymorphisms in the Spanish CD population. A case-control study, including 415 CD patients and 433 ethnically matched healthy controls, and a familial study, including parents of 145 of those CD patients, was performed. Six MYO9B variants previously associated with CD were analyzed: rs2305767, rs2279003, rs962917, rs1457092, rs2305765 and rs2305764. No MYO9B variants or MYO9B haplotypes were found associated with CD, either before or after stratification of the patients for the human leucocyte antigen (HLA)-DQ2-positive risk factor. The family study revealed no distorted transmission of the aforementioned MYO9B polymorphisms or haplotypes. Our results support a negligible influence of this gene on CD predisposition.     

Common gene variants interactions related to uric acid transport are associated with knee osteoarthritis susceptibility

Background: The presence of genetic variants in uric acid (UA) transporters can be associated with hyperuricemia, and therefore with an increased risk of monosodium urate (MSU) crystal precipitation. The inflammatory process triggered by these crystals leads to cartilage damage, which, in turn, could promote knee osteoarthritis (KOA).

Objective: To determine whether genetic polymorphisms of the UA transporters and their interactions are associated with KOA.

Materials and Methods: Two hundred forty-three unrelated Mexican-mestizo individuals were recruited for this case-control study. Ninety-three of them were KOA patients but without gout, and one hundred and fifty healthy individuals with no symptoms or signs of KOA were recruited as controls. Forty-one single-nucleotide polymorphisms (SNPs) involved in the UA transporters were genotyped with OpenArray technology in a QuantStudio 12K flex-System with both cases and controls.

Results: After adjusting by age, gender, BMI, and ancestry, significant associations were found for eight SNPs: rs1260326 (GCKR), rs780093 (GCKR), rs17050272 (INHBB), rs1471633 (PDZK1), rs12129861 (PDZK1), rs7193778 (IGF1R), rs17786744 (STC1), and rs1106766 (R3HDM2). With respect to gene–gene interactions, the pairwise interactions of rs112129861 (PDZK1) and rs7193778 (IGF1R); rs17050272 (INHBB) and rs1106766 (R3HDM2); rs1106766 (R3HDM2) and rs780093 (GCKR); rs1260326 (GCKR) and rs17786744 (STC1); and rs17786744 (STC1) and rs1106766 (R3HDM2) make it possible to visualize the synergistic or antagonistic effect of their genotypes or alleles on KOA development.

Conclusions: Our preliminary results show that the common gene variants related to UA transport are associated with KOA in the Mexican population. Further studies must be carried out to corroborate it.     

Contribution of variants in and near the IRF6 gene to the risk of nonsyndromic cleft lip with or without cleft palate in a Malay population

Several studies have shown evidence for the contribution of interferon regulatory factor 6 (IRF6) variants to the risk of nonsyndromic oral clefts in Asians; however, this has not included the Malay population. The current study attempts to address this research gap using allele and haplotype transmission disequilibrium analyses. The results showed a strong transmission distortion for multiple haplotypes to patients with nonsyndromic cleft lip with or without cleft palate. Haplotypes carrying the 243 bp allele of D1S2136 and common alleles at the rs861019 and rs2235371 were over‐transmitted to patients. By contrast, haplotypes consisting of the 251 bp allele of D1S2136 and the rare allele at rs2235371 were more under‐transmitted. Furthermore, several variants and haplotypes showed excess maternal transmission, but none of them attained statistical significance in maternal relative risk analyses. In contrast, a significant child genotype effect was observed for several haplotypes, indicating fetal genotype could be the major genetic contribution rather than maternal genotype. The present study therefore further supports a role for IRF6 variants in clefting in this Southeast Asian population. Overall, Asian genetic backgrounds are most likely more susceptible to the haploinsufficiency of IRF6 variants. These variants may contribute to the condition either themselves, or they may be in linkage disequilibrium with other casual variants. © 2011 Wiley‐Liss, Inc.     

Genetic polymorphisms in cell cycle regulatory genes MDM2 and TP53 are associated with susceptibility to lung cancer

The tumor suppressor TP53 pathway plays a crucial role in preventing carcinogenesis through its ability to impose cell cycle arrest and apoptosis following DNA damage and oncogene activation. MDM2 is a key negative regulator of the TP53 pathway and is overexpressed in many cancers as oncoprotein. We investigated the association between genetic variation in the promoter region of MDM2 (c.-5+309G>T, rs2279744:g.G>T) and the coding region of TP53 (c.215G>C, rs1042522:g.G>C, designated Arg72Pro) and the risk of developing lung cancer. The genotypes of 1,106 patients and 1,420 controls were determined by tetra-primer amplification refractory mutation system (ARMS)-PCR or PCR-based restriction fragment length polymorphism (RFLP). Associations with risk of lung cancer were estimated by logistic regression. We observed an increased lung cancer risk associated with the MDM2 GG (odds ratio [OR] = 1.83, 95% confidence interval [CI] = 1.45-2.32) and TG (OR = 1.33, 95% CI = 1.09-1.63) genotypes. An increased risk was also associated with the TP53 Pro/Pro genotype (OR = 1.47, 95% CI = 1.17-1.85, P = 0.003) compared to the Arg/Arg genotype. The gene-gene interaction of MDM2 and TP53 polymorphisms increased lung cancer risk in a supermultiplicative manner (OR for the presence of both MDM2 GG and TP53 Pro/Pro genotypes = 4.56, 95% CI = 2.76-7.54). Significant interactions were observed between these polymorphisms (respectively and jointly) and smoking (OR = 10.41, 95% CI = 5.26-20.58) for smokers with both the MDM2 GG and TP53 Pro/Pro genotypes. In conclusion, genetic polymorphisms in cell cycle regulatory genes MDM2 and TP53 contribute to the risk of developing lung cancer.     

Functional polymorphisms in CD86 gene are associated with susceptibility to pneumonia‐induced sepsis

Sepsis is an illness in which the body has a severe response to bacteria or other germs. A bacterial infection in the body such as lungs may set off the response that leads to the disease. CD86 (B7‐2) is expressed on various immune cells and plays critical roles in immune responses. Genetic polymorphisms in CD86 gene may affect the development of several diseases. Here, we evaluated the association between two CD86 polymorphisms (rs1915087C/T and rs2332096T/G) and susceptibility to pneumonia‐induced sepsis. CD86 rs1915087C/T and rs2332096T/G were identified in 186 pneumonia‐induced septic patients and 196 healthy controls in the Chinese population. Results revealed that subjects with rs1915087CT and TT genotypes had significantly lower risk of pneumonia‐induced sepsis than those with CC genotype [odds ratio (OR) = 0.58, 95% confidence interval (CI), 0.37–0.91, p = 0.017, and OR = 0.40, 95%CI, 0.21–0.76, p = 0.005]. However, prevalence of rs2332096GG genotype and G allele were significantly increased in patients than in healthy controls (OR = 2.75, 95%CI, 1.46–5.16, p = 0.001, and OR = 1.65, 95%CI, 1.21–2.24, p = 0.001]. We further investigated functions of these two polymorphisms by assessing gene expression in peripheral blood mononuclear cells and in monocytes. Data showed subjects carrying rs2332096GG genotype had significantly decreased level of CD86 in monocytes than those carrying rs2332096TT genotype. These results indicate that CD86 polymorphisms are associated with susceptibility to pneumonia‐induced sepsis and may affect gene expression in monocytes.