In vitro production of IFN-gamma correlates with CA repeat polymorphism in the human IFN-gamma gene.

The DNA sequence of the human IFN-gamma gene shows the presence of a variable-length CA repeat in the first intron of the gene. We investigated the allele distribution of this microsatellite region in 164 unrelated healthy individuals, and the association with interferon-gamma (IFN-gamma) production. In vitro production of IFN-gamma showed a significant correlation with the presence of allele #2.     

CA repeat allele polymorphism in the first intron of the human interferon-gamma gene is associated with lung allograft fibrosis.

Interferon-gamma (IFN-gamma) is an inflammatory cytokine that has been implicated in the development of fibrosis in inflamed tissues. In this study we have analysed the association between genetically-determined high IFN-gamma production and development of fibrosis in lung transplants. The human IFN-gamma gene has a variable length CA repeat in the first intron. Our previous study showed that polymorphism of this microsatellite is associated with individual variation in the levels of IFN-gamma production. In vitro production of IFN-gamma showed significant correlation with presence of allele #2 (p < 0.01). In this study allele #2 was found to be associated with allograft fibrosis defined by transbronchial biopsy. An analysis of two groups of lung transplant recipients showed a significant increase in the frequency of allele #2 in the group which developed fibrosis after transplantation compared to the group that did not (p < 0.005). We postulate that the production of IFN-gamma, which is under genetic control, can influence the development of fibrosis in lung allografts.     

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。     

In vitro production of IFN-γ correlates with CA repeat polymorphism in the human IFN-γ gene

The DNA sequence of the human IFN-γ gene shows the presence of a variable-length CA repeat in the first intron of the gene. We investigated the allele distribution of this microsatellite region in 164 unrelated healthy individuals, and the association with interferon-γ (IFN-γ) production. In vitro production of IFN-γ showed a significant correlation with the presence of allele #2.     

Association analysis of the monoamine oxidase A and B genes with attention deficit hyperactivity disorder (ADHD) in an Irish sample: preferential transmission of the MAO-A 941G allele to affected children.

Pharmacological and genetic studies suggest the importance of the dopaminergic, serotonergic, and noradrenergic systems in the pathogenesis of attention deficit hyperactivity disorder (ADHD). Monoamine oxidases A and B (MAO-A and MAO-B) degrade biogenic amines such as dopamine and serotonin and thereby control the levels of these neurotransmitters in the central nervous system. We examined four polymorphisms in the MAO-A gene (30 bp promoter VNTR, CA microsatellite in intron 2, 941G/T SNP in exon 8, and A/G SNP in intron 12) as well as two markers in the MAO-B gene (CA microsatellite in intron 2 and T/C SNP in intron 13) for association with ADHD in an Irish sample of 179 nuclear families. TDT analysis of the examined MAO-A markers revealed a significant association of the more active MAO-A 941G allele with the disorder (chi2 = 5.1, P = 0.03, OR = 1.7). In addition, haplotype analysis revealed a significantly increased transmission of a haplotype consisting of the shorter allele of the promoter VNTR (allele 1), the 6-repeat allele of the CA microsatellite and the G-allele of the 941G/T SNP (famhap global statistic 34.54, P = 0.01) to ADHD cases. No significant distortion in the number of transmitted alleles was observed between the two examined MAO-B polymorphisms and ADHD. These findings suggest the importance of the 941G/T MAO-A polymorphism in the development of ADHD at least in the Irish population.     

Histamine N-methyltransferase functional polymorphism: lack of association with schizophrenia

Histamine is a central nervous system (CNS) neurotransmitter that has been implicated in the pathophysiology of schizophrenia. Histamine N-methyltransferase (HNMT) terminates the neurotransmitter actions of histamine in the mammalian CNS, and levels of HNMT activity in human tissues are controlled, in part, by inheritance. A common C314T polymorphism in the HNMT gene causes a Thr105Ile change in encoded amino acid. The T314 allele results in decreased levels of both HNMT enzyme activity and immunoreactive protein. There is also a polymorphic CA repeat in intron 5 of the HNMT gene. The frequencies of alleles for the functional C314T polymorphism and the polymorphic CA repeat were compared between 171 schizophrenia cases and 171 ethnically matched controls to test for possible disease association. No significant difference was found between the two groups in the frequency of the T314 allele in patients with schizophrenia and controls (0.068 vs. 0.078, respectively). Allele frequencies for the polymorphic HNMT CA repeat also failed to show significant differences between cases and matched controls.     

3' polymorphisms of ETS1 are associated with different clinical phenotypes in SLE

A microsatellite repeat polymorphism was identified in the 3' flanking region of the human ETS1 gene. Sequencing revealed two CA repeat segments in close proximity. Seven different alleles comprising various combinations of CA repeat units were identified in a healthy control population. Because ETS1 plays a role in lymphocyte development and function, apoptosis, and inflammation, we examined whether any of these polymorphisms were associated with a systemic inflammatory condition, systemic lupus erythematosus (SLE). Inheritance of this disease is polygenic and a recent genome-wide screen for SLE susceptibility loci revealed linkage with chromosome 11q14-23, the region in which the ETS1 gene lies. This region has also been identified as a general autoimmune susceptibility region. None of the seven distinct ETS1 alleles appeared statistically more frequently in SLE patients than controls, however, two alleles were associated with particular clinical manifestations. Allele 1 is associated with discoid lesions and allele 7 is associated with vasculitis. While this polymorphism does not directly affect the coding region of ETS1, it may be a marker for overexpression of a particular isoform or inheritance of another polymorphism which does affect function. These data suggest that ETS1 may be involved in the phenotypic expression of systemic lupus erythematosus.     

Association of IFN-gamma and IFN regulatory factor 1 polymorphisms with childhood atopic asthma

BACKGROUND: IFN-gamma and related molecules play important roles in the differentiation and function of TH2 cells. OBJECTIVE: We sought to determine whether IFNG and related genes contribute to any susceptibility to atopic asthma, a representative TH2-dominant disorder. METHODS: We investigated the association of IFNG (CA repeat polymorphism within the first intron), IRF1 (GT repeat polymorphism within the intron 7), IFNGR1 (Val 14 Met), and IFNGR2 (Gln 64 Arg) gene polymorphisms with atopic asthma in the Japanese child population. RESULTS: A significant association (P =.0018) was observed between IFNG gene polymorphism and atopic asthma. The tendency was more prominent in patients with age of onset of 3 years or younger (P =.0004) or patients with a family history of allergic diseases (P =.0038). Furthermore, there was a significant association between IRF1 gene whole-allele distribution and atopic asthma (P =.044). The tendency was more prominent in patients with onset at 3 years of age or less (P =.0058). On the other hand, IFNGR1 and IFNGR2 gene polymorphisms showed no association with atopic asthma. CONCLUSION: These results suggested that among IFNG and related genes, IFNG and IRF1 genes confer genetic susceptibility to atopic asthma in Japanese children.     

The natural history of a microsatellite located in the HLA DQ region

Microsatellite sequences are very polymorphic stretches of di or more nucleotide repeats that are intensively used in gene mapping studies. In this study, we have characterized the polymorphism of a CA repeat sequence (DQCAR) located between DQA1 and DQB1. This allowed us to study the value of microsatellite typing for association studies and to speculate on the evolution and mutagenicity of dinucleotide sequences in the human genome.

The linkage disequilibrium pattern of 14 DQCAR alleles was established using 941 samples oligotyped at the DRB1, DQA1 and DQB1 level. Samples included unrelated subjects from Japan, Papua New Guinea, African American and Caucasians, 10th WS cell lines and patients with various Class II associated diseases. DQCAR typing was performed as described previously (Human Immunol, 42(3); 209-220, 1995). We also PCR amplified, cloned and sequenced various DQCAR size alleles in a subset of samples.

The most striking finding of this study was the discovery that DQCAR variation differed greatly between DQ1 and non DQ1 haplotypes. Almost all DQ1 samples shared a single DQCAR allele (DQCAR 103). In contrast, non DQ1 haplotypes displayed a large amount of additional DQCAR variation, with for example up to 8 alleles in association with DQB1^*0301. We also explored the value of DQCAR typing in a few selected autoimmune disorders but could not detect a tighter association than with HLA class II typing alone.

DQCAR sequencing results were very informative to explain the lack of DQCAR polymorphism in DQCAR103-DQ1 haplotypes. In the low variation DQ1 haplotypes, the stretch of CA was interrupted by a C to A mutation, thus leading to short CA repeat stretches flanking a triple A sequence. In contrast, all DQCAR mutating alleles had relatively longer perfect CA repeat sequences. Other sequence changes were also observed in the flanking area of the microsatellite where CA to GA conversions were frequently observed. These results suggest that sequence polymorphisms within individual microsatellite alleles may drastically influence the mutation rate of each allele. This may have consequences for disease association studies using microsatellite markers.     

Molecular analysis of the oligodendrocyte myelin glycoprotein gene in autistic disorder

We previously observed in four autistic patients a new allele (GXAlu 5) of the GXAlu microsatellite marker located in intron 27b of the neurofibromatosis type 1 (NF1) gene (17q11.2). This large intron contains the OMGP gene, coding for the oligodendrocyte myelin glycoprotein expressed by neurons and oligodendrocytes. In the present work, we analysed the distribution of a coding single nucleotide polymorphism (OMGP62) of the OMGP gene, the nearest gene to the GXAlu marker, in a control population (n=101) and in an autistic group (n=65). We observed no significant difference in allele distribution comparing these two groups (chi(2)=1.81; P=0.179). When distinguishing an autistic group with a developmental quotient (DQ) higher than 30 (n=37) and one with a DQ lower than 30 (n=28), we observed an association between allele A and the group with the highest DQ (P=0.015). We found no other polymorphism using SSCP screening and DNA sequencing in the OMGP coding region in 16 autistic patients bearing OMGP62 allele A.     

广东汉族人群MICA和MICB微卫星多态性分布

目的　调查广东地区汉族人群 MICA基因第 5外显子和 MICB基因第 1内含子微卫星多态性分布。方法　应用聚合酶链反应和荧光 ( 6 - FAM)自动化检测技术 ,对广东地区共 10 6名无亲缘关系样本进行 MICA和 MICB微卫星基因分型 ,并计算这两个微卫星的基因频率、基因型频率、个体鉴别力、期望杂合性、多态性信息含量和非父排除率。结果　MICA和 MICB微卫星基因型分布符合 Hardy- Weinberg平衡。MICA A5基因频率最高为 0 .2 877,A4基因频率则最低为 0 .132 1;A5 - 5 .1( 14 .15 % )和 A5 - 5 ( 10 .38% )基因型分布频率较高。 MICB CA14等位基因频率最高为 0 .32 5 5 ,CA19、CA2 8等位基因频率最低为0 .0 0 4 7,未检出 CA2 7。 CA14 - CA14 ( 14 .15 % )基因型分布频率较高。结论　 MICA基因第 5外显子和MICB基因第 1内含子微卫星适合作为中国人群的遗传标志 ,用于人类学、遗传疾病基因连锁分析、法医学亲子鉴定和个体识别等研究领域     

Promoter and intron-1 region polymorphisms in the IFNG gene in patients with hepatitis E

Allelic and genotype variations in the promoter region and the dinucleotide (CA)(n) repeat region in intron 1 of the interferon-g (IFNG) gene were analysed by direct sequencing and simple sequence length polymorphism (SSLP), respectively, in patients with acute hepatitis, and the prevalence was compared with that in healthy controls. Our results showed a significant association of heterozygous genotypes (CA)12/(CA)14 and (CA)12/(CA)16 in intron 1 of the IFNG gene in all categories of patients with acute hepatitis, classified on the basis of presence or absence of hepatitis E virus (HEV), in comparison with healthy controls. A novel polymorphism, -288 A-->T [from the translational start site, as per Human Genome Organization (HUGO) nomenclature], in the promoter region of the IFNG gene leading to a loss of the consensus domain for the interferon-stimulated response element (ISRE), as predicted by in silico analysis, was observed in 12.5% of patients with acute HEV infection. However, no significant difference in allele or genotype frequency was observed for the -288 promoter polymorphism, although the heterozygous -288 A/T genotype showed a moderate risk in patients with acute HEV infection alone (P = 0.29, odds ratio = 1.964, confidence interval = 0.46-8.45). The data suggest that the genotype at intron 1 of IFNG might affect susceptibility to acute hepatitis in HEV infection, which warrants further elucidation in a larger sample and also functional studies.     

A CA repeat polymorphism of the IFN-gamma gene is associated with susceptibility to type 1 diabetes.

Recent studies have shown that loci outside the HLA region are involved in determining susceptibility to type 1 diabetes. Polymorphisms in the coding and noncoding regions of the genes encoding cytokines may be involved in modulating the immune response to self and nonself antigens. There is increasing evidence that an imbalance and disruption of the Thl and Th2 T cell subsets play a key role in the development of experimental and clinical type 1 diabetes. The aim of this study was to investigate the frequency of a CA dinucleotide repeat polymorphism in the interferon-gamma (IFN-gamma) gene (IFNG) and a C(-590)T polymorphism of the interleukin-4 (IL-4) gene in 236 Caucasoid patients with type 1 diabetes. There was a highly significant increase in the 3/3 IFNG genotype in the patients compared with normal healthy controls (34.3% vs. 13.5%, p<0.0001) as well as a significant increase in allele 3 of the IFNG locus in the patients compared with controls (51.9% vs. 31.7%, p<0.00001). In contrast, no significant differences were found in the frequency of the C(-590)T IL-4 polymorphism between patients and controls. These results suggest that polymorphisms of the IFNG gene may modify the function of this proinflammatory mediator and the response to pancreatic islet beta cells.     

Association of interferon-γ and interferon regulatory factor 1 polymorphisms with asthma in a family-based association study in Taiwan

BACKGROUND: Asthma is a multi-factorial disorder caused by complex interactions between genetic and environmental factors. IFN-gamma and IFN regulatory factor 1 (IRF-1) affect Th1/Th2 cytokine balance, and influence the differentiation of Th2 cells, which influence the development of asthma. OBJECTIVE: This study investigated CA repeats polymorphism of the IFN-gamma gene and GT repeats polymorphism of the IRF-1 gene, which may predispose individuals to asthma pathogenesis. METHODS: In the present study, we used the transmission/disequilibrium test (TDT) to investigate the relationship between asthma and the IFN-gamma and IRF-1 polymorphisms by studying 348 subjects composed of 232 parents and 116 asthmatic children. RESULTS: For global TDT test, IFN-gamma CA repeats and IRF-1 GT repeat polymorphisms showed a significant association with asthma in children (P=0.009 and 0.017, respectively). We demonstrated that 13 CA repeats (138 bp) of IFN-gamma gene and 11 GT repeats (306 bp) of IRF-1 gene are significantly preferentially transmitted to asthmatic children (T/NT=89/61, chi2=8.43, P<0.005 and T/NT=75/49, chi2=8.18, P<0.005, respectively). The offspring will have an increased risk of asthma when their parents transmit IFN-gamma 13 CA repeats (OR=1.83, P=0.009) and IRF1 11 GT repeats (OR=1.88, P=0.007) to them. But we observed that the IFN-gamma and IRF-1 polymorphisms are not associated with IgE concentrations. CONCLUSION: These findings provide strong evidence of which IFN-gamma CA repeat and IRF-1 GT repeat polymorphisms influence the risk of asthma for children in Taiwan.     

Association of TNF-alpha, TNF-beta, IFN-gamma and IL-1Ra gene polymorphisms with Graves' disease in the Thai population

Cytokines play a key role in the regulation of immune and inflammatory responses. Therefore, cytokine genes are potentially related to susceptibility to Graves' disease (GD). The aim of this study was to investigate the putative functional polymorphisms within tumor necrosis factor-alpha (TNF-alpha), tumor necrosis factor-beta (TNF-beta), interferon-gamma (IFN-gamma), and interleukin-1 receptor antagonist (IL-1Ra) genes, in patients with GD (n = 137) compared to a healthy Thai control group (n = 137). The results showed no statistically significant difference between the study groups for TNF-beta (Ncol site in intron 1), IFN-gamma (+874 in intron 1), and IL-1Ra (variable numbers of tandem repeats in intron 2) gene polymorphisms. Only the -863A allele within the promoter region of the TNF-alpha gene, which may affect the affinity of the promoter nuclear factor (NF)-kappab interaction, was found to be increased in GD patients compared to the controls (p = 0.009, OR = 1.8, 95% CI = 1.15 to 2.84). The effect of the -863A allele of the TNF-alpha gene was similar to the autosomal dominance mode of inheritance (p = 0.01, OR = 2, 95% CI = 1.16 to 3.44). This polymorphism may be involved in the susceptibility to GD in part through its higher promoter activity of TNF-alpha production.     

Global profiling of EGFR gene mutation,amplification, regulation and tissue protein expression in unknown primary carcinomas: to target or not to target?

Introduction Epidermal growth factor receptor (EGFR) signalling contributes to malignant transformation and survival. We studied molecular predictors of benefit from EGFR-modulating therapies in patients with cancer of unknown primary (CUP). Materials and methods Tumours from paraffin-embedded biopsies of 50 patients with CUP were stained for EGFR protein by immunohistochemistry. Polymerase chain reaction amplification, single-strand conformational polymorphism and direct sequencing were used to study EGFR intron 1 cytosine-adenosine (CA) repeat length as well as exon 18, 19, 21 activating mutations and amplification. Results Thirty-seven tumours (74%) expressed EGFR protein but only six (12%) strongly. Regarding intron 1 CA repeat length, we detected five alleles with CA repeat numbers 16–20, allele 16 being the most common (39%). All samples were heterozygous, the commonest genotype consisting of 16/18 dinucleotides (78%). Five samples had three intron 1 alleles and were associated with EGFR overexpression in 40% of cases. There was no evidence of EGFR exon 18, 19, 21 amplification. Two mutations were detected: Exon 21 2508 C > T, a silent nucleotide polymorphism (R836R) and a G > A substitution in sequences flanking exon 19 (IVS19 + 24G > A) resulting in aberrant mRNA splicing. Neither EGFR protein expression nor CA repeat length were prognostic factors for survival. Conclusions Our data depict absence of molecular predictors of benefit from EGFR modulation in patients with CUP. Study of its molecular pathophysiology and targeting other molecular pathways may be warranted instead.