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PubMed2004

Genome-wide profiling of papillary thyroid cancer identifies MUC1 as an independent prognostic marker.

Clinicopathological variables used at present for prognostication and treatment selection for papillary thyroid carcinomas (PTCs) do not uniformly predict tumor behavior, necessitating identification of novel prognostic markers. Complicating the assessment is the long natural history of PTC and our rudimentary knowledge of its genetic composition. In this study we took advantage of differences in clinical behavior of two distinct variants of PTC, the aggressive tall-cell variant (TCV) and indolent conventional PTC (cPTC), to identify molecular prognosticators of outcome using complementary genome wide analyses. Comparative genome hybridization (CGH) and cDNA microarray (17,840 genes) analyses were used to detect changes in DNA copy number and gene expression in pathological cPTC and TCV. The findings from CGH and cDNA microarray analyses were correlated and validated by real-time PCR and immunohistochemical analyses on a series of 100 cases of cPTC and TCV. Genes identified by this approach were evaluated as prognostic markers in cPTC by immunohistochemistry on tissue arrays. CGH identified significant differences in the presence (76 versus 27%; P = 0.001) and type of DNA copy number aberrations in TCV compared with cPTC. Recurrent gains of 1p34-36, 1q21, 6p21-22, 9q34, 11q13, 17q25, 19, and 22 and losses of 2q21-31, 4, 5p14-q21, 6q11-22, 8q11-22, 9q11-32, and 13q21-31 were unique to TCV. Hierarchical clustering of gene expression profiles revealed significant overlap between TCV and cPTC, but further analysis identified 82 dysregulated genes differentially expressed among the PTC variants. Of these, MUC1 was of particular interest because amplification of 1q by CGH correlated with MUC1 amplification by real-time PCR analysis and protein overexpression by immunohistochemistry in TCV (P = 0.005). Multivariate analysis revealed a significant association between MUC1 overexpression and treatment outcome, independent of histopathological categorization (P = 0.03). Analysis of a validation series containing a matched group of aggressive and indolent cPTCs confirmed the association between MUC1 overexpression and survival (relative risk, 2.3; 95% confidence interval, 1.1-5.5; P = 0.03). Our data suggest that MUC1 dysregulation is associated with aggressive behavior of PTC and may serve as a prognostic marker and potential therapeutic target in this disease.

Carcinoma, Papillary↗
PubMed1999

Donor G protein beta3 subunit 825TT genotype is associated with reduced kidney allograft survival.

Recent studies have identified a novel polymorphism (C825T) of the gene encoding the beta3 subunit of heterotrimeric G proteins (Gbeta3), associated with enhanced activation of G proteins, which appears to be more common in hypertensive patients. In the present study, the relationship between this genetic variant and kidney allograft survival was examined over the first 3 yr after transplantation, in 320 consecutive Caucasian patients recruited from the Berlin-Steglitz transplantation center between 1988 and 1993. Clinical parameters, transplantation data, and details of graft survival were retrieved from clinical records. After multivariate adjustment for covariates (Cox hazard regression), the Gbeta3 825TT donor-genotype was associated with a significantly decreased graft survival representing a relative risk of graft loss of 2.2 (95% confidence interval, 1.1 to 4.8) compared to TC and CC grafts within the observation period. This association between donor TT genotype and graft survival remained stable even after stepwise exclusion of covariates from the multivariate model. In contrast, there was no significant relationship between recipient genotype and allograft function. These findings indicate that individuals receiving renal allografts from donors homozygous for the Gbeta3-825T allele may have an increased risk of developing allograft failure. Additional studies on the role of this genetic marker as well as the role of pertussis toxin-sensitive G proteins in the development of chronic rejection appear warranted.

Adult↗
PubMed1999

Alpha1-antitrypsin deficiency allele carriers among lung cancer patients.

Lung cancer (LC) and chronic obstructive pulmonary lung diseases (COPDs; including emphysema and chronic bronchitis) share a common etiology. Despite the known associations of alpha1-antitrypsin deficiency (alpha1AD) with COPD and COPD with LC, few studies examined the association of alpha1AD alleles and LC. We hypothesize that heterozygous individuals who carry a deficient allele of the alpha1AD gene Pi (protease inhibitor locus) are at an increased risk of developing LC. The Pi locus is highly polymorphic with >70 variants reported. There are at least 10 alleles associated with deficiency in alpha1-antitrypsin. Using an exact binomial test, we compared the alpha1AD carrier rate in 260 newly diagnosed Mayo Clinic LC patients to the reported carrier rate in Caucasians in the United States (7%). alpha1AD carrier status, determined by isoelectric focusing assay, was examined with respect to the history of cigarette smoking, COPD, and histological types. Thirty-two of the 260 patients (12.3%; 95% confidence interval, 8.6-16.9%) carried an alpha1AD allele, which was significantly higher than expected (P = 0.002). Twenty-four of the 32 carriers had allele S, 6 had allele Z, and 2 had allele I. Patients who never smoked cigarettes were three times more likely to carry a deficient allele (20.6%; P = 0.008), although smokers had a higher carrier rate (11.1%; P = 0.025) when compared with the 7% rate. Patients with squamous cell or bronchoalveolar carcinoma had a significantly higher carrier rate than expected (15.9% and 23.8%, P < or = 0.01, respectively). Our preliminary findings suggest that individuals who carry an alpha1AD allele may have an increased risk for developing LC, specifically squamous cell or bronchoalveolar carcinoma.

Adenocarcinoma, Bronchiolo-Alveolar↗
PubMed2001

An intronic poly (AT) polymorphism of the DNA repair gene XPC and risk of squamous cell carcinoma of the head and neck: a case-control study.

Inherited polymorphisms of DNA repair genes may contribute to variations in DNA repair capacity and genetic susceptibility to cancer. In a hospital-based case-control study of 287 non-Hispanic white patients with newly diagnosed SCCHN and 311 control subjects matched on age, sex, ethnicity, and smoking status, we investigated the role of a newly identified variant allele of XPC, XPC-PAT+. We found that the frequency of the XPC-PAT+ allele was higher in the cases (0.409) than in the controls (0.333; P = 0.007). Fifty cases (17.4%) and 37 controls (11.9%) were XPC-PAT+/+, and 135 (47.0%) cases and 133 controls (42.8%) were XPC-PAT+/-. XPC-PAT+/- and XPC-PAT+/+ subjects were at significantly increased risk for SCCHN [adjusted odds ratios = 1.44 and 1.85, respectively (95% confidence intervals, 1.01-2.05 and 1.12-3.05, respectively; trend test, P = 0.007)]. We did not find ethnic difference in the frequency of XPC-PAT+ allele among four groups aged between 19 and 75 years: non-Hispanic whites, 294; African-Americans, 178; Hispanic-Americans, 103; and native Chinese, 119 (0.333, 0.281, 0.296, and 0.353, respectively). The case-control findings support the hypothesis that the XPC-PAT+ allele may contribute to the risk of developing SCCHN.

Aged↗
PubMed2006

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

MOTIVATION: Algorithmic and modeling advances in the area of protein-protein interaction (PPI) network analysis could contribute to the understanding of biological processes. Local structure of networks can be measured by the frequency distribution of graphlets, small connected non-isomorphic induced subgraphs. This measure of local structure has been used to show that high-confidence PPI networks have local structure of geometric random graphs. Finding graphlets exhaustively in a large network is computationally intensive. More complete PPI networks, as well as PPI networks of higher organisms, will thus require efficient heuristic approaches. RESULTS: We propose two efficient and scalable heuristics for finding graphlets in high-confidence PPI networks. We show that both PPI and their model geometric random networks, have defined boundaries that are sparser than the 'inner parts' of the networks. In addition, these networks exhibit 'uniformity' of local structure inside the networks. Our first heuristic exploits these two structural properties of PPI and geometric random networks to find good estimates of graphlet frequency distributions in these networks up to 690 times faster than the exhaustive searches. Our second heuristic is a variant of a more standard sampling technique and it produces accurate approximate results up to 377 times faster than the exhaustive searches. We indicate how the combination of these approaches may result in an even better heuristic. AVAILABILITY: Supplementary information is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/Supplementary.pdf. Software implementing the algorithms is available at http://www.cs.toronto.edu/~natasha/BIOINF-2005-0946/estimate_grap-hlets.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed2004

G20210A prothrombin gene polymorphism and coronary ischaemic syndromes: a phenotype-specific meta-analysis of 12 034 subjects.

OBJECTIVE: To investigate the possible link between the G20210A prothrombin gene variant and different forms of ischaemic heart disease. DESIGN: Phenotype-specific meta-analysis of 19 studies published within March 2002, globally including 4944 patients and 7090 controls. Sample size, inclusion criteria, geographical location, clinical presentation, age, cardiovascular risk factors, and angiographic extent of disease were extracted from each study. Analyses were done according to Mantel-Haenszel. RESULTS: Overall, the odds ratio (OR) for unspecified ischaemic heart disease associated with the 20210A allele was 1.21 (95% confidence interval (CI) 0.99 to 1.59, n = 12 034). Similar findings were seen for acute coronary syndromes (unstable angina and myocardial infarction) and for myocardial infarction without age limits (OR 1.24, 95% CI 0.98 to 1.63, n = 10 240; and OR 1.19, 95% CI 0.93 to 1.58, n = 9765). The effects were similar in male and female subjects. In the 1931 subjects < 55 years of age, the OR for myocardial infarction increased to 1.77 (95% CI 1.16 to 3.42) and in the 1359 subjects < 45 years to 2.30 (95% CI 1.27 to 4.59). No significant association was found between the 20210A allele and the presence of angiographically documented coronary disease (OR 1.08, 95% CI 0.70 to 1.64, n = 3444). However, patients with 0/1 vessel disease at angiography showed a greater prevalence of the A allele than those with multivessel disease (relative risk 2.0, 95% CI 1.2 to 3.1, n = 2376). CONCLUSIONS: G20210A prothrombin gene polymorphism may represent a modest but significant risk factor for myocardial infarction at young ages and favour the expression of ischaemic heart disease among individuals who have a limited extent of coronary atherosclerosis at angiography.

Adult↗
PubMed2005

PGC-1alpha Gly482Ser polymorphism associates with hypertension among Danish whites.

PGC-1alpha is a coactivator of numerous transcription factors and is expressed in tissues with high energy demands and abundant in mitochondria. It is induced in the myocardium on fasting and physical exercise, and cardiac-specific overexpression stimulates mitochondrial biogenesis in mice. The common Gly482Ser polymorphism of PGC-1alpha has previously shown association with arterial hypertension among Austrian men. Thus, we aimed at investigating this relationship in the Danish white population. The Gly482Ser polymorphism was genotyped in a total of 2562 Danish white subjects using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) and a GenoView locked nucleic acid assay (LNA), and the relationships of this variant with blood pressure levels and arterial hypertension were analyzed. Furthermore, we performed a combined analysis of the data from the present study in combination with previously published results. The Ser/Ser genotype was significantly associated with a reduced risk of hypertension and with lower systolic, diastolic, and mean arterial blood pressure levels, predominantly among women. Finally, in a combined analysis using data obtained in both sexes, the Ser/Ser genotype group had an estimated odds ratio of 0.70 (95% confidence interval, 0.56 to 0.86) for hypertension compared with Gly/X carriers (P=0.001). In conclusion, the Ser allele of PGC-1alpha Gly482Ser confers a significantly reduced risk of hypertension in whites. Further studies are needed to elucidate the differential role of this polymorphism in men and women.

Adult↗
PubMed2006

Paraoxonase gene polymorphisms and sporadic ALS.

BACKGROUND: The human paraoxonase (PON) gene family consists of three members, PON1, PON2, and PON3, located adjacent to each other on chromosome 7. PON catalytic activity may be influenced by frequent amino acid variants. Chronic exposure to certain chemicals or to environmental factors causing enhanced lipid peroxidation metabolized by paraoxonases may be a risk factor for sporadic ALS (sALS). OBJECTIVE: The aim of this study was to examine the association between PON1 Q192R, PON1 L55M, and PON2 C311S functional polymorphisms and the risk of sALS in a Polish population. METHODS: The authors included 185 patients with a definite or probable diagnosis of sALS (El Escorial Criteria) and 437 healthy controls of similar age and gender. The paraoxonase polymorphisms were studied by PCR and restriction enzyme digestion. RESULTS: Using logistic regression analyses, the C allele of the C311S polymorphism was associated with sALS in dominant and additive models, whereas the R allele of the Q192R polymorphism was associated with sALS in recessive, additive, and dominant models. The authors compared the distribution of haplotypes between cases and controls. The R-C haplotype was overrepresented among cases (odds ratio 3.44, 95% CI: 1.55 to 7.62, p = 0.002). CONCLUSIONS: Frequent amino acid variants in the paraoxonase 1 and paraoxonase 2 genes are associated with sporadic ALS in a Polish population.

Adult↗
PubMed1999

FokI polymorphism at translation initiation site of the vitamin D receptor gene predicts bone mineral density and vertebral fractures in postmenopausal Italian women.

A novel T/C polymorphism (ATG to ACG) at the translation initiation site of the vitamin D receptor (VDR) gene, defined by FokI restriction endonuclease, has been recently associated with variation in bone mineral density (BMD) and rates of bone loss in a group of postmenopausal Mexican-American women. The presence of the restriction site, designated as f, allows protein translation to initiate from the first ATG, while the allele lacking the site, indicated as F, initiates translation at a second ATG. In this study, we investigated the role of FokI polymorphism in a group of 400 postmenopausal women of Italian descent stratified for BMD into osteoporotic (n = 164), osteopenic (n = 117), and normal (n = 119) groups. There were 159 (41%) FF homozygotes, 55 (14%) ff homozygotes, and 186 (45%) Ff heterozygotes. In the whole population, we observed a weak association between FokI polymorphism and lumbar BMD (p = 0.06, analysis of covariance [ANCOVA]) but not with femoral neck BMD (p = 0.5, ANCOVA). Interestingly, the effect of FokI genotypes on lumbar BMD was influenced by the years since menopause such that differences in BMD related to different VDR allelic variants were greater among women in the first 5 years of menopause (p = 0.04, ANCOVA), progressively declining afterward. In addition, a significantly higher prevalence of ff genotype in osteoporotic than in osteopenic and normal women was observed (p = 0.04, Chi-square test). Finally, ff genotype resulted significantly over-represented in the group of women with a vertebral fracture as compared with controls (p = 0.003, Chi-square test), equivalent to a relative risk of 2.58 (95% confidence intervals 1.36-4.91). We conclude that in this population, FokI polymorphism at the VDR gene locus accounts for a part of the heritable component of BMD at the lumbar spine.

Aged↗
PubMed2003

Genetic polymorphisms of cytochromes P450: CYP2C9, CYP2C19, and CYP2D6 in Croatian population.

AIM: To determine the prevalence of most common mutations of cytochrome P450 (CYP), ie, allelic variants of CYP2C9, CYP2C19, and CYP2D6, and to predict genotype frequency in the Croatian population. METHODS: CYP genotype was determined in 200 non-related Croatian citizens. DNA isolated from blood samples was used for the analysis of the most common allelic variants of CYP2C9, CYP2C19, and CYP2D6 by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS: For 200 subjects genotyped for CYP2C9, the allele frequencies of CYP2C9*1 (wt), CYP2C9*2, and CYP2C9*3 were 0.74, 0.165, and 0.095, respectively. Among them, 3.5% of subjects were predicted to be poor metabolizers. For CYP2C19, the most frequent alleles were CYP2C19*1 and CYP2C19*2, with frequencies of 0.85 and 0.15, respectively; 3% of subjects were predicted to be poor metabolizers. For CYP2D6, the most frequent alleles were CYP2D6*1 (frequency 0.765), CYP2D62* (0.04), CYP2D6*3 (0.0275), CYP2D6*4 (0.14), CYP2D6*5 ( 0.01), and CYP2D6*6 (0.015). Out of these, 3% were predicted to be poor metabolizers, and 4% were predicted to be ultra-rapid metabolizers. CONCLUSION: The prevalence of allelic variants and predicted genotypes in the Croatian population is in accordance with the other European populations, and it can be interpolated between the values for mid-European and Mediterranean populations.

Aryl Hydrocarbon Hydroxylases↗
PubMed2006

[Study on the relations between genetic polymorphisms in methylenetetrahydrofolate reductase, methionine synthase and the risk of pancreatic cancer].

OBJECTIVE: To determine whether genetic polymorphisms in methylenetetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MS A2756G) were associated with the risks of pancreatic cancer. METHODS: A hospital-based, case-control study consisting of 101 incident pancreatic cancer cases and 337 controls matched on age, sex and race was conducted to investigate the association between polymorphism in MTHFR and MS, and susceptibility to pancreatic cancer. Genotypes of MTHFR C677T, A1298C and MS A2756G were analyzed by polymerase chain reasction-restriction fragment length polymorphism methods. RESULTS: It was found that multivariate-adjusted odds ratio (ORs; 95% confidence interval) for MTHFR-677CT and 677TT compared with 677CC were 2.17 (1.26 - 3.85) and 3.53 (1.85 - 6.84) respectively, which was in a manner of allele-dose relationship. However, no significant association between the A1298C genotype alone and the risk of cancer was observed which seemed that this polymorphism had a combined effect with the C677T polymorphism. A significant gene-environment interaction was observed between C677T polymorphism and cigarette smoking or alcohol intake. Subjects with variant genotypes who smoked > 17 pack-years had highest risk for developing the cancer, with the OR of 5.58 (2.53 - 12.30). Similarly, the OR (3.27, 1.51 - 7.23) for subjects with variant genotypes of alcohol drinker was significantly higher than that for subjects either having the variant genotype or being drinkers. No association was found between MS A2756G polymorphism and risk of pancreatic cancer in the study. CONCLUSION: These findings supported the hypothesis that genetic polymorphisms in MTHFR C677T might contribute to the risk of developing pancreatic cancer.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗
PubMed2001

Influenza A infection is an important cause of febrile seizures.

OBJECTIVES: To compare the incidence of febrile seizures in children hospitalized for influenza A infection with parainfluenza and adenovirus infection and to examine the hypothesis that children hospitalized for influenza A (variant Sydney/H3N2) during the 1998 season in Hong Kong had more frequent and refractory seizures when compared with other respiratory viruses, including the A/Wuhan H3N2 variant that was present in the previous year. METHODS: Medical records of children between 6 months and 5 years of age admitted for influenza A infection in 1998 were reviewed. For comparison, records of children of the same age group with influenza A infection in 1997, and with parainfluenza and adenovirus infections between 1996 and 1998 were reviewed. Children who were afebrile or who had an underlying neurologic disorder were excluded. RESULTS: Of children hospitalized for influenza A in 1998 and 1997, 54/272 (19.9%) and 27/144 (18.8%) had febrile seizures, respectively. The overall incidence of febrile seizures associated with influenza A (19.5%) was higher than that in children hospitalized for parainfluenza (18/148; 12.2%) and adenovirus (18/199; 9%) infection, respectively. In children who had febrile seizures, repeated seizures were more commonly associated with influenza A infection than with parainfluenza or adenovirus infection (23/81 [28%] vs 3/36 [8.3%], odds ratio [OR] 4.3, 95% confidence interval: 1.2 to 15.4). Alternatively, children with influenza A infection had a higher incidence (23/416, 5.5%) of multiple seizures during the same illness than those with adenovirus or parainfluenza infection (3/347, 0.86%; OR 6.7, 95% confidence interval: 2.0-22.5.) The increased incidence of febrile seizures associated with influenza A was not attributable to differences in age, gender, or family history of febrile seizure. Multivariate analysis, adjusted for peak temperature and duration of fever, showed that hospitalized children infected with infection A had a higher risk of febrile seizures than those who were infected with parainfluenza or adenovirus (OR 1.97). Influenza A infection was a significant cause of febrile seizure admissions. Of 250 and 249 children admitted to Queen Mary Hospital for febrile seizures in 1997 and 1998, respectively, influenza A infection accounted for 27 (10.8%) admissions in 1997 and 54 (21.7%) in 1998. During months of peak influenza activity, it accounted for up to 35% to 44% of febrile seizure admissions. In contrast, parainfluenza, adenovirus, respiratory syncytial virus, and influenza B had a smaller contribution to hospitalizations for febrile seizures, together accounting for only 25/250 (10%) admissions in 1997 and 16/249 (6.4%) in 1998. CONCLUSION: The influenza A Sydney variant (H3N2) was not associated with an increased risk of febrile seizures when compared with the previous influenza A Wuhan variant (H3N2) or H1N1 viruses. However, in hospitalized children, influenza A is associated with a higher incidence of febrile seizures and of repeated seizures in the same febrile episode than are adenovirus or parainfluenza infections. The pathogenesis of these observations warrants additional studies. Complex febrile seizures, particularly multiple febrile seizures at the time of presentation, have been thought to carry an adverse long-term prognosis because of its association with a higher incidence of epilepsy. Repeated febrile seizures alone, particularly if associated with influenza A infection, may not be as worrisome as children with complex febrile seizures because of other causes, which requires additional investigation. This may subsequently have an impact on reducing the burden of evaluation in a subset of children with complex febrile seizures.

Adenoviridae Infections↗
PubMed2003

Risk factors for neural tube defects: associations between uncoupling protein 2 polymorphisms and spina bifida.

BACKGROUND: Polymorphisms in the mitochondrial membrane transporter gene UCP2 are capable of affecting energy metabolism, body weight regulation, and possibly preventing the buildup of reactive oxygen species, all factors that could contribute to neural tube defect risk through maternal obesity and diabetes. METHODS: Genomic DNA was extracted from newborn screening blood spots obtained from infants with spina bifida and nonmalformed control infants. Genotype frequencies of two genetic variants in the UCP2 gene, an amino acid substitution of valine for alanine at codon 55 in exon 4, and a 45-base pair insertion/deletion in the 3' untranslated region of exon 8,were determined by restriction enzyme digestion of PCR amplification products. RESULTS: We found the frequency of the 3' untranslated region deletion homozygous genotype (256/256) as well as the A55V homozygous (Val/Val) genotype to be higher in SB infants than in controls (odds ratio [OR], 3.1; 95% confidence interval [CI], 0.9-10.4 and OR = 2.0; 95% CI = 0.3-11.1, respectively). Additionally, the frequency of the combined homozygous 256/256,+ / + genotype was higher in cases and resulted in more than a threefold higher spina bifida risk (OR = 3.6; 95% CI = 1.0-13.1). CONCLUSIONS: These data are the first to suggest that polymorphisms in the UCP2 gene may be genetic risk factors of spina bifida.

California↗
PubMed1997

Allelic association of a dopamine transporter gene polymorphism in alcohol dependence with withdrawal seizures or delirium.

Hereditary factors confer susceptibility to alcohol dependence. Alcohol mediates its reinforcing effects by enhancing dopamine activity in the mesolimbic dopamine system. The role of the dopamine transporter in terminating dopaminergic activity in synaptic neurotransmission suggests that variants of the dopamine transporter gene (DAT1) might contribute to individual differences in vulnerability to addictive behavior. Our population-based association study investigated whether variants of DAT1 confer susceptibility to alcohol dependence in 293 alcoholics and clinically more homogeneous subgroups formed by: positive family history, early age-at-onset, delirium, withdrawal seizures, antisocial tendencies, type 1 and 2 alcoholics. Analyzing a VNTR polymorphism in the 3' untranslated region of DAT1, we found a significantly increased prevalence of the nine-repeat allele in 93 alcoholics displaying withdrawal seizures or delirium, compared with 93 ethnically matched nonalcoholic controls (p = 0.003; OR = 2.44; 95% confidence interval: 1.35-4.43). Our data provide evidence that a major genetic determinant of DAT1 influences vulnerability to severe alcohol withdrawal symptoms.

Adult↗
PubMed2004

Single-nucleotide promoter polymorphism alters transcription of neuronal nitric oxide synthase exon 1c in infantile hypertrophic pyloric stenosis.

Infantile hypertrophic pyloric stenosis (IHPS), characterized by enlarged pyloric musculature and gastric-outlet obstruction, is associated with altered expression of neuronal nitric oxide synthase (nNOS). Here we have studied molecular mechanisms by which nNOS gene expression is altered in pyloric tissues of 16 infants with IHPS and 9 controls. A significant decreased expression of total nNOS mRNA was found by quantitative RT-PCR in IHPS after normalization against GAPDH, which predominantly affected exon 1c with a reduction of 88% compared with controls (P < 0.001). After normalization against the neuronal-specific gene PGP9.5, expression of exon 1c was still decreased (P < 0.001), whereas expression of exon 1f was increased significantly (P = 0.001), indicating a compensatory up-regulation of this nNOS mRNA variant. DNA samples of 16 IHPS patients and 81 controls were analyzed for nNOS exon 1c promoter mutations and single-nucleotide polymorphism (SNP). Sequencing of the 5'-flanking region of exon 1c revealed mutations in 3 of 16 IHPS tissues, whereas 81 controls showed the wild-type sequence exclusively. Carriers of the A allele of a previously uncharacterized nNOS exon 1c promoter SNP (-84G --> A) had increased risk for development of IHPS (odds ratio, 8.0; 95% confidence interval, 2.5-25.6). Reporter gene assays revealed an unchanged promoter activity for mutations but a approximately 30% decrease for the -84A SNP (P < 0.001). In summary, our findings indicate that genetic alterations in the nNOS exon 1c regulatory region influence expression of the nNOS gene and may contribute to the pathogenesis of IHPS.

Base Sequence↗
PubMed2001

Association between a single-nucleotide polymorphism in the promoter of the human interleukin-3 gene and rheumatoid arthritis in Japanese patients, and maximum-likelihood estimation of combinatorial effect that two genetic loci have on susceptibility to the disease.

Genetic variants of interleukin-3 (IL-3), a well-studied cytokine, may have a role in the pathophysiology of rheumatoid arthritis (RA); but reports on this association sometimes conflict. A case-control study was designed to investigate association between RA and a single-nucleotide polymorphism (SNP) in the IL-3 promoter region. Comparison of cases of RA versus control individuals yielded a chi(2) value of 14.28 (P=.0002), with a genotype odds ratio of 2.24 (95% confidence interval [95%CI] 1.44-3.49). When female cases with earlier onset were compared with female control individuals, the SNP revealed an even more significant correlation, with chi2=21.75 (P=.000004) and a genotype odds ratio of 7.27 (95%CI 2.80-18.89). The stronger association that we observed in this clinically distinct subgroup (females with early onset), within a region where linkage disequilibrium was not significantly extended, suggested that the genuine RA locus should locate either within or close to the IL-3 gene. Combined genotype data on SNPs on eight other candidate genes were combined with our IL-3 results, to estimate relationships between pairs of loci and RA, by maximum-likelihood analysis. The utility of combining the genotype data in this way to identify possible contributions of various genes to this disease is discussed.

Age of Onset↗
PubMed2004

Gene-gene interaction in folate-related genes and risk of neural tube defects in a UK population.

OBJECTIVE: To investigate the contribution of polymorphic variation in genes involved in the folate-dependent homocysteine pathway in the aetiology of neural tube defects (NTD). DESIGN: Case-control association study. SUBJECTS: A total of 530 individuals from families affected by NTD, 645 maternal controls, and 602 healthy newborn controls from the northern UK. MAIN OUTCOME MEASURES: Seven polymorphisms in six genes coding for proteins in the folate-dependent homocysteine pathway (MTHFR 677C-->T, MTHFR 1298A-->C, MTRR 66A-->G, SHMT 1420C-->T, CbetaS 844ins68, GCPII 1561C-->T, RFC-1 80G-->A). The impact of each polymorphism and the effect of gene-gene interactions (epistasis) upon risk of NTD were assessed using logistic regression analysis. RESULTS: The MTHFR 677C-->T polymorphism was shown to represent a risk factor in NTD cases (CC v CT+TT odds ratio (OR) 2.03 [95% confidence interval (CI) 1.09, 3.79] p = 0.025) and the MTRR 66A-->G polymorphism was shown to exert a protective effect in NTD cases (AA v AG+GG OR 0.31 [95% CI 0.10, 0.94] p = 0.04). When statistical tests for interaction were conducted, three genotype combinations in cases (MTRR/GCPII; MTHFR 677/CbetaS; MTHFR 677/MTRR) and one combination in case mothers (CbetaS/RFC-1) were shown to elevate NTD risk. Maternal-fetal interaction was also detected when offspring carried the MTHFR 677C-->T variant and mothers carried the MTRR 66A-->G variant, resulting in a significantly elevated risk of NTD. CONCLUSION: Both independent genetic effects and gene-gene interaction were observed in relation to NTD risk. Multi-locus rather than single locus analysis might be preferable to gain an accurate assessment of genetic susceptibility to NTD.

Case-Control Studies↗
PubMed2003

The topoisomerase IIalpha expression correlates with survival in patients with advanced Hodgkin's lymphoma.

PURPOSE: Topoisomerase (Topo) II isoenzymes are the targets for drugs, such as epidophyllotoxins and doxorubicin. The aim of this study was to determine whether the expression of Topo IIalpha and Ki67 in advanced Hodgkin's disease (HD) played a role as a prognostic factor or predictor of response to treatment. EXPERIMENTAL DESIGN: Forty-two patients who were homogeneously treated and had a long-term follow-up were selected for the study. Immunohistochemistry of paraffin-embedded tissue sections was performed. The effect of patient and tumor characteristics on failure-free survival (FFS) and overall survival were evaluated in a univariate analysis using the Cox proportional hazards model. The Cox model was also implemented in a multivariate analysis using stepwise selection. RESULTS: Positive nuclear staining for Topo IIalpha in Reed-Stemberg or Reed-Stemberg variant cells was seen in 90% of HD cases, and coexpression of Ki67 and Topo IIalpha in 79%. No significant difference in the percentage of Topo IIalpha-positive cells was detected among histological HD subtypes. In the univariate analysis for FFS, the male gender, high lactate dehydrogenase, and Topo IIalpha < 30% were associated with more relapses. In the multivariate analysis for FFS, only Topo IIalpha < 30% was statistically associated with shorter FFS, with relative risk of 3 (95% confidence interval, 1.26-7.15; P = 0.013). In uni- and multivariate analyses for overall survival, only Topo IIalpha was associated with shorter survival. CONCLUSIONS: Topo IIalpha expression could be useful in advanced HD to identify patients with a higher risk of relapse and lesser overall survival. It is of potential utility in the design of specific treatments.

Adolescent↗