The independence assumption for a case-only analysis of statistical interaction, i. e. that genetic (G) and environmental exposures (E) are not associated in the source population, is often checked in surrogate populations. Few studies have examined G-E association in empirical data, particularly in controls from population-based studies, the type of controls expected to provide the most valid surrogate estimates of G-E association. We used controls from two population-based case-control studies to evaluate G-E independence for 43 selected genetic polymorphisms and smoking behavior. The odds ratio (ORz) was used to estimate G-E association and, therefore, the magnitude of bias introduced into the case-only odds ratio (COR). Odds ratios of moderate magnitude [mmORz], defined as ORz≤0.7 or ORz≥1.4, were found at least one of the six smoking measures (ever, former, current, cig/day, years smoked, pack-years) for 45% and 59% of the SNPs examined in the control groups of two independently conducted North Carolina studies, respectively. Consequently, case-only estimates of G-E interaction in the context of a multiplicative benchmark would be biased for these SNPs and smoking measures. MmORzs were found more often for smoking amount than smoking status. We recommend that a stand-alone case-only study should only be conducted when G-E independence can be verified for each polymorphism and exposure metric with population-specific data. Our results suggest that ORz is specific to each underlying population rather than an estimate of a ‘universal’ ORz for that SNP and smoking measure. Further, misspecification of smoking is likely to introduce bias into the COR.
Case-only; controls; gene-environment interaction; genetic polymorphisms; smoking
Several investigations demonstrated that the polymorphisms of multidrug resistance gene (MDR1) gene contribute to interindividual variability in bioavailability and tissue distribution of its substrates. Genotyping of closely spaced single-nucleotide polymorphism (SNP) markers frequently yields highly correlated data, owing to extensive linkage disequilibrium (LD) between markers. The product of multidrug resistance gene (P-gp) is an important molecule, which regulating the bioavailability of many drugs, including calcineurin inhibitors. It also reported that some MDR1 gene polymorphisms (such as 3435C>T) was associated with significantly reduced intestinal P-gp expression in T/T homozygotes. The aim of this study is to develop genotyping assays for polymorphisms of the MDR1 gene, which are believed to have functional properties and to assess the distribution of variant alleles in renal patients (UK Caucasoid). A total of ten polymorphisms in the MDR-1 gene were selected for analysis. Haplotype assays were performed by using EH programme in 172 individuals. The following possible haplotype was apparent (G-41, C-145, C-129, C+139, C+1236, G+2677, G+2956, C+3435, C+4030 and A+4036). This finding suggests the importance of haplotype assignment for the MDR1 gene.
MDR; gene; single-nucleotide polymorphism; linkage disequilibrium; haplotype; immunosuppressive
Osteosarcoma (OS) is a rare malignant bone tumor with an overall incidence rate of 4.6 cases per million children aged 0-19 years in the United States. While the etiology of OS is largely unknown, its distinctive age-incidence pattern suggests that growth and development is crucial in genesis. Prior studies have suggested that variants in genes in the estrogen metabolism (ESTR) and insulin-like growth factor/growth hormone (IGF/GH) pathways are associated with OS. We examined 798 single nucleotide polymorphisms (SNPs) in 42 genes from these pathways in a case-parent study (229 complete triads and 56 dyads) using buccal cell samples. Relative risks (RR) and 95% confidence intervals (CI) associated with transmitting one or two copies of the variant were estimated using log-linear models. After Bonferroni correction, 1 SNP within the ESTR pathway (rs1415270: RR = 0.50 and 8.37 for 1 and 2 vs. 0 copies, respectively; p = 0.010), and two SNPs in the IGF/GH pathway (rs1003737: RR = 0.91 and 0.0001 for 1 and 2 vs. 0 copies, respectively; p <0.0001 and rs2575352: RR = 2.62 and 0.22 for 1 and 2 vs. 0 copies; p < 0.0001) were significantly associated with OS incidence. These results confirm previous findings that variation in the estrogen metabolism and bone growth pathways influence OS risk and further support a biologically and epidemiologically plausible role in OS development.
Osteosarcoma; case-parent study; growth and development; insulin-like growth factor pathway; estrogen metabolism pathway
Background: Recent studies suggested that gamma-glutamyl transferase (GGT) and C-reactive protein (CRP) are good markers of metabolic abnormalities. We assessed the link between GGT, CRP and common metabolic abnormalities, as well their link to related diseases, such as cancer and cardiovascular disease (CVD). Methods: We selected 333,313 subjects with baseline measurements of triglycerides (TG), total cholesterol (TC), glucose, GGT and CRP in the Swedish AMORIS study. Baseline measurement of BMI was available for 63,900 persons and 77,944 had baseline measurements of HDL. Pearson correlation coefficients between CRP, GGT, and metabolic components (TG, HDL, BMI and TC) were calculated. To investigate the combined effect of GGT and CRP we created a score ranging from 0 to 6 and used Cox proportional hazard models to evaluate its association with CVD and cancer. Results: 21,216 individuals developed cancer and 47,939 CVD. GGT and TG had the strongest correlation (r=0.22). An increased risk of cancer was identified with elevated levels of GGT or CRP or both markers (GGT-CRP score ≥3); the greatest risk of cancer was found when GGT-CRP score = 6 (HR: 1.40 (95%CI: 1.31-1.48) and 1.60 (1.47-1.76) compared to GGT-CRP score = 0, respectively). Conclusion: While GGT and CRP have been shown to be associated with metabolic abnormalities previously, their association to the components investigated in this study was limited. Results did demonstrate that these markers were predictive of associated diseases, such as cancer.
GGT; CRP; metabolic abnormalities; cardiovascular disease; cancer
CLU, PICALM and CR1 were identified as genetic risk factors for late onset Alzheimer’s disease (AD) in two large genome wide association studies (GWAS) published in 2009, but the variants that convey this alteration in disease risk, and how the genes relate to AD pathology is yet to be discovered. A next generation sequencing (NGS) project was conducted targeting CLU, CR1 and PICALM, in 96 AD samples (8 pools of 12), in an attempt to discover rare variants within these AD associated genes. Inclusion of repetitive regions in the design of the SureSelect capture lead to significant issues in alignment of the data, leading to poor specificity and a lower than expected depth of coverage. A strong positive correlation (0.964, p<0.001) was seen between NGS and 1000 genome project frequency estimates. Of the ~170 “novel” variants detected in the genes, seven SNPs, all of which were present in multiple sample pools, were selected for validation by Sanger sequencing. Two SNPs were successfully validated by this method, and shown to be genuine variants, while five failed validation. These spurious SNP calls occurred as a result of the presence of small indels and mononucleotide repeats, indicating such features should be regarded with caution, and validation via an independent method is important for NGS variant calls.
Next generation sequencing; Alzheimer’s disease; genes; CLU; PICALM; CR1
To understand the change of the dominant serogroup of Shigella spp., their antimicrobial resistance over more than two decades in Tianjin, their phylogenetic similarity and to determine their evolutionary biology by using REP-PCR and MLST in order to study their epidemiological character. Multi-locus Sequence Typing was performed to determine their lineage and phylogenetic similarity. REP-PCR typing was used to study the homology of their genomic DNA. The isolated rate of group D Shigella in 2009 and 2010 had obviously increased. Antimicrobial susceptibility test results showed that the resistant rates of the 1981-1983 Shigella flexneri to tetracycline, streptomycin and chloramphenicol varied from 76.47 to 100%, they were all sensitive to other antibiotics. During 2009-2010, the resistance rates of the isolated Shigella flexneri to gentamicin, amikacin, third and fourth Generation Cephalosporins and quinolones had increased. MLST results produced five sequence types and two sequence type complexes. REP-PCR showed DNA band similarities between the 1981-1983 and 2009-2010 strains. The dominant serogroup of Shigella in Tianjin has changed from Shigella flexneri to Shigella sonnei. Increased drug resistance of Shigella flexneri is higher than Shigella sonnei because a great variety of antibiotics has been used. The MLST results showed that the 1981-1983 strains had the same sequence type with some of the 2009-2010 strains. Combination of MLST and REP-PCR produced better discriminatory power than using either method alone.
Shigella; multidrug resistance; REP-PCR; multi-locus sequence typing
Receptor for advanced glycation end products (RAGE) plays an important role in promoting chronic inflammation with activation of NF-κB. Soluble form of RAGE (sRAGE) represents a naturally occurring competitive inhibitor of RAGE-mediated events. In a colonoscopy-based case-control study, we examined the associations of plasma levels of sRAGE, sTNF-αRI, sTNF-αRII, sIL-6R, EGF, IFNα2, G-CSF, MCP1, TNFβ, and VEGF with risk of colorectal adenoma. We prospectively identified 158 cases with colorectal adenoma and 203 polyp-free controls who were frequency-matched according to age, sex, race, and time of blood draw. Exposure information was collected using a questionnaire and fasting plasma samples were obtained before the colonoscopy. We used Luminex bead-based multiplex assays to determine level of biomarkers. Multivariate logistic regression model was used to estimate odds ratio (OR) and its 95% confidence interval (CI). Cases had insignificant lower levels of sRAGE, and higher levels of EGF and VEGF than controls. When the highest compared with the lowest category, the OR (95% CI) of colorectal adenoma was 0.55 (0.31-0.96) (P trend = 0.03) for sRAGE and 1.75 (1.05-2.93) (P trend =0.04) for VEGF, adjusting for age, smoking status, hypertension and type 2 diabetes. The inverse association between sRAGE and colorectal adenoma was seen only among those without hypertension (P interaction = 0.02). An inverse association between sRAGE and colorectal adenoma was in line with an inverse association between sRAGE and colorectal cancer previously reported. This study supported the involvement of RAGE-NF-kB related inflammatory mechanism in the formation of colorectal adenoma.
Case-control; colorectal adenoma; risk; inflammation; sRAGE; VEGF; NF-kB
Accumulating evidence suggests that placental abruption has a complex multifactorial pathogenesis that involves cardiovascular risk and metabolic dysfunction. However, comprehensive assessment of variations in genes involved in cardiometabolic traits associated with the risk of placental abruption is lacking. We conducted a case-control study investigating associations of variations in maternal cardiometabolic genes (characterized using 217,697 SNPs on the Illumina Cardio-Metabo Chip) with risk of placental abruption. A total of 253 abruption cases and 258 controls were selected from among participants enrolled in the Peruvian Abruptio Placentae Epidemiology Study in Lima, Peru. In the genome-wide association analyses, top hits did not surpass genome-wide significance. However, we observed suggestive associations of placental abruption with several SNPs, including SNPs in SMAD2 (P-value=1.88e-6), MIR17HG (P-value=7.8e-6], and DGKB (P-value=8.35e-6] loci. In candidate gene analyses, we observed associations of variations in a priori selected genes involved in coagulation, rennin-angiotensin, angiogenesis, inflammation, and B-vitamin metabolism with the risk of abruption. Our study suggests that variations in maternal cardiovascular and metabolic genes may be associated with risk of placental abruption. Future studies with large sample sizes are warranted.
Placental abruption; pregnancy complications; Cardio-Metabo chip; genetic association; single nucleotide polymorphism; genome-wide association study
The purpose of the present study was to analyze the associations between specific genetic markers and early disc degeneration (DD) or early disc degeneration progression (DDP) defined by magnetic resonance imaging (MRI).
We selected eleven of the most promising single nucleotide polymorphisms (SNP) and compared the distributions of these genetic markers between groups defined by MRI in a Danish adolescent population (N=166) over a three-year follow-up period.
We observed a ten-fold higher annual incidence of endplate changes than previously reported in adults. The gender difference in IL1A rs1800587 association with DD remained significant and another association with DDP emerged in follow-up assessment. Among girls, the rs1800587 T-allele was associated both with DD (OR 2.82 [95% CI 1.29-6.16]) and with DDP (OR 2.45 [95% CI 1.03-5.82]). Among boys, the IL6 rs1800795 genotype G/C was protective in both DD (OR 0.26 [95% CI 0.09-0.72]) and DDP (OR 0.32 [95% CI 0.12-0.88]) with the IL6 rs1800797 genotype G/A was associated with a decreased likelihood of DD (OR 0.27 [95% CI 0.10-0.77]). Gender-genotype interactions were significant for polymorphisms in both IL1A and IL6. Correction for multiple testing weakened the associations for IL6 polymorphisms.
We conclude that gender specific effects in lumbar disc degeneration and its progression are possible. However, further evaluations in larger populations are needed. Our results provide some support to the hypothesis that early disc degeneration is an especially important phase in the cascade of degenerative disc disease.
Disc degeneration; disc degeneration progression; adolescents; genetics; interleukins
Glial cell-derived neurotrophic factor (GDNF) and brain-derived neurotrophic factor (BDNF) play key roles in the early development of the central auditory pathway and the inner ear. Both have been successfully employed to treat experimental forms of hearing loss and are likely to operate in a broad spectrum of auditory phenotypes, including phantom perceptions of sound. We conducted a genetic association study addressing five biallelic candidate variants in 240 Caucasian subjects who had been diagnosed with tinnitus for more than 6 months.
Allele frequencies were determined for three GDNF and two BDNF markers, including a functional missense substitution (V66M). When data were compared to previously examined control populations, no significant allelic associations were noted after corrections for multiple testing. However, using a multiple regression approach and scores from a validated self-report questionnaire, GDNF and BDNF genotypes jointly predicted tinnitus severity in women (N=69, uncorrected p=0.04) but not in men (N=171, n.s.).
The present findings serve as an incentive for further explorations of neurotrophic factors' role in predicting clinical features of tinnitus. Possible implications of sexually dimorphic at-risk genotypes are discussed with regard to hearing and neural plasticity.
BDNF; GDNF; tinnitus; sexual dimorphism; genetic variation
This study sought to determine the role of copy number variants (CNV) combined with other genetic variants in the Glutathione S-transferases Mu class1 (GSTM1) promoter in the development of urinary bladder cancer. TaqMan real-time PCR and direct sequencing were used to determine genetic variants. Haploblocks and haplotype were constructed and estimated by Haploview and Phase, respectively. Logistic regression revealed a significantly decreased bladder cancer risk in subjects with at least 2 copies of GSTM1 (OR=0.56; 95%CI=0.39-0.81) but not in those with 1 copy of the gene. GSTM1 promoter screening revealed an insertion variant (-1543TTCT) and 14 single nucleotide polymorphisms (SNPs) (-1529C>G, -1490A>G, -1143A>G, -888A>T, -498G>C, -486C>G, -471C>T, -426G>A, -344C>T, -343A>T, -341C>T, -339C>T, -304G>A, and -164C>T). Four haploblocks were evident by Haploview. There was no significant association between any single SNP/haplotype and bladder cancer risk. However, when stratified by copy number, the two copy carriers with the -1543 insertion had decreased bladder cancer risk (OR, 0.58; 95%CI, 0.32-0.10) and similar results were found in two copy carriers with -888 A, -486G, - 344 C, -343 A, -341 C allele and haplotype INS-1543-C-1529-A-1429 in LD block 1, A-1143-A-888 in LD block 2, C-498-G-486-T-471 in LD block 3, C-344-A-343-C-341-C-339 and C-344-A-343-C-341-T-339 in LD block 4. These results suggest that GSTM1 CNV is a better predictor of bladder cancer susceptibility than measuring presence/absence of GSTM1 and other genetic variants also can modify bladder cancer risk.
Glutathione-S-transferase M1; Copy number variant; single nucleotide polymorphism; bladder cancer
Recent genomic studies have identified risk SNPs in or near eight genes associated with testicular germ cell tumors (TGCT). Mouse models suggest a role for Dnd1 epigenetics in TGCT susceptibility, and we have recently reported that transgenerational inheritance of epigenetic events may be associated with familial TGCT risk. We now investigate whether aberrant promoter methylation of selected candidate genes is associated with familial TGCT risk. Pyrosequencing assays were designed to evaluate CpG methylation in the promoters of selected genes in peripheral blood DNA from 153 TGCT affecteds and 116 healthy male relatives from 101 multiple-case families. Wilcoxon rank-sum tests and logistic regression models were used to investigate associations between promoter methylation and TGCT. We also quantified gene product expression of these genes, using quantitative PCR. We observed increased PDE11A, SPRY4 and BAK1 promoter methylation, and decreased KITLG promoter methylation, in familial TGCT cases versus healthy male family controls. A significant upward risk trend was observed for PDE11A when comparing the middle and highest tertiles of methylation to the lowest [odds ratio (OR) =1.55, 95% confidence intervals (CI) 0.82-2.93, and 1.94, 95% CI 1.03-3.66], respectively; P
trend=0.042). A significant inverse association was observed for KITLG when comparing the middle and lowest tertiles to the highest (OR=2.15, 95% CI 1.12-4.11, and 2.15, 95% CI 1.12-4.14, respectively; P
trend=0.031). There was a weak inverse correlation between promoter methylation and KITLG expression. Our results suggest that familial TGCT susceptibility may be associated with promoter methylation of previously-identified TGCT risk-modifying genes. Larger studies are warranted.
Promoter methylation; testicular germ cell tumors; familial testicular cancer; epidemiology; candidate gene
A growing body of evidence suggests that mitochondrial dysfunction is associated with oxidative stress and impaired differentiation and invasion of trophoblasts, both of which have been related to preeclampsia pathogenesis. However, studies that examined circulating mitochondrial DNA (mtDNA) copy number in relation to preeclampsia are limited. Therefore, we examined association of maternal whole blood mtDNA copy number (a novel biomarker of systemic mitochondrial dysfunction) with the odds of preeclampsia. This case-control study was comprised of 144 preeclampsia cases and 407 normotensive controls. Real-time quantitative polymerase chain reaction (PCR) was used to assess the relative copy number of mtDNA in maternal whole blood samples collected at delivery. Logistic regression procedures were used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Median mtDNA copy number was significantly higher among preeclamptic women compared with controls (271.5 vs. 239.3, Mann-Whitney U test p-value <0.001). There was evidence of a linear trend in higher odds of preeclampsia with increasing quartiles of mtDNA copy number (P for trend=0.03) after controlling for confounders. The adjusted ORs for the successive quartiles of mtDNA copy number, compared with the referent (first quartile) were 1.30 (95%CI 0.66-2.56), 1.93 (95%CI 1.02-3.67) and 1.86 (95%CI 1.00-3.48). Our findings suggest that maternal mitochondrial dysfunction may contribute to the pathogenesis of preeclampsia. However, replication in prospective studies is needed to further investigate this relationship.
Mitochondria; DNA; mitochondrial DNA; preeclampsia; pregnancy
Telomeres are repetitive non-coding DNA sequences at the ends of chromosomes that provide protection against chromosomal instability. Telomere length and stability are influenced by proteins, including telomerase which is partially encoded by the TERT gene. Genetic variation in the TERT gene is associated with ovarian cancer risk, and predicts survival in lung cancer and glioma. We investigated whether genetic variation in five telomere maintenance genes was associated with survival among 1480 cases of invasive epithelial ovarian cancer in the population-based New England Case-Control Study. Cox proportional hazard models were used to calculate hazard ratios and 95% confidence intervals. Overall we observed no significant associations between SNPs in telomere maintenance genes and mortality using a significance threshold of p=0.001. However, we observed some suggestive associations in subgroup analyses. Future studies with larger populations may further our understanding of what role telomeres play in ovarian cancer survival.
Ovarian cancer; survival; telomere length; SNPs; telomeres
Total motile count (TMC) is a useful tool for sperm evaluation, comprising both quantitative and motility parameters. Although frequently used, TMC has not yet been evaluated as a contributory variable for intracytoplasmic sperm injection (ICSI) cycles. In this study we evaluate the possible role of TMC as a prognostic parameter in cycles designated for ICSI. We also test the existence of a possible TMC-threshold value that might be predictive for ICSI cycle outcome in the everyday practice. This is a retrospective cohort study in which the research question is addressed by a locally weighted regression (LOESS) analysis. Primary outcome measures are fertilization rate, good quality embryos rate and implantation rate. A total of 666 patients were included, contributing 1456 cycles. The effect of TMC over the fertilization rate was significant, depicting an inverted U-shaped curve: with up to approximately 10 million motile sperm, fertilization rates increased as TMC increased, but from this point on decreased. A slight increment in the rate of good embryo formation with increasing value of TMC was noted, but this did not reach a statistical significance. TMC values demonstrated no effect in the case of implantation rates. ICSI may offer an advantage related to fertilization rates for the sub-fertile male population, with a motile sperm count up to 10 million.
Male infertility; sperm motility; ICSI; fertilization; embryo Implantation
Telomeres cap the ends of chromosomes and help maintain genomic stability and integrity. Telomere length (TL) has been linked to a number of diseases, including a variety of cancers; however, the association between TL and risk for colorectal cancer is unclear.
We investigate the association between genetic, diet, and lifestyle factors and TL and the association between TL and colorectal cancer using data from a population-based case-control study of colon (249 cases and 371 controls) and rectal cancer (276 cases and 372 controls) conducted in Utah. DNA samples came from immortalized cell lines for colon cancer and directly from whole blood for rectal cancer. We genotyped 11 single nucleotide polymorphisms in five genes associated with telomeres, TERT, MEN1, MRE11A, RECQL5, and TNKS.
TL was measured using quantitative PCR. TERT rs2853676 (p=0.044) and RECQL5 rs820152 (p=0.001) were associated with TL at <0.05 level of significance. After adjusting for age and sex, BMI and cigarette smoking were significantly inversely associated with TL among controls. Use of aspirin/NSAIDs interacted significantly with TERT rs10069690 and rs2242652 to alter TL. Longer TL was significantly associated with reduced colon cancer risk after adjusting for age and sex (OR = 0.94 95% confidence intervals 0.89-0.99 per decile of TL). Further adjustment for BMI and cigarette smoking attenuated the association so that it was no longer significant.
In summary several genetic and lifestyle factors were observed to influence TL. These factors also appear to confound associations between TL and colon cancer.
TERT; MEN1; RECQL5; MRE11A; TNKS; Colorectal cancer; telomere length
This study examined whether carotid artery intimal-medial thickness (cIMT) is associated with genetic variations (SNPs) in a hemodynamics-responsive gene pathway.
Subjects were Cardiovascular Health Study participants free of cardiovascular events at baseline (N=3388). Genotype was measured using Illumina 370CNV HumanHap chip. Carotid IMT was measured using ultrasound. Estimated mean differences in cIMT per additional minor allele for 366 SNPs in MAP2K5, MAPK7, MEF2A/C, and KLF2 were adjusted for sex, age, clinic, and medication use. SNP-SNP interactions were examined using logic regression for 71 tagSNPs.
None of the associations was significant after correction for multiple comparisons; smallest P-value=0.065 for MAP2K5 and common cIMT. The best-performing logic regression tree combined two SNPs in MAP2K5—rs745212 and rs12905175— and common cIMT; this association was not significant, corrected P-value=0.062.
There was not strong evidence of association between genetic variants in a hemodynamics-responsive gene pathway and atherosclerosis among older adults.
Cardiovascular Health Study (CHS); candidate gene study; carotid intima-media thickness (cIMT); hemodynamics response; fluid shear stress; endothelium / endothelial cells; Kruppel-like factor 2 (KLF2); Mitogen-activated protein kinase 7 (MAPK7); Myocyte-specific enhancer factor 2 A/C (MEF2A/C); Mitogen-activated protein kinase kinase 5 (MAP2K5)
S-adenosylmethionine (SAM) is a primary methyl donor for the methylation of many molecules including DNA. DNA methylation is believed to play an important role in functions of cells and genes. Dietary, genetic and metabolic factors that influence systematic SAM levels are not fully understood. We conducted cross-sectional analysis to evaluate associations between plasma concentrations of one-carbon metabolism nutrients and metabolites and plasma SAM concentrations using healthy individuals within the Singapore Chinese Health Study. Plasma SAM, betaine, choline, folate, total homocysteine (Hcy), methionine, S-adenosylhomocysteine (SAH), vitamin B6 and vitamin B12 concentrations were quantified. Genotypes of methionine adenosyltransferases (MAT1A, MAT2A and MAT2B) were also determined. Linear regression and path analysis were performed to depict the directed dependencies in one-carbon metabolism. Age and body mass index were positively associated while cigarette smoking were inversely associated with plasma SAM concentrations. Plasma choline, methionine and SAH were positively and strongly associated with plasma SAM after adjustment for confounders. Plasma betaine and folate were positively associated with plasma SAM only in men. Men carrying the variant MAT1A genotypes had lower plasma SAM concentrations than men carrying the wild type genotype (p for gene x gender interaction = 0.02). This effect modification by gender was restricted to individuals with low plasma methionine. In conclusion, plasma choline, methionine and SAH were strongly associated with plasma SAM concentrations. The MAT1A genetic polymorphism may impact plasma SAM concentrations in men with low plasma methionine concentrations.
One-carbon metabolism; plasma SAM; MAT genetic polymorphism; path analysis
To examine the blood leukocyte expression of 22 sex steroid metabolic/signaling genes according to female reproductive status.
Michigan Fisheaters’ Cohort participants underwent blood collection during the luteal phase of the menstrual cycle or randomly in non-menstruating participants. Gene expression (GE) was measured using Taqman hydrolysis probes and quantitative RT-PCR. Repeatability of four genes was determined in a subgroup.
Five premenstrual, 57 premenopausal (20 users of systemic hormonal contraception), and 43 postmenopausal females participated. After Bonferroni correction for multiple comparisons of median GE between groups, three findings remained significant: greater GE of AhR in postmenopausal women than in premenopausal non-users of systemic hormonal contraception; and greater GE of ESR2 and HSD17B7 in premenstrual girls compared to postmenopausal women. Modest intra-class correlations were identified for CYP 19, ESR1, and ESR2 GE measured both in 2007 and 2010, but no intra-class correlation over the same time period was found for CYP17.
There was little differential variation of blood leukocyte sex steroid GE between premenopausal women in the luteal phase of the menstrual cycle and postmenopausal women for most genes analyzed, but it will be necessary to make statistical adjustments in future epidemiologic studies in two circumstances: 1) when comparing AhR GE in premenopausal women non-users of systemic hormone contraception with postmenopausal women and 2) when comparing ESR2 and HSD17B7 GE in studies that include premenstrual girls. Developmental differences may explain the differential GE found in ESR2 and HSD17B7 in premenstrual girls compared with postmenopausal women.
Steroid gene expression; blood leukocyte gene expression; female reproductive status
Colorectal adenoma (CRA) and colorectal cancer (CRC) risks have been linked to the intake of red and processed meat. Heterocyclic aromatic amines (HCA) formed herein during high temperature cooking, are metabolized by a variety of enzymes, and allelic variation in the coding genes could influence individual CRA risk. Associations of polymorphisms in NAT1, NAT2, GSTA1, SULT1A1, CYP1A2, UGT1A7, UGT1A9, GSTP1 genes with colorectal adenoma risk were investigated in a nested case-control study of the EPIC-Heidelberg cohort including 428 cases matched by age, sex and year of recruitment with one or two controls (n=828) with negative colonoscopy per case. Genoyping was preformed with the Sequenom MassArray system and the LightCycler 480. Conditional logistic regression was used to compute odds ratios (OR) and corresponding 95% confidence intervals (CI). For rs15561 (NAT1) and rs1057126 (NAT1), the rarer allel was significantly inversely associated with adenoma risk OR=0.80 (95% CI 0.65-0.97) and (OR=0.81 (95% CI 0.65-0.99) and, respectively). For the combined NAT2 alleles encoding for enzymes with medium (versus slow) activity we also observed a significantly inverse association with adenoma risk (OR=0.75; 95% CI 0.85-0.97). In addition, homozygous carriers of the A allele of rs3957357 (GSTA1), i.e., those with a decreased enzyme activity, had a decreased risk of colorectal adenoma with an OR of 0.68 (95% CI 0.50-0.92; AA versus GG/GA). Polymorphisms in the other tested genes did not modify the risk of colorectal adenomas. In conclusion, polymorphisms in NAT1, NAT2, and GSTA1 are related to colorectal adenoma risk in this German cohort.
Colorectal adenoma; genetic polymorphisms; NAT1; NAT2; GSTA1
A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy volunteers were noted. Our data demonstrated that the allele frequencies of COMT and CYP2D6*10 in the Filipino healthy volunteers were similar with other Asians but markedly different from Caucasian populations.
Allele frequency; catechol-O-methyltransferase; CYP2D6*10; polymorphism; Filipino
While the association between obesity and endometrial cancer (EC) is well established, the underlying mechanisms require further study. We assessed possible links between lipid profiles and EC risk, while also taking into account BMI, parity, and menopausal status at baseline.
Using the information available from the Swedish Apolipoprotein MOrtality RISk (AMORIS) study we created a cohort of 225,432 women with baseline values for glucose, triglycerides (TG), and total cholesterol (TC). Two subgroups of 31,792 and 26,317 had, in addition, baseline measurements of HDL, LDL, apolipoprotein A-I and apoB and BMI, respectively. We used Multivariate Cox proportional hazards models to analyze quartiles and dichotomized values of these lipid components for a link to EC risk.
During mean follow-up of 12 years (SD: 4.15), 1,144 persons developed endometrial cancer. A statistically significant association was found between TG and EC risk when using both quartiles and a clinical cut-off (Hazard Ratio (HR): 1.10 (95%CI: 0.88-1.37), 1.34 (1.09-1.63), and 1.57 (1.28-1.92)) for the 2nd, 3rd, and 4th quartile, compared to the 1st, with P-value for trend: <0.001). The association remained after exclusion of the first three years of follow-up. Also total cholesterol and TG/HDL ratio were positively associated with EC risk, but no link was found for the other lipid components studied.
This detailed analysis of lipid components showed a consistent relation between TG levels and EC risk. Future research should continue to analyze the metabolic pathway and its relation to EC risk, as a pathway to further understand the relation of obesity and disease.
Lipid profiles; risk factor; endometrial cancer; Swedish AMORIS study
Kaposi's sarcoma (KS) associated with HHV8 is one of the common connective tissue malignancies especially in immunocompromised patients. The aim of the present study was to determine the common HHV8 genotypes in hospitalized patients in Tehran, Iran. A total of 36 archival paraffin-embedded KS tissue samples of patients with common characterization of KS were collected between 1999 to 2010 from hospitals in Tehran, Iran. After identifying the presence of HHV8 by amplification of its ORF 26 region, the ORF K1 region was amplified, sequenced and used for phylogenetic analysis. Among 30 ORF 26 positive cases, ORF K1 was amplified successfully in 14 cases. Consistent with other studies in Asia, subtype A (9 cases; 64.28%) and subtype C (5 cases; 35.71%) were detected by phylogenetic analysis. This result is in concordance with results from other countries of the region, however the ratio of genotype A to C is higher in our study compared to another study in the country.
Kaposi's sarcoma; HHV8; PCR; Tehran
The glutathione S-transferase (GST) supergene family is made up of four gene families responsible for the biotransformation of drugs and other xenobiotics. Genetic variations in this supergene family influence individual detoxification levels and may contribute to the development of cancer. A hospital-based case-control study was conducted to evaluate the association between GST polymorphism among Filipino patients positive for hepatitis B virus (HBV DNA) and clinically diagnosed as either with chronic active hepatitis, liver cirrhosis, and hepatocellular carcinoma as well as normal individuals negative for HBV infection. Multiplex PCR was used to detect the presence or absence of the GSTT1 and GSTM1 polymorphisms in peripheral blood. DNA sequencing of the S gene region of the virus was used to determine the predominant genotype found among HBV-infected patients. Our results showed that the odds of having a chronic liver disease is only 0.95 (95% CI 0.58-1.57) among those with GSTT1 null genotype compared to those with GSTT1+ genotype. On the other hand, the odds of chronic liver disease is 17.85 times (95% CI 7.34-43.45) for those with GSTM1 null genotype compared to those with GSTM1+ genotype. Using the GSTT1+/GSTM1+ genotype as the reference, both GSTT1+/GSTM1- (OR 16.61; 95% CI 6.69-41.22) and GSTT1-/GSTM1- (OR 11.91; 95% CI 4.48-31.66) genotypes seem to be risk factors for chronic liver disease. From our observations, we conclude that polymorphism in GSTM1 null genotype (OR 17.85; 95% CI 7.34-43.45) seem to be associated with an increased risk of chronic liver disease among Filipinos.
GSTT1; GSTM1; chronic liver disease; hepatitis B virus; polymorphism; Filipino
The IL4 gene is located on chromosome 5q23.3-31.2. Polymorphisms within this cytokine gene, like the derivative allele T of IL4-590, have been reported as being associated to elevated IgE serum levels and asthma. In the present work, the allelic and genotypic frequency of the IL4-590 and IL4 RP2 polymorphisms was carried out in 599 individuals from Madeira, Azores, Portugal mainland, Cape Verde and Guinea-Bissau and in a sample of 101 asthmatics from Madeira population. In all populations the polymorphisms were in LD and presented a significant dissimilar allelic and genotypic distribution (p<0.05) except between mainland Portugal and Madeira when compared to Azores. Significant differences regarding both loci were found between Madeira population and the group of asthmatics. Genotype 183183TT frequency is higher for African populations while 253253CC prevails in Caucasian populations. The existence of a Hardy-Weinberg Disequilibrium in Guinea-Bissau population not observed in neutral markers leads to the hypothesis of natural selection occurring in these loci probably associated to a rapid population growth an hypothesis strengthened by neutral STRs D5S818 and CSF1PO gene diversity.
IL4-590; IL4 RP2; D5S818; CSF1PO; Asthma; Madeira; Azores; Portugal mainland; Cape Verde; Guinea-Bissau