Fangyi Gu

Eighteen Insulin-like Growth Factor Pathway Genes, Circulating Levels of IGF-I and Its Binding Protein, and Risk of Prostate and Breast Cancer

Background: Circulating levels of insulin-like growth factor I (IGF-I) and its main binding protein, IGF binding protein 3 (IGFBP-3), have been associated with risk of several types of cancer. Heritable factors explain up to 60% of the variation in IGF-I and IGFBP-3 in studies of adult twins. Methods: We systematically examined common genetic variation in 18 genes in the IGF signaling pathway for associations with circulating levels of IGF-I and IGFBP-3. A total of 302 single nucleotide polymorphisms (SNP) were genotyped in >5,500 Caucasian men and 5,500 Caucasian women from the Breast and Prostate Cancer Cohort Consortium. Results: After adjusting for multiple testing, SNPs in the IGF1 and SSTR5 genes were significantly associated with circulating IGF-I (P < 2.1 × 10−4); SNPs in the IGFBP3 and IGFALS genes were significantly associated with circulating IGFBP-3. Multi-SNP models explained R2 = 0.62% of the variation in circulating IGF-I and 3.9% of the variation in circulating IGFBP-3. We saw no significant association between these multi-SNP predictors of circulating IGF-I or IGFBP-3 and risk of prostate or breast cancers. Conclusion: Common genetic variation in the IGF1 and SSTR5 genes seems to influence circulating IGF-I levels, and variation in IGFBP3 and IGFALS seems to influence circulating IGFBP-3. However, these variants explain only a small percentage of the variation in circulating IGF-I and IGFBP-3 in Caucasian men and women. Impact: Further studies are needed to explore contributions from other genetic factors such as rare variants in these genes and variation outside of these genes. Cancer Epidemiol Biomarkers Prev; 19(11); 2877–87. ©2010 AACR.

Genetic variants in DNA repair pathway genes and risk of esophageal squamous cell carcinoma and gastric adenocarcinoma in a Chinese population

The DNA repair pathways help to maintain genomic integrity and therefore genetic variation in the pathways could affect the propensity to develop cancer. Selected germline single nucleotide polymorphisms (SNPs) in the pathways have been associated with esophageal cancer and gastric cancer (GC) but few studies have comprehensively examined the pathway genes. We aimed to investigate associations between DNA repair pathway genes and risk of esophageal squamous cell carcinoma (ESCC) and GC, using data from a genome-wide association study in a Han Chinese population where ESCC and GC are the predominant cancers. In sum, 1942 ESCC cases, 1758 GC cases and 2111 controls from the Shanxi Upper Gastrointestinal Cancer Genetics Project (discovery set) and the Linxian Nutrition Intervention Trials (replication set) were genotyped for 1675 SNPs in 170 DNA repair-related genes. Logistic regression models were applied to evaluate SNP-level associations. Gene- and pathway-level associations were determined using the resampling-based adaptive rank-truncated product approach. The DNA repair pathways overall were significantly associated with risk of ESCC (P = 6.37 × 10(-4)), but not with GC (P = 0.20). The most significant gene in ESCC was CHEK2 (P = 2.00 × 10(-6)) and in GC was CLK2 (P = 3.02 × 10(-4)). We observed several other genes significantly associated with either ESCC (SMUG1, TDG, TP53, GTF2H3, FEN1, POLQ, HEL308, RAD54B, MPG, FANCE and BRCA1) or GC risk (MRE11A, RAD54L and POLE) (P < 0.05). We provide evidence for an association between specific genes in the DNA repair pathways and the risk of ESCC and GC. Further studies are warranted to validate these associations and to investigate underlying mechanisms.

Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence.

We conducted a 1000 Genomes–imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerström Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P=8.0 × 10−9 across all the samples for rs2273500-C (frequency=0.15; odds ratio=1.12 and 95% confidence interval=1.08–1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P=7.3 × 10−4). Importantly, rs2273500-C was associated with increased lung cancer risk (N=28 998, odds ratio=1.06 and 95% confidence interval=1.00–1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single ‘cigarettes per day’ item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.

Identifying biomarkers of dietary patterns by using metabolomics

BACKGROUND Healthy dietary patterns that conform to national dietary guidelines are related to lower chronic disease incidence and longer life span. However, the precise mechanisms involved are unclear. Identifying biomarkers of dietary patterns may provide tools to validate diet quality measurement and determine underlying metabolic pathways influenced by diet quality. OBJECTIVE The objective of this study was to examine the correlation of 4 diet quality indexes [the Healthy Eating Index (HEI) 2010, the Alternate Mediterranean Diet Score (aMED), the WHO Healthy Diet Indicator (HDI), and the Baltic Sea Diet (BSD)] with serum metabolites. DESIGN We evaluated dietary patterns and metabolites in male Finnish smokers (n = 1336) from 5 nested case-control studies within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study cohort. Participants completed a validated food-frequency questionnaire and provided a fasting serum sample before study randomization (1985-1988). Metabolites were measured with the use of mass spectrometry. We analyzed cross-sectional partial correlations of 1316 metabolites with 4 diet quality indexes, adjusting for age, body mass index, smoking, energy intake, education, and physical activity. We pooled estimates across studies with the use of fixed-effects meta-analysis with Bonferroni correction for multiple comparisons, and conducted metabolic pathway analyses. RESULTS The HEI-2010, aMED, HDI, and BSD were associated with 23, 46, 23, and 33 metabolites, respectively (17, 21, 11, and 10 metabolites, respectively, were chemically identified; r-range: -0.30 to 0.20; P = 6 × 10-15 to 8 × 10-6). Food-based diet indexes (HEI-2010, aMED, and BSD) were associated with metabolites correlated with most components used to score adherence (e.g., fruit, vegetables, whole grains, fish, and unsaturated fat). HDI correlated with metabolites related to polyunsaturated fat and fiber components, but not other macro- or micronutrients (e.g., percentages of protein and cholesterol). The lysolipid and food and plant xenobiotic pathways were most strongly associated with diet quality. CONCLUSIONS Diet quality, measured by healthy diet indexes, is associated with serum metabolites, with the specific metabolite profile of each diet index related to the diet components used to score adherence. This trial was registered at clinicaltrials.gov as NCT00342992.

Common genetic variants in the 9p21 region and their associations with multiple tumours

Background:The chromosome 9p21.3 region has been implicated in the pathogenesis of multiple cancers.Methods:We systematically examined up to 203 tagging SNPs of 22 genes on 9p21.3 (19.9–32.8 Mb) in eight case–control studies: thyroid cancer, endometrial cancer (EC), renal cell carcinoma, colorectal cancer (CRC), colorectal adenoma (CA), oesophageal squamous cell carcinoma (ESCC), gastric cardia adenocarcinoma and osteosarcoma (OS). We used logistic regression to perform single SNP analyses for each study separately, adjusting for study-specific covariates. We combined SNP results across studies by fixed-effect meta-analyses and a newly developed subset-based statistical approach (ASSET). Gene-based P-values were obtained by the minP method using the Adaptive Rank Truncated Product program. We adjusted for multiple comparisons by Bonferroni correction.Results:Rs3731239 in cyclin-dependent kinase inhibitors 2A (CDKN2A) was significantly associated with ESCC (P=7 × 10−6). The CDKN2A-ESCC association was further supported by gene-based analyses (Pgene=0.0001). In the meta-analyses by ASSET, four SNPs (rs3731239 in CDKN2A, rs615552 and rs573687 in CDKN2B and rs564398 in CDKN2BAS) showed significant associations with ESCC and EC (P<2.46 × 10−4). One SNP in MTAP (methylthioadenosine phosphorylase) (rs7023329) that was previously associated with melanoma and nevi in multiple genome-wide association studies was associated with CRC, CA and OS by ASSET (P=0.007).Conclusion:Our data indicate that genetic variants in CDKN2A, and possibly nearby genes, may be associated with ESCC and several other tumours, further highlighting the importance of 9p21.3 genetic variants in carcinogenesis.

Polymorphisms in genes involved in DNA repair, cell growth, oxidative stress and inflammatory response, and melanoma risk

Few genetic risk factors for melanoma have been examined and confirmed. We examined five important candidate genes (MGMT, ICAM-5, VEGF, MPO, and TNF-α) involved in direct reversal DNA repair, cell growth, oxidative stress, and inflammatory response, in relation to melanoma susceptibility. Eight candidate SNPs in the five genes were selected according to previous studies (MGMT 84Leu>Phe (rs12917), MGMT 143Ile>Val (rs2308321) [1], VEGF 398G>C (rs2010963), VEGF 1967C>T (rs3025039) [2], MPO −764T>C (rs2243828) [3], TNF-α−487A>G (rs1800629) [4] and ICAM5 301Val>Ile (rs1056538), ICAM5 −542C>G (rs281439) [5]). Due to genotyping difficulty, the MPO −463G>A (rs2333227) was replaced by the MPO −764 T>C (rs2243828). Genotyping concordance between the two SNPs was 100%. (http://snp500cancer.nci.nih.gov). We investigated the associations between these genetic variants and melanoma susceptibility in a nested case-control study of 219 incident melanoma cases and 219 matched controls within the Nurses’ Health Study (NHS) Cohort. The detailed information about the study population and laboratory assays were described elsewhere [6]. The detailed statistical analyses have been published previously [6]. We used unconditional logistic regression to evaluate the association between genotype and melanoma risk, firstly adjusting for matching factors (age and race (Caucasians and missing)), and then additionally adjusting for other melanoma risk factors. We evaluated the interactions between SNPs and melanoma risk factors (constitutional susceptibility score and cumulative sun exposure with a bathing suit) on melanoma susceptibility. We used the expectation maximization algorithm to estimate haplotype frequencies in cases and controls for the SNPs MGMT 84Leu>Phe and 143Ile>Val. We also explored the potential modification by antioxidants intake on the association between the MPO polymorphism and melanoma risk (See previous report for data collection and analysis [7]). No departure from the Hardy-Weinberg Equilibrium among controls was observed for all the 8 SNPs. We observed that the MGMT 84Leu>Phe polymorphism was associated with melanoma susceptibility. The Phe carriers had a higher risk of melanoma than non-carriers (84Leu/Leu) with OR (95%CI) 1.55 (0.99–2.44). The association was attenuated in the multivariate model. The MGMT gene encodes a direct reversal DNA repair protein that removes alkyl or methyl adducts from the O6 position of guanine to an internal cysteine residue at codon 145 of the protein [2]. An animal study suggested that MGMT protein prevents N-nitroso-N-methylurea-initiated skin carcinogenesis through avoiding tumor initiation triggered by alkylation damage [8]. There are three common non-synonymous polymorphisms in the MGMT gene, 84Leu>Phe, 143Ile>Val, and 178 Lys>Arg, and the latter two are in linkage disequilibrium. The Leu84 and Ile143 are close to the reactive cysteine in the 3D structure and may have subtle functional consequences [1]. The minor alleles in the 84Leu>Phe and 143Ile>Val polymorphisms were reported to be inversely associated with the capacity to repair tobacco-induced DNA damage [9]. This evidence suggests that these two minor alleles may confer a higher cancer susceptibility. Consistently, we observed a higher risk of melanoma for the 84Phe carriers and the 143Val carriers compared to their wildtypes. The 84Phe carriers had about a 50% increased risk of melanoma compared to non-carriers (84Leu/Leu). The 143Val carriers had an OR of 1.34(0.86–2.09) for melanoma risk compared to non-carriers (143Ile/Ile). Comparing to the common haplotype 84Leu/143Ile, the haplotype 84Phe/143Ile and 84Leu/143Val had an OR (95%CI) of 1.75 (1.11–2.76) and 2.00 (1.21–3.29), respectively. These associations remained significant after adjusting for other risk factors. Our results combined with the functional results of these two SNPs suggest that alkylation-related DNA damage (or other damage repaired by MGMT) may be involved in melanoma carcinogenesis. Because the ICAM expression in melanocytes was shown to be inhibited by alpha-melanocyte-stimulating hormone (α-MSH), a sun exposure–induced ligand for skin pigmentation [10], we evaluated the interactions between the ICAM5 variants and the constitutional susceptibility score and cumulative sun exposure with a bathing suit on melanoma risk. Comparing to the first tertiles, the ORs (95%CIs) of the third tertiles were 3.25(1.44–7.36) for constitutional susceptibility score and 3.03(1.71–5.39) for cumulative sun exposure with a bathing suit. In the interaction analysis, the highest risk of melanoma was observed among women with the ICAM5 301 Val/Val genotype and highest susceptibility (OR, 5.73; 95%CI, 1.62–20.31) or greatest sun exposure (OR, 4.83; 95%CI, 1.79–13.06). The interactions did not approach statistical significance (Table 2). Table 2 Interaction between ICAM5 301 Val>Ile and risk factors on melanoma risk We did not observe significant results for SNPs in other genes (Table 1), or the interaction between the MPO polymorphism and dietary intake of antioxidants on melanoma risk. Table 1 Polymorphisms in selected candidate genes and melanoma risk In conclusion, this is the first study of the MGMT, ICAM5, and MPO genetic polymorphisms in relation to melanoma susceptibility. We found a borderline-significant association between the MGMT84 Leu>Phe and melanoma risk, and significant associations between the MGMT haplotypes and melanoma risk. A higher risk of melanoma was observed among 84Phe or 143Val carriers who have lower alkylation-damage-repair capacity. The statistical power of our study to detect a modest association is limited, and larger studies are warranted to confirm these findings.

Insulin-like growth factor pathway genes and blood concentrations, dietary protein, and risk of prostate cancer in the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)

It has been hypothesized that a high intake of dairy protein may increase prostate cancer risk by increasing the production of insulin‐like growth factor 1 (IGF‐1). Several single nucleotide polymorphisms (SNPs) have been weakly associated with circulating concentrations of IGF‐1 and IGF binding protein 3 (IGFBP‐3), but none of these SNPs was associated with risk of prostate cancer. We examined whether an association between 16 SNPs associated with circulating IGF‐1 or IGFBP‐3 concentrations and prostate cancer exists within subgroups defined by dietary protein intake in 5,253 cases and 4,963 controls of European ancestry within the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). The BPC3 includes nested case–control studies within large North‐American and European cohorts. Per‐allele odds ratios for prostate cancer for the SNPs were compared across tertiles of protein intake, which was expressed as the percentage of energy derived from total, animal, dairy or plant protein sources, using conditional logistic regression models. Total, animal, dairy and plant protein intakes were significantly positively associated with blood IGF‐1 (p < 0.01), but not with IGFBP‐3 concentrations (p > 0.10) or with risk of prostate cancer (p > 0.20). After adjusting for multiple testing, the SNP‐prostate cancer associations did not differ by intakes of protein, although two interactions by intake of plant protein were of marginal statistical significance [SSTR5 (somatostatin receptor 5)‐rs197056 (uncorrected p for interaction, 0.001); SSTR5‐rs197057 (uncorrected p for interaction, 0.002)]. We found no strong evidence that the associations between 16 IGF pathway SNPs and prostate cancer differed by intakes of dietary protein.

Common genetic variants in the 8q24 region and risk of papillary thyroid cancer

Single nucleotide polymorphisms (SNPs) in the 8q24 chromosomal region identified from genome‐wide scans have been associated with the risk of several cancers, including breast (rs1562430), prostate (rs1447295), and colon (rs6983267). A genome‐wide scan in 26 families with papillary thyroid cancer (PTC) also found susceptibility loci in 8q24, supporting a closer evaluation of this chromosomal region in relation to the risk of sporadic PTC.

Insulin-like growth factor pathway genes and blood concentrations, dietary protein and risk of prostate cancer in the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)

It has been hypothesized that a high intake of dairy protein may increase prostate cancer risk by increasing the production of insulin‐like growth factor 1 (IGF‐1). Several single nucleotide polymorphisms (SNPs) have been weakly associated with circulating concentrations of IGF‐1 and IGF binding protein 3 (IGFBP‐3), but none of these SNPs was associated with risk of prostate cancer. We examined whether an association between 16 SNPs associated with circulating IGF‐1 or IGFBP‐3 concentrations and prostate cancer exists within subgroups defined by dietary protein intake in 5,253 cases and 4,963 controls of European ancestry within the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). The BPC3 includes nested case–control studies within large North‐American and European cohorts. Per‐allele odds ratios for prostate cancer for the SNPs were compared across tertiles of protein intake, which was expressed as the percentage of energy derived from total, animal, dairy or plant protein sources, using conditional logistic regression models. Total, animal, dairy and plant protein intakes were significantly positively associated with blood IGF‐1 (p < 0.01), but not with IGFBP‐3 concentrations (p > 0.10) or with risk of prostate cancer (p > 0.20). After adjusting for multiple testing, the SNP‐prostate cancer associations did not differ by intakes of protein, although two interactions by intake of plant protein were of marginal statistical significance [SSTR5 (somatostatin receptor 5)‐rs197056 (uncorrected p for interaction, 0.001); SSTR5‐rs197057 (uncorrected p for interaction, 0.002)]. We found no strong evidence that the associations between 16 IGF pathway SNPs and prostate cancer differed by intakes of dietary protein.

Sleep Duration and Cancer in the NIH-AARP Diet and Health Study Cohort

Background Very few studies have examined sleep duration in relation to cancer incidence with the exception of breast cancer. Methods We assessed the associations between sleep duration and incidences of total and 18 site-specific cancers in the NIH-AARP Health and Diet Study cohort, with 173,327 men and 123,858 women aged 51–72 years at baseline. Self-reported sleep duration categories were assessed via questionnaire. We used multivariable Cox proportional hazards regression to estimate hazard ratios (HR) and 95% confidence intervals (CI), using 7–8 hours/night as the reference. Results We observed a significantly increased risk of stomach cancer among male short sleepers (multivariable HR5-6 vs. 7–8 hours = 1.29; 95%CI: 1.05, 1.59; Ptrend = 0.03). We also observed suggestive associations in either short or long sleepers, which did not reach overall significance (Ptrend >0.05), including increased risks in male short sleepers for cancers of head and neck (HR<5vs.7-8 hours = 1.39; 95%CI:1.00–1.95), bladder (HR5-6vs.7-8 hours = 1.10; 95%CI:1.00–1.20), thyroid (HR<5 vs. 7–8 hours = 2.30; 95%CI:1.06, 5.02), Non-Hodgkin Lymphoma (NHL) (HR5-6vs.7-8 hours = 1.17; 95%CI:1.02–1.33), and myeloma (HR<5vs.7-8 hours = 2.06; 95%CI:1.20–3.51). In women, the suggestive associations include a decreased total cancer risk (HR<5vs.7-8 hours = 0.9; 95%CI:0.83–0.99) and breast cancer risk (HR<5vs.7-8 hours = 0.84; 95%CI:0.71–0.98) among short sleepers. A decreased ovarian cancer risk (HR≥ 9 vs. 7–8 hours = 0.50; 95%CI:0.26–0.97) and an increased NHL risk (HR≥ 9 vs. 7–8 hours = 1.45; 95%CI:1.00–2.11) were observed among long sleepers. Conclusion In an older population, we observed an increased stomach cancer risk in male short sleepers and suggestive associations with short or long sleep duration for many cancer risks in both genders.