Genomic copy number alterations in clear cell renal carcinoma: associations with case characteristics and mechanisms of VHL gene inactivation

Array comparative genomic hybridization was used to identify copy number alterations in clear cell renal cell carcinoma (ccRCC) patient tumors to identify associations with patient/clinical characteristics. Of 763 ccRCC patients, 412 (54%) provided frozen biopsies. Clones were analyzed for significant copy number differences, adjusting for multiple comparisons and covariates in multivariate analyses. Frequent alterations included losses on: 3p (92.2%), 14q (46.8%), 8p (38.1%), 4q (35.4%), 9p (32.3%), 9q (31.8%), 6q (30.8%), 3q (29.4%), 10q (25.7%), 13q (24.5%), 1p (23.5%) and gains on 5q (60.2%), 7q (39.6%), 7p (30.6%), 5p (26.5%), 20q (25.5%), 12q (24.8%), 12p (22.8%). Stage and grade were associated with 1p, 9p, 9q, 13q and 14q loss and 12q gain. Males had more alterations compared with females, independent of stage and grade. Significant differences in the number/types of alterations were observed by family cancer history, age at diagnosis and smoking status. Von Hippel-Lindau (VHL) gene inactivation was associated with 3p loss (P Collapse

Key Words

• renal cancer
• epidemiology
• vhl

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MESH Headings Collapse

Grants

• HHSN261200800001C NCI NIH HHS
• HHSN261200800001E NCI NIH HHS

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Xenobiotic metabolizing gene variants and renal cell cancer: a multicenter study

BACKGROUND

The countries of Central and Eastern Europe have among the highest worldwide rates of renal cell cancer (RCC). Few studies have examined whether genetic variation in xenobiotic metabolic pathway genes may modify risk for this cancer.

METHODS

The Central and Eastern Europe Renal Cell Cancer study was a hospital-based case-control study conducted between 1998 and 2003 across seven centers in Central and Eastern Europe. Detailed data were collected from 874 cases and 2053 controls on demographics, work history, and occupational exposure to chemical agents. Genes [cytochrome P-450 family, N-acetyltransferases,

NAD(P)H

quinone oxidoreductase I (NQO1), microsomal epoxide hydrolase (mEH), catechol-O-methyltransferase (COMT), uridine diphosphate-glucuronosyltransferase (UGT)] were selected for the present analysis based on their putative role in xenobiotic metabolism. Haplotypes were calculated using fastPhase. Odds ratios and 95% confidence intervals were estimated by unconditional logistic regression adjusted for country of residence, age, sex, smoking, alcohol intake, obesity, and hypertension.

RESULTS

We observed an increased risk of RCC with one SNP. After adjustment for multiple comparisons it did not remain significant. Neither NAT1 nor NAT2 slow acetylation was associated with disease.

CONCLUSION

We observed no association between this pathway and renal cell cancer.

Von Hippel-Lindau (VHL) inactivation in sporadic clear cell renal cancer: associations with germline VHL polymorphisms and etiologic risk factors

Renal tumor heterogeneity studies have utilized the von Hippel-Lindau VHL gene to classify disease into molecularly defined subtypes to examine associations with etiologic risk factors and prognosis. The aim of this study was to provide a comprehensive analysis of VHL inactivation in clear cell renal tumors (ccRCC) and to evaluate relationships between VHL inactivation subgroups with renal cancer risk factors and VHL germline single nucleotide polymorphisms (SNPs). VHL genetic and epigenetic inactivation was examined among 507 sporadic RCC/470 ccRCC cases using endonuclease scanning and using bisulfite treatment and Sanger sequencing across 11 CpG sites within the VHL promoter. Case-only multivariate analyses were conducted to identify associations between alteration subtypes and risk factors. VHL inactivation, either through sequence alterations or promoter methylation in tumor DNA, was observed among 86.6% of ccRCC cases. Germline VHL SNPs and a haplotype were associated with promoter hypermethylation in tumor tissue (OR = 6.10; 95% CI: 2.28-16.35, p = 3.76E-4, p-global = 8E-5). Risk of having genetic VHL inactivation was inversely associated with smoking due to a higher proportion of wild-type ccRCC tumors [former: OR = 0.70 (0.20-1.31) and current: OR = 0.56 (0.32-0.99); P-trend = 0.04]. Alteration prevalence did not differ by histopathologic characteristics or occupational exposure to trichloroethylene. ccRCC cases with particular VHL germline polymorphisms were more likely to have VHL inactivation through promoter hypermethylation than through sequence alterations in tumor DNA, suggesting that the presence of these SNPs may represent an example of facilitated epigenetic variation (an inherited propensity towards epigenetic variation) in renal tissue. A proportion of tumors from current smokers lacked VHL alterations and may represent a biologically distinct clinical entity from inactivated cases.

Abstract B25: Kidney cancer and female reproductive factors in two prospective cohorts

Introduction: The unexplained two-fold lower incidence of kidney cancer in women compared to men and findings from clinical and experimental studies have generated interest in the role of female reproductive factors and exogenous hormones on kidney cancer development. Endocrine system involvement in kidney cancer development is biologically plausible since sex hormone receptors have been detected in normal and malignant renal tissue, exogenous estrogens have been shown to promote and induce kidney cancer formation, and anatomic changes to the kidney during pregnancy may make nephrons more vulnerable to inflammation and oxidative stress. Findings from several epidemiologic studies suggest that parity may be associated with kidney cancer, but case numbers have generally been small. Associations with other reproductive factors have been sparse and inconsistently reported. Therefore, we conducted a pooled analysis of two large prospective studies to evaluate whether hormone-related factors are associated with risk of kidney cancer in women.

Methods: We investigated the relationship between female reproductive factors and exogenous hormones and kidney cancer risk in two large prospective cohort studies: the NIH-AARP Diet and Health Study (NIH-AARP: 601 cases) and the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO: 191 cases). Study-specific hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated by Cox regression. Data from both studies were pooled and aggregate HRs were estimated. We also conducted meta-analyses of all case-control and cohort studies to summarize our new findings and previously reported associations between kidney cancer risk and select reproductive factors. Random-effects models were fit to estimate summary relative risks (RRs) and odds ratios (ORs) for cohort and case-control studies separately.

Results: The analysis included 283,952 post-menopausal women, with 792 incident kidney cancer cases. Parity was not associated with risk of kidney cancer in either study (pooled HR = 1.15, 95% Cl = 0.91–1.44). Risk for kidney cancer was significantly elevated, however, in both cohorts among women who had undergone a hysterectomy (pooled HR = 1.33,95% Cl = 1.15–1.53). After allowing for a 10 year lag between study baseline and diagnosis of kidney cancer, associations remained significantly elevated (pooled HR = 1.31,95% Cl = 1.14–1.51), suggesting the elevation in association was not due to detection bias. For women with a history of endometriosis, a significant increase in risk (HR = 1.69,95% Cl = 1.09–2.62) was observed in PLCO, the only cohort that collected data on this condition.

A meta-analysis of epidemiologic studies provided additional support for an association with hysterectomy (all cohort studies: summary RR = 1.29,95% Cl = 1.14–1.47; excluding NIH-AARP and PLCO Results: summary RR = 1.23,95% Cl = 0.99–1.52; case-control studies: OR = 1.39,95% Cl = 1.17–1.64).

Conclusion: Our findings from two large prospective cohorts and a meta-analysis of epidemiologic studies suggests that hysterectomy is associated with increased kidney cancer risk.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr B25.

A case-control study of reproductive factors and renal cell carcinoma among black and white women in the United States

OBJECTIVE

Renal cell carcinoma (RCC) incidence is higher among blacks than whites in the United States and has been associated with the frequency and timing of childbirth among women in some epidemiologic studies. We investigated whether reproductive factors are associated with RCC, overall and by race, within a population-based case-control study.

METHODS

Between 2002 and 2007, 497 female cases of incident RCC (136 black, 361 white) and 546 female controls (273 black, 273 white) within the Detroit and Chicago metropolitan areas were enrolled. Information on reproductive history and other factors was collected through in-person interviews. Multivariate-adjusted odds ratios (OR) and 95% confidence intervals (CI) were computed using unconditional logistic regression.

RESULTS

Reduced RCC risk was observed among women aged ≥30 years at first live birth, relative to an age of <20 years (OR 0.5, 95% CI 0.3-0.9). This association was present among both white (OR 0.4, 95% CI 0.2-0.9) and, though not statistically significant, black women (OR 0.6, 95% CI 0.2-1.8). In analyses restricted to clear cell adenocarcinoma, the most common RCC histological subtype, the association was particularly strong (OR 0.3, 95% CI 0.2-0.8). We did not observe clear evidence of association with RCC for other reproductive factors.

CONCLUSIONS

Our findings further support an association between late maternal age at first birth and reduced RCC risk, and suggest that the association may be particularly strong for clear cell adenocarcinoma.

Comprehensive analysis of 5-aminolevulinic acid dehydrogenase (ALAD) variants and renal cell carcinoma risk among individuals exposed to lead

Background

Epidemiologic studies are reporting associations between lead exposure and human cancers. A polymorphism in the 5-aminolevulinic acid dehydratase (ALAD) gene affects lead toxicokinetics and may modify the adverse effects of lead.

Methods

The objective of this study was to evaluate single-nucleotide polymorphisms (SNPs) tagging the ALAD region among renal cancer cases and controls to determine whether genetic variation alters the relationship between lead and renal cancer. Occupational exposure to lead and risk of cancer was examined in a case-control study of renal cell carcinoma (RCC). Comprehensive analysis of variation across the ALAD gene was assessed using a tagging SNP approach among 987 cases and 1298 controls. Occupational lead exposure was estimated using questionnaire-based exposure assessment and expert review. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression.

Results

The adjusted risk associated with the ALAD variant rs8177796^CT/TT was increased (OR = 1.35, 95%CI = 1.05–1.73, p-value = 0.02) when compared to the major allele, regardless of lead exposure. Joint effects of lead and ALAD rs2761016 suggest an increased RCC risk for the homozygous wild-type and heterozygous alleles (^GGOR = 2.68, 95%CI = 1.17–6.12, p = 0.01; ^GAOR = 1.79, 95%CI = 1.06–3.04 with an interaction approaching significance (p_int = 0.06).. No significant modification in RCC risk was observed for the functional variant rs1800435^(K68N). Haplotype analysis identified a region associated with risk supporting tagging SNP results.

Conclusion

A common genetic variation in ALAD may alter the risk of RCC overall, and among individuals occupationally exposed to lead. Further work in larger exposed populations is warranted to determine if ALAD modifies RCC risk associated with lead exposure.

Occupational exposure to dusts and risk of renal cell carcinoma

BACKGROUND

Occupational exposures to dusts have generally been examined in relation to cancers of the respiratory system and have rarely been examined in relation to other cancers, such as renal cell carcinoma (RCC). Although previous epidemiological studies, though few, have shown certain dusts, such as asbestos, to increase renal cancer risk, the potential for other occupational dust exposures to cause kidney damage and/or cancer may exist. We investigated whether asbestos, as well as 20 other occupational dust exposures, were associated with RCC risk in a large European, multi-center, hospital-based renal case-control study.

METHODS

General occupational histories and job-specific questionnaires were reviewed by occupational hygienists for subject-specific information. Odds ratios (ORs) and 95% confidence intervals (95% CIs) between RCC risk and exposures were calculated using unconditional logistic regression.

RESULTS

Among participants ever exposed to dusts, significant associations were observed for glass fibres (OR: 2.1; 95% CI: 1.1-3.9), mineral wool fibres (OR: 2.5; 95% CI: 1.2-5.1), and brick dust (OR: 1.5; 95% CI: 1.0-2.4). Significant trends were also observed with exposure duration and cumulative exposure. No association between RCC risk and asbestos exposure was observed.

CONCLUSION

Results suggest that increased RCC risk may be associated with occupational exposure to specific types of dusts. Additional studies are needed to replicate and extend findings.

Renal cancer risk and occupational exposure to polycyclic aromatic hydrocarbons and plastics

OBJECTIVE

To investigate whether occupational exposure to polycyclic aromatic hydrocarbons and certain plastic monomers increased renal cell carcinoma (RCC) risk.

METHODS

Unconditional logistic regression was used to calculate RCC risk in relation to exposure.

RESULTS

No association between RCC risk and having ever been occupationally exposed to any polycyclic aromatic hydrocarbons or plastics was observed. Duration of exposure and average exposure also showed no association with risk. Suggestive positive associations between RCC risk and cumulative exposure to styrene (P-trend = 0.02) and acrylonitrile (P-trend = 0.06) were found. Cumulative exposure to petroleum/gasoline engine emissions was inversely associated with risk (P-trend = 0.02).

CONCLUSIONS

Results indicate a possible association between occupational styrene and acrylonitrile exposure and RCC risk. Additional studies are needed to replicate findings, as this is the first time these associations have been reported and they may be due to chance.

Occupational trichloroethylene exposure and renal carcinoma risk: evidence of genetic susceptibility by reductive metabolism gene variants

Trichloroethylene (TCE) is a suspected renal carcinogen. TCE-associated renal genotoxicity occurs predominantly through glutathione S-transferase (GST) conjugation and bioactivation by renal cysteine beta-lyase (CCBL1). We conducted a case-control study in Central Europe (1,097 cases and 1,476 controls) specifically designed to assess risk associated with occupational exposure to TCE through analysis of detailed job histories. All jobs were coded for organic/chlorinated solvent and TCE exposure (ever/never) as well as the frequency and intensity of exposure based on detailed occupational questionnaires, specialized questionnaires, and expert assessments. Increased risk was observed among subjects ever TCE exposed [odds ratio (OR) = 1.63; 95% confidence interval (95% CI), 1.04-2.54]. Exposure-response trends were observed among subjects above and below the median exposure [average intensity (OR = 1.38; 95% CI, 0.81-2.35; OR = 2.34; 95% CI, 1.05-5.21; P(trend) = 0.02)]. A significant association was found among TCE-exposed subjects with at least one intact GSTT1 allele (active genotype; OR = 1.88; 95% CI, 1.06-3.33) but not among subjects with two deleted alleles (null genotype; OR = 0.93; 95% CI, 0.35-2.44; P(interaction) = 0.18). Similar associations for all exposure metrics including average intensity were observed among GSTT1-active subjects (OR = 1.56; 95% CI, 0.79-3.10; OR = 2.77; 95% CI, 1.01-7.58; P(trend) = 0.02) but not among GSTT1 nulls (OR = 0.81; 95% CI, 0.24-2.72; OR = 1.16; 95% CI, 0.27-5.04; P(trend) = 1.00; P(interaction) = 0.34). Further evidence of heterogeneity was seen among TCE-exposed subjects with >or=1 minor allele of several CCBL1-tagging single nucleotide polymorphisms: rs2293968, rs2280841, rs2259043, and rs941960. These findings provide the strongest evidence to date that TCE exposure is associated with increased renal cancer risk, particularly among individuals carrying polymorphisms in genes that are important in the reductive metabolism of this chemical, and provides biological plausibility of the association in humans.

Occupational sunlight exposure and risk of renal cell carcinoma

BACKGROUND

Recent findings indicate that vitamin D obtained from ultraviolet (UV) exposure may reduce the risk of several different cancers. Vitamin D is metabolized to its active form within the kidney, which is the major organ for vitamin D metabolism and activity. Because both the incidence of renal cell carcinoma (RCC) and the prevalence of vitamin D deficiency have increased over the past few decades, in the current study, the authors explored whether occupational UV exposure was associated with RCC risk.

METHODS

A hospital-based, case-control study of 1097 patients with RCC (cases) and 1476 controls was conducted in 4 Central and Eastern European countries. Demographic and occupational information was collected to examine the association between occupational UV exposure and RCC risk.

RESULTS

A significant reduction (24%-38%) in the risk of RCC was observed with increasing occupational UV exposure among men who participated in the study. No association between UV exposure and RCC risk was observed among women who participated. When the analyses were stratified by latitude as another estimate of sunlight intensity, a stronger reduction (71%-73%) in the risk of RCC was observed between UV exposure and cancer risk among men who resided at the highest latitudes.

CONCLUSIONS

The current results suggested that, among men, there is an inverse association between occupational UV exposure and the risk of RCC. Replication studies are warranted to confirm these results.

Abstract 915: Xenobiotic metabolizing gene variants, occupational chemical exposures, and renal cell cancer

The countries of Central and Eastern Europe have among the highest worldwide rates of renal cell cancer. Few studies have examined whether genetic variation in xenobiotic metabolic pathway genes may modify risk for this cancer.

The Central and Eastern Europe Renal Cell Cancer study was a hospital-based case-control study conducted between 1998 and 2003 across seven centers in central and eastern Europe. The study centers were in the Czech Republic (Ceske, Prague, Olomouc, Brno), Poland (Lodz), Romania (Bucharest), and Russia (Moscow). Incident cases of primary kidney cancer were recruited and underwent an in-person interview in which detailed data were collected on demographics as well as work history and occupational exposure to chemical agents. Genes (cytochrome P-450 family, N-acetyltransferases, NAD(P)H:quinone oxidoreductase I (NQO1), microsomal epoxide hydrolase (mEH), catechol-O-methyltransferase (COMT)) were selected for the present analysis based on their putative role in xenobiotic metabolism. Genotyping (874 cases and 2396 controls) was conducted with a GoldenGate® Oligo Pool All (OPA) assay by Illumina® and the 5’ nuclease assay (Taqman, Applied Biosystems). Haplotypes were calculated using fastPhase. Odds ratios (OR) and 95% confidence intervals (CI) were estimated by unconditional logistic regression adjusted for country of residence, age, and sex.

We observed an increased risk of renal cell cancer (RCC) with two NAT1 SNPs (NAT1A40T, OR=1.36, CI 1.00, 1.86; NAT1R187Q, OR=1.65, CI 1.01, 2.71) and with CYP1B1V432L (OR=1.14, CI 1.01, 1.28). The slow (NAT1*14) phenotype was associated with increased risk of RCC (OR=1.69, CI 1.00-2.86) in comparison to normal phenotype (NAT1*4, *3, *11). Among persons with NAT1*14 phenotype, occupational exposure to trichloroethylene (OR=9.94, CI 1.15, 86.1) and chlorinated solvents (OR=9.79, CI 1.13, 84.8) conferred an increased risk of RCC. Among those with the CYP1B1V432L variant, occupational exposure to trichloroethylene (OR=1.68, CI 1.21, 2.34) and chlorinated solvents (OR=1.58, CI 1.14, 2.19) also had increased risk of RCC.

These results require replication, but provide evidence that the relationship between certain agents and RCC may be modified by particular variants in xenobiotic metabolism genes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 915.

Variants in blood pressure genes and the risk of renal cell carcinoma

Hypertension is a known risk factor for renal cell carcinoma (RCC), although the underlying biological mechanisms of its action are unknown. To clarify the role of hypertension in RCC, we examined the risk of RCC in relation to 142 single-nucleotide polymorphisms (SNPs) in eight genes having a role in blood pressure control. We analyzed 777 incident and histologically confirmed RCC cases and 1035 controls who completed an in-person interview as part of a multi-center, hospital-based case-control study in Central Europe. Genotyping was conducted with an Illumina GoldenGate Oligo Pool All assay using germ line DNA. Of the eight genes examined, AGT (angiotensinogen) was most strongly associated with RCC (minimum P-value permutation test = 0.02). Of the 17 AGT tagging SNPs considered, associations were strongest for rs1326889 [odds ratio (OR) = 1.35, 95% confidence interval (CI) = 1.15-1.58] and rs2493137 (OR = 1.31, 95% CI = 1.12-1.54), which are located in the promoter. Stratified analysis revealed that the effects of the AGT SNPs were statistically significant in participants with hypertension or high body mass index (BMI) (> or =25 kg/m(2)), but not in subjects without hypertension and with a normal BMI (<25 kg/m(2)). Also, haplotypes with risk-conferring alleles of markers located in the promoter and intron 1 regions of AGT were significantly associated with RCC compared with the common haplotype in subjects with hypertension or high BMI (global P = 0.003). Our findings suggest that common genetic variants of AGT, particularly those in the promoter, increase RCC risk among subjects who are hypertensive or overweight.

Vitamin d pathway genes, diet, and risk of renal cell carcinoma

Mediated by binding to the high-affinity vitamin D receptor (VDR), vitamin D forms a heterodimer complex with the retinoid-X-receptor (RXR). Variation in both genes has been shown to modify renal cell carcinoma (RCC) risk. Therefore, we investigated whether VDR and RXRA polymorphisms modify associations between RCC risk and frequency of dietary intake of vitamin D and calcium rich foods, and occupational ultraviolet exposure among 777 RCC case and 1035 controls from Central and Eastern Europe. A positive association was observed in this population between increasing dietary intake frequency of yogurt, while an inverse association was observed with egg intake frequency. RXRA polymorphisms, located 3' of the coding sequence, modified associations between specific vitamin D rich foods and RCC risk, while RXRA polymorphisms, located in introns 1 and 4, modified associations with specific calcium rich foods. Results suggest that variants in the RXRA gene modified the associations observed between RCC risk and calcium and vitamin D intake.

Toxic effects of cobalt chloride on hematological factors of common carp (Cyprinus carpio)

In this study, we investigate the toxic effects of cobalt chloride on some hematological factors of the carp Cyprinus carpio, such as white blood cell count, red blood cell count, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin, and mean corpuscular hemoglobin concentration. At first, LC50 of cobalt in C. carpio was measured during 96 h after exposure. Also, physicochemical parameters of water including pH, dissolved oxygen, viscosity, temperature, and conductivity were monitored, continuously. The results showed that LC50 values of cobalt in C. carpio were 327 and 328 mg/L in two replicates, respectively. Then, the changes in some hematological factors in the five treatment groups placed under concentration of 100, 200, 300, 400, and 500 mg/L cobalt were compared with the control group. Based on hematological tests conducted in this research, exposure of carp to 500- and 300-mg/L concentrations of cobalt in 48 h showed significant difference (p<0.05) in white blood cell count. The concentration of 500 mg/L cobalt in 24 h showed a significant difference in the amount of hemoglobin, number of red blood cells, and hematocrit level as compared with the control group. The concentration of 100 mg/L cobalt in 48 h did not show a significant difference in comparison with the control group (p>0.05). Also, the concentration of 500 mg/L cobalt in 24 h showed a significant difference in the amount of mean corpuscular volume and mean corpuscular hemoglobin as compared with the control group and other treatments. Also, the percentage of mean corpuscular hemoglobin concentration in a concentration of 200 mg/L cobalt in 24 h showed a significant difference as compared with the control group and other treatments.

Apolipoprotein E/C1 locus variants modify renal cell carcinoma risk

Lipid peroxidation is considered a unifying mechanistic pathway through which known risk factors induce renal cell carcinoma (RCC). We hypothesized that genes selected a priori for their role in lipid peroxidation would modify cancer risk. We genotyped 635 single nucleotide polymorphisms (SNP) in 38candidate genes in 777 Caucasian RCC cases and 1,035 controls enrolled in a large European case-control study. Top candidate SNPs were confirmed among 718 Caucasian cases and 615 controls in a second study in the United States. Two of the three SNPs (rs8106822 and rs405509) that replicated in the U.S. study were within a regulatory region of the APOE promoter. The OR for rs8106822 A>G variant was 1.22(AG) and 1.41(GG) (P(trend) = 0.01) in the European study, 1.05(AG) and 1.51(GG) (P(trend) = 0.03) in the U.S. study, and 1.15(AG) and 1.44(GG) (P(trend) = 0.001) among 1,485 cases and 1,639 controls combined. The rs405509 G>T variant was associated with risk in the European (OR, 0.87(TG); OR, 0.71(TT); P(trend) = 0.02), the U.S. (OR, 0.68(TG); OR, 0.71(TT); P(trend) = 0.02), and both studies combined (OR(TG), 0.79; OR(TT), 0.71; P(trend) = 0.001), as was the G-G haplotype (r(2) = 0.64; P= 4.7 x 10(-4)). This association is biologically plausible as SNP rs405509 was shown to modify protein binding and transcriptional activity of the APOE protein in vitro and is in linkage disequilibrium with key known variants defining the e2, e3, and e4 alleles that modify risk of atherosclerosis, Alzheimer's disease risk, and progression to AIDS. In two large case-control studies, our findings further define a functional region of interest at the APOE locus that increases RCC susceptibility.

Analysis of SNPs and haplotypes in vitamin D pathway genes and renal cancer risk

In the kidney vitamin D is converted to its active form. Since vitamin D exerts its activity through binding to the nuclear vitamin D receptor (VDR), most genetic studies have primarily focused on variation within this gene. Therefore, analysis of genetic variation in VDR and other vitamin D pathway genes may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. RCC cases (N = 777) and controls (N = 1,035) were genotyped to investigate the relationship between RCC risk and variation in eight target genes. Minimum-p-value permutation (Min-P) tests were used to identify genes associated with risk. A three single nucleotide polymorphism (SNP) sliding window was used to identify chromosomal regions with a False Discovery Rate of <10%, where subsequently, haplotype relative risks were computed in Haplostats. Min-P values showed that VDR (p-value = 0.02) and retinoid-X-receptor-alpha (RXRA) (p-value = 0.10) were associated with RCC risk. Within VDR, three haplotypes across two chromosomal regions of interest were identified. The first region, located within intron 2, contained two haplotypes that increased RCC risk by approximately 25%. The second region included a haplotype (rs2239179, rs12717991) across intron 4 that increased risk among participants with the TC (OR = 1.31, 95% CI = 1.09-1.57) haplotype compared to participants with the common haplotype, TT. Across RXRA, one haplotype located 3' of the coding sequence (rs748964, rs3118523), increased RCC risk 35% among individuals with the variant haplotype compared to those with the most common haplotype. This study comprehensively evaluated genetic variation across eight vitamin D pathway genes in relation to RCC risk. We found increased risk associated with VDR and RXRA. Replication studies are warranted to confirm these findings.

Occupation and renal cell cancer in Central and Eastern Europe

OBJECTIVE

Central and Eastern Europe has among the highest rates of renal cell cancer worldwide. Few studies have been conducted in these areas to investigate the possible role of occupational exposures in renal cell cancer aetiology. The purpose of this study was to examine the association of renal cell cancer with employment in specific occupations and industries.

METHODS

From 1999 to 2003, we conducted a hospital-based case-control study in seven areas of the Czech Republic, Poland, Romania and Russia. A detailed occupational history was collected from renal cell cancer cases and controls, together with information on potential confounders. Odds ratios (ORs) and 95% CI of cancer risk were calculated for having ever been employed in selected jobs and industries, with follow-up analyses examining duration of employment.

RESULTS

A total of 992 histologically confirmed incident renal cell cancer cases and 1459 controls were included in the analysis. An increased risk of renal cell cancer was observed for workers in agricultural labour and animal husbandry (OR 1.43; 95% CI 1.05 to 1.93), particularly among women employed as general farm workers (OR 2.73; 95% CI 1.05 to 7.13). Risk gradients for agricultural work increased with longer employment. An overall increased risk of renal cell cancer was seen among architects and engineers (OR 1.89; 95% CI 1.35 to 2.65), and mechanical engineers (OR 1.71; 95% CI 1.03 to 2.84).

CONCLUSIONS

Our data suggest an association between renal cell cancer and agricultural work, particularly among female workers.

An analysis of growth, differentiation and apoptosis genes with risk of renal cancer

We conducted a case-control study of renal cancer (987 cases and 1298 controls) in Central and Eastern Europe and analyzed genomic DNA for 319 tagging single-nucleotide polymorphisms (SNPs) in 21 genes involved in cellular growth, differentiation and apoptosis using an Illumina Oligo Pool All (OPA). A haplotype-based method (sliding window analysis of consecutive SNPs) was used to identify chromosome regions of interest that remained significant at a false discovery rate of 10%. Subsequently, risk estimates were generated for regions with a high level of signal and individual SNPs by unconditional logistic regression adjusting for age, gender and study center. Three regions containing genes associated with renal cancer were identified: caspase 1/5/4/12(CASP 1/5/4/12), epidermal growth factor receptor (EGFR), and insulin-like growth factor binding protein-3 (IGFBP3). We observed that individuals with CASP1/5/4/12 haplotype (spanning area upstream of CASP1 through exon 2 of CASP5) GGGCTCAGT were at higher risk of renal cancer compared to individuals with the most common haplotype (OR:1.40, 95% CI:1.10–1.78, p-value = 0.007). Analysis of EGFR revealed three strong signals within intron 1, particularly a region centered around rs759158 with a global p = 0.006 (GGG: OR:1.26, 95% CI:1.04–1.53 and ATG: OR:1.55, 95% CI:1.14–2.11). A region in IGFBP3 was also associated with increased risk (global p = 0.04). In addition, the number of statistically significant (p-value<0.05) SNP associations observed within these three genes was higher than would be expected by chance on a gene level. To our knowledge, this is the first study to evaluate these genes in relation to renal cancer and there is need to replicate and extend our findings. The specific regions associated with risk may have particular relevance for gene function and/or carcinogenesis. In conclusion, our evaluation has identified common genetic variants in CASP1, CASP5, EGFR, and IGFBP3 that could be associated with renal cancer risk.

Abstract PR-6: Variation in VDR pathway genes and renal cancer risk

PR-6

The conversion of vitamin D to its main biologically active form, 1,25-dihydroxy vitamin D, occurs in the kidney. Since the most biologically active form of vitamin D exerts its activity through binding to the intracellular vitamin D receptor (VDR), most studies of genetic susceptibility have primarily focused on variation within the VDR gene. But, the concert of genes that interact with VDR are vast; therefore, an analysis of genetic variation in VDR and other genes in its pathway may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. In this case-control study, we investigated the relationship between RCC risk and 139 single nucleotide polymorphisms (SNPs) in 8 target genes (VDR, RXRA, RXRB, CYP24A1, GC, STAT1, THRAP4 and TRAP5) of the expanded vitamin D pathway from subjects residing in Central and Eastern Europe. 1,097 RCC cases and 1,476 controls were recruited for this study where genomic DNA was analyzed using an Illumina Oligo Pool-All (OPA) assay. First, the minimum-p-value permutation (Min-P) test was used to identify genes that were associated with RCC risk and that remained significant at a cut off level of 10%. Next, a haplotype-based sliding window analysis of three consecutive SNPs was used to identify chromosome regions of interest that remained significant at a False Discovery Rate (FDR) of 10%. For these regions, haplotype relative risks were computed using the HaploStats package in R. Significant Min-P values were observed for two genes, which were selected for in-depth analysis: VDR (P-value: 0.024) and RXRA (P-value: 0.100). Two chromosomal regions of interest within the VDR gene were identified using the haplotype-based sliding window technique. The first region identified two haplotypes within intron 2, centered around rs4760648, that significantly increased RCC risk (haplotype 1: OR= 1.25; 95% CI= 1.04-1.50 and hapotype 2: OR= 1.26; 95% CI= 1.02-1.54) when compared to patients with the most common referent haplotype. The second signal identified a haplotype (rs886441 and rs12717991) located within intron 4 of the VDR gene that was associated with increased risk among participants with the TG (OR= 1.29; 95%CI= 1.08-1.54) haplotype compared to participants with most common referent haplotype, CA. The global p-values in R for these haplotypes were 0.025 and 0.028, respectively. Across the RXRA gene, a single haplotype located downstream, 3’ of the coding sequence, centered around rs3118523 was shown to increase RCC risk (OR= 1.41; 95% CI= 1.10-1.82) among individuals with the variant haplotype compared to those with the most common haplotype. This is the first study to our knowledge to comprehensively evaluate genetic variation in VDR and other pathway genes in relation to RCC risk. While replication and fine mapping studies will be required to confirm these findings, this study suggests that genes in the vitamin D pathway may modify RCC risk.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):PR-6.

Abstract A89: Association of genes involved in lipid metabolism-peroxidation and risk of renal cancer in the Central European Renal Cancer Case-Control Study

A89

Recent descriptive studies have reported increases in kidney cancer incidence since the 1970s in the United States and globally. Lipid peroxidation has been suggested as a unifying mechanistic pathway by which several known risk factors including obesity, hypertension, and chemicals directly damage cells of the proximal renal tubules and induce renal carcinogenesis. This study investigated the association between renal cell cancer (RCC) risk and variation in genes that modify the effects of lipid peroxidation, inflammation, and oxidative stress. We conducted a case-control study of RCC (987 cases and 1298 controls) from Central and Eastern Europe and analyzed genomic DNA for 635 single nucleotide polymorphisms (SNPs) thirty-eight candidate genes using an Illumina Oligo Pool-All (OPA). First, the minimum p-value permutation test (MINP) was used to identify genes that remained significant with an FDR&lt;5%. Subsequently, a haplotype-based sliding window analysis of three consecutive SNPs was used to identify chromosome regions of interest that remained significant at a FDR&lt;5%. Six genes were selected for in-depth analysis after multiple testing correction of the single marker associations: APOE, GPX4, NOS2A and PTGS2. The overall gene-level p-values for these genes were 0.017, 0.020, 0.055 and 0.069 using the MINP test, respectively. The minimum FDR-adjusted p-values in a sliding window haplotype analysis were 0.0005, 0.0007, 0.0002 and 1.09x10-5, respectively. For these regions, age-, sex- and center-adjusted haplotype relative risks were computed using the HaploStats package in R. After adjustment, a strong signal centered around the promoter region of APOE gene (rs405509) remained significantly associated with decreased risk of RCC compared to persons homozygous for the referent haplotype (OR=0.73 95% CI:0.59-0.91); global p=0.001). A second haplotype window spanning from IVS7+11 to IVS12-52 of the NOS2A gene that was significantly associated with increased risk (OR=1.36 (95% CI:1.05-1.78); p-global p-0.006). Additional haplotype windows spanning the trans-membrane and tyrosine kinase domains of INSR (rs28601) and intron 2 of LEPR (rs970467) genes also were investigated further (FDR-adjusted p &lt;0.05). After adjustment in Haplostats, two additional high risk haplotypes were identified that were significantly associated with risk. To our knowledge this is the first and largest study of RCC conducted to evaluate these genes in relation to RCC. Although replication and fine mapping studies will be required to confirm these findings, this study supports the hypothesis variation in genes influencing lipid metabolism/peroxidation may increase susceptibility to sporadic kidney cancer.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):A89.

Improved identification of von Hippel-Lindau gene alterations in clear cell renal tumors

PURPOSE

To provide a comprehensive, thorough analysis of somatic mutation and promoter hypermethylation of the von Hippel-Lindau (VHL) gene in the cancer genome, unique to clear cell renal cancer (ccRCC). Identify relationships between the prevalence of VHL gene alterations and alteration subtypes with patient and tumor characteristics.

EXPERIMENTAL DESIGN

As part of a large kidney cancer case-control study conducted in Central Europe, we analyzed VHL mutations and promoter methylation in 205 well-characterized, histologically confirmed patient tumor biopsies using a combination of sensitive, high-throughput methods (endonuclease scanning and Sanger sequencing) and analysis of 11 CpG sites in the VHL promoter.

RESULTS

We identified mutations in 82.4% of cases, the highest VHL gene mutation prevalence reported to date. Analysis of 11 VHL promoter CpG sites revealed that 8.3% of tumors were hypermethylated and all were mutation negative. In total, 91% of ccRCCs exhibited alteration of the gene through genetic or epigenetic mechanisms. Analysis of patient and tumor characteristics revealed that certain mutation subtypes were significantly associated with Fuhrman nuclear grade, metastasis, node positivity, and self-reported family history of RCC.

CONCLUSION

Detection of VHL gene alterations using these accurate, sensitive, and practical methods provides evidence that the vast majority of histologically confirmed ccRCC tumors possess genetic or epigenetic alteration of the VHL gene and support the hypothesis that VHL alteration is an early event in ccRCC carcinogenesis. These findings also indicate that VHL molecular subtypes can provide a sensitive marker of tumor heterogeneity among histologically similar ccRCC cases for etiologic, prognostic, and translational studies.