A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age

Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control women. The combined discovery and replication sets identified 72 new SNPs associated with EOBC (P < 4 × 10(-8)) located in six genomic regions previously reported to contain SNPs associated largely with later-onset breast cancer (LOBC). SNP rs2229882 and 10 other SNPs on chromosome 5q11.2 remained associated (P < 6 × 10(-4)) after adjustment for the strongest published SNPs in the region. Thirty-two of the 82 currently known LOBC SNPs were associated with EOBC (P < 0.05). Low power is likely responsible for the remaining 50 unassociated known LOBC SNPs. The gene-based analysis identified an association between breast cancer and the phosphofructokinase-muscle (PFKM) gene on chromosome 12q13.11 that met the genome-wide gene-based threshold of 2.5 × 10(-6). In conclusion, EOBC and LOBC seem to have similar genetic etiologies; the 5q11.2 region may contain multiple distinct breast cancer loci; and the PFKM gene region is worthy of further investigation. These findings should enhance our understanding of the etiology of breast cancer.

Abstract 08: Differential DNA methylation related to arsenic exposure and tobacco smoking

Background: Chronic arsenic exposure through drinking water is a growing public health issue affecting millions of people worldwide, including 35 to 57 million in Bangladesh. While tobacco smoking is beginning to decline in some Western populations, it is increasing in the Bangladeshi population as well as other developing nations. Arsenic and tobacco are known human carcinogens, with epigenetic modification suggested to underlie their mechanisms of carcinogenesis.

Objectives: Among a random sample of 413 adult participants (218 males and 195 females) in the Bangladesh Vitamin E and Selenium Trial (BEST)'an NCI-funded 6-year chemoprevention trial of 7,000 individuals with arsenical skin lesions, we evaluated the association between chronic arsenic exposure, tobacco smoking, and epigenome-wide DNA methylation at baseline.

Design and Methods: BEST participants, aged 25-65 years at enrollment, have been chronically exposed to naturally-occurring arsenic through the consumption of groundwater. Individual-level arsenic exposure was measured by urinary total arsenic and blood arsenic concentrations. Cigarette smoking was ascertained as current, former, and never smoker. DNA methylation status was assessed from whole blood DNA using the Illumina Infinium HumanMethylation450 BeadChip, which measures methylation of 485,577 CpG sites. Linear regression models were used to examine the associations between arsenic as well as tobacco smoking with each CpG site, adjusted for sex, age, and batch. Bonferroni correction was applied to the level of significance to account for multiple comparisons in detecting differential methylation.

Results: The mean urinary total arsenic concentration in the study sample was 307.8±370.0 μg/g, and the mean blood arsenic concentration was 9.4±11.3 μg/L. The Pearson correlation coefficient between the two arsenic measures was 0.88. In adjusted analyses, we observed 5 differentially methylated CpG sites with urinary total arsenic concentration and 12 differentially methylated CpG sites with blood arsenic concentration. Methylation of PLA2G2C cg04605617 was the most significantly associated site for both urinary (P=2.35 × 10-12) and blood arsenic concentrations (P=6.07 × 10-13). The prevalence of smoking was 66.5% among men and 4.6% among women; therefore, differential methylation was examined in male participants only for the tobacco smoking analyses. In adjusted analyses, we observed 42 differentially methylated CpG sites with ever versus never tobacco smoking. Methylation of AHRR cg05575921was the most significantly associated site (P=1.48 × 10-35) with tobacco smoking.

Conclusion: Significant associations between arsenic exposure and the phospholipase A2 pathway were observed in this study. Additionally, a significant association between tobacco smoking and the aryl hydrocarbon receptor pathway was observed in this study among males. Our results suggest that these inflammation-related epigenetic modifications may be important pathways underlying arsenic and tobacco carcinogenesis and may inform future interventions for these environmental carcinogens.

Citation Format: Maria Argos, Farzana Jasmine, Lin Chen, Rachelle Brutus, Shantanu Roy, Vesna Slavkovich, Joseph Graziano, Muhammad Kibriya, Habibul Ahsan. Differential DNA methylation related to arsenic exposure and tobacco smoking. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 08.