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Metabolomic profiles in breast cancer:a pilot case-control study in the breast cancer family registry.

ABSTRACT: BACKGROUND:Metabolomics is emerging as an important tool for detecting differences between diseased and non-diseased individuals. However, prospective studies are limited. METHODS:We examined the detectability, reliability, and distribution of metabolites measured in pre-diagnostic plasma samples in a pilot study of women enrolled in the Northern California site of the Breast Cancer Family Registry. The study included 45 cases diagnosed with breast cancer at least one year after the blood draw, and 45 controls. Controls were matched on age (within 5 years), family status, BRCA status, and menopausal status. Duplicate samples were included for reliability assessment. We used a liquid chromatography/gas chromatography mass spectrometer platform to measure metabolites. We calculated intraclass correlations (ICCs) among duplicate samples, and coefficients of variation (CVs) across metabolites. RESULTS:Of the 661 named metabolites detected, 338 (51%) were found in all samples, and 490 (74%) in more than 80% of samples. The median ICC between duplicates was 0.96 (25th - 75th percentile: 0.82-0.99). We observed a greater than 20% case-control difference in 24 metabolites (p < 0.05), although these associations were not significant after adjusting for multiple comparisons. CONCLUSIONS:These data show that assays are reproducible for many metabolites, there is a minimal laboratory variation for the same sample, and a large between-person variation. Despite small sample size, differences between cases and controls in some metabolites suggest that a well-powered large-scale study is likely to detect biological meaningful differences to provide a better understanding of breast cancer etiology.

SUBMITTER: Dougan MM

PROVIDER: S-EPMC5935968 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Both protein-truncating variants and some missense substitutions in CHEK2 confer increased risk of breast cancer. However, no large-scale study has used full open reading frame mutation screening to assess the contribution of rare missense substitutions in CHEK2 to breast cancer risk. This absence has been due in part to a lack of validated statistical methods for summarizing risk attributable to large numbers of individually rare missense substitutions.Previously, we adapted an in silico assessment of missense substitutions used for analysis of unclassified missense substitutions in BRCA1 and BRCA2 to the problem of assessing candidate genes using rare missense substitution data observed in case-control mutation-screening studies. The method involves stratifying rare missense substitutions observed in cases and/or controls into a series of grades ordered a priori from least to most likely to be evolutionarily deleterious, followed by a logistic regression test for trends to compare the frequency distributions of the graded missense substitutions in cases versus controls. Here we used this approach to analyze CHEK2 mutation-screening data from a population-based series of 1,303 female breast cancer patients and 1,109 unaffected female controls.We found evidence of risk associated with rare, evolutionarily unlikely CHEK2 missense substitutions. Additional findings were that (1) the risk estimate for the most severe grade of CHEK2 missense substitutions (denoted C65) is approximately equivalent to that of CHEK2 protein-truncating variants; (2) the population attributable fraction and the familial relative risk explained by the pool of rare missense substitutions were similar to those explained by the pool of protein-truncating variants; and (3) post hoc power calculations implied that scaling up case-control mutation screening to examine entire biochemical pathways would require roughly 2,000 cases and controls to achieve acceptable statistical power.This study shows that CHEK2 harbors many rare sequence variants that confer increased risk of breast cancer and that a substantial proportion of these are missense substitutions. The study validates our analytic approach to rare missense substitutions and provides a method to combine data from protein-truncating variants and rare missense substitutions into a one degree of freedom per gene test.

Project description:The carcinogenesis process is associated with inflammation, which can be modified by diet. There is limited evidence regarding the inflammatory status and diet in association with breast cancer (BC). The aim of this study was to investigate the association of hybrid dietary-blood inflammatory profiles (HD-BIPs) with postmenopausal breast cancer occurrence. The case-control study was conducted among 420 women (230 controls, 190 primary BC cases) aged 40-79 years from north-eastern Poland. Blood levels of C-reactive protein (CRP), interleukin-6 (IL-6) and leukocyte count were marked in 129 postmenopausal women (82 controls, 47 cases). The 62-item food frequency questionnaire (FFQ-6) was used to the dietary data collection. Two HD-BIPs were found using the Principal Component Analysis (PCA). The "Pro-healthy/Neutral-inflammatory" profile was characterized by the frequent consumption of wholemeal cereals/coarse groats, legumes, vegetables, fruits, nuts/seeds and fish. The "Unhealthy/Pro-inflammatory" profile was characterized by the frequent consumption of red/processed meats, animal fats, sugar/honey/sweets, refined cereals/fine groats, and an increased concentration of CRP, IL-6 and granulocyte-to-lymphocyte ratio. The lower odds ratio (OR) of breast cancer was associated with the higher adherence to the "Pro-healthy/Neutral-inflammatory" profile (OR = 0.38; 95% Cl: 0.18-0.80; p < 0.01 for the higher level vs. lower level, crude model; OR for one-point score increment: 0.61; 95% Cl: 0.42-0.87; p < 0.01, adjusted model). The higher OR of breast cancer was associated with the higher adherence to the "Unhealthy/Pro-inflammatory" profile (OR = 3.07; 95%Cl: 1.27-7.44; p < 0.05 for the higher level v.s. lower level, adjusted model; OR for one-point score increment: 1.18; 95%Cl: 1.02-1.36; p < 0.05, adjusted model). This study revealed that the consumption of highly processed, high in sugar and animal fat foods should be avoided because this unhealthy diet was positively associated with postmenopausal breast cancer occurrence through its pro-inflammatory potential. Instead, the frequent consumption of low-processed plant foods and fish should be recommended since this pro-healthy diet was inversely associated with the cancer occurrence even though its anti-inflammatory potential has not been confirmed in this study sample.

Project description:INTRODUCTION:The MRE11A-RAD50-Nibrin (MRN) complex plays several critical roles related to repair of DNA double-strand breaks. Inherited mutations in the three components predispose to genetic instability disorders and the MRN genes have been implicated in breast cancer susceptibility, but the underlying data are not entirely convincing. Here, we address two related questions: (1) are some rare MRN variants intermediate-risk breast cancer susceptibility alleles, and if so (2) do the MRN genes follow a BRCA1/BRCA2 pattern wherein most susceptibility alleles are protein-truncating variants, or do they follow an ATM/CHEK2 pattern wherein half or more of the susceptibility alleles are missense substitutions? METHODS:Using high-resolution melt curve analysis followed by Sanger sequencing, we mutation screened the coding exons and proximal splice junction regions of the MRN genes in 1,313 early-onset breast cancer cases and 1,123 population controls. Rare variants in the three genes were pooled using bioinformatics methods similar to those previously applied to ATM, BRCA1, BRCA2, and CHEK2, and then assessed by logistic regression. RESULTS:Re-analysis of our ATM, BRCA1, and BRCA2 mutation screening data revealed that these genes do not harbor pathogenic alleles (other than modest-risk SNPs) with minor allele frequencies>0.1% in Caucasian Americans, African Americans, or East Asians. Limiting our MRN analyses to variants with allele frequencies of <0.1% and combining protein-truncating variants, likely spliceogenic variants, and key functional domain rare missense substitutions, we found significant evidence that the MRN genes are indeed intermediate-risk breast cancer susceptibility genes (odds ratio (OR)=2.88, P=0.0090). Key domain missense substitutions were more frequent than the truncating variants (24 versus 12 observations) and conferred a slightly higher OR (3.07 versus 2.61) with a lower P value (0.029 versus 0.14). CONCLUSIONS:These data establish that MRE11A, RAD50, and NBN are intermediate-risk breast cancer susceptibility genes. Like ATM and CHEK2, their spectrum of pathogenic variants includes a relatively high proportion of missense substitutions. However, the data neither establish whether variants in each of the three genes are best evaluated under the same analysis model nor achieve clinically actionable classification of individual variants observed in this study.

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Metabolomic profiles in breast cancer:a pilot case-control study in the breast cancer family registry.

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