methscore: a comprehensive R function for DNA methylation-based health predictors

MOTIVATION

DNA methylation-based predictors of various biological metrics have been widely published and are becoming valuable tools in epidemiologic studies of epigenetics and personalized medicine. However, generating these predictors from original source software and web servers is complex and time consuming. Furthermore, different predictors were often derived based on data from different types of arrays, where array differences and batch effects can make predictors difficult to compare across studies.

RESULTS

We integrate these published methods into a single R function to produce 158 previously published predictors for chronological age, biological age, exposures, lifestyle traits and serum protein levels using both classical and principal component-based methods. To mitigate batch and array differences, we also provide a modified RCP method (ref-RCP) that normalize input DNA methylation data to reference data prior to estimation. Evaluations in real datasets show that this approach improves estimate precision and comparability across studies.

AVAILABILITY AND IMPLEMENTATION

The function was included in software package ENmix, and is freely available from Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).

Diet quality and cardiovascular disease risk among breast cancer survivors in the Pathways Study

BACKGROUND

Women with breast cancer are at higher risk of cardiovascular disease (CVD) compared with women without breast cancer. Whether higher diet quality at breast cancer diagnosis lowers this risk remains unknown. We set out to determine if higher diet quality at breast cancer diagnosis was related to lower risk of CVD and CVD-related death.

METHODS

This analysis included 3415 participants from the Pathway Study, a prospective cohort of women diagnosed with invasive breast cancer at Kaiser Permanente Northern California between 2005 and 2013 and followed through December 31, 2021. Scores from 5 diet quality indices consistent with healthy eating were obtained at the time of breast cancer diagnosis. Scores were categorized into ascending quartiles of concordance for each diet quality index, and multivariable adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated. P values were 2-sided.

RESULTS

The Dietary Approaches to Stop Hypertension diet quality index was associated with lower risk of heart failure (HR = 0.53, 95% CI = 0.33 to 0.87; Ptrend = .03), arrhythmia (HR = 0.77, 95% CI = 0.62 to 0.94; Ptrend = .008), cardiac arrest (HR = 0.77, 95% CI = 0.61 to 0.96; Ptrend = .02), valvular heart disease (HR = 0.79, 95% CI = 0.64 to 0.98; Ptrend = .046), venous thromboembolic disease (HR = 0.75, 95% CI = 0.60 to 0.93; Ptrend = .01), and CVD-related death (HR = 0.70, 95% CI = 0.50 to 0.99; Ptrend = .04), when comparing the highest with lowest quartiles. Inverse associations were also found between the healthy plant-based dietary index and heart failure (HR = 0.60, 95% CI = 0.39 to 0.94; Ptrend = .02), as well as the alternate Mediterranean dietary index and arrhythmia (HR = 0.74, 95% CI = 0.60 to 0.93; Ptrend = .02).

CONCLUSION

Among newly diagnosed breast cancer patients, higher diet quality at diagnosis was associated with lower risk of CVD events and death.

Circulating Leukocyte Subsets Before and After a Breast Cancer Diagnosis and Therapy

Importance

Changes in leukocyte composition often precede chronic disease onset. Patients with a history of breast cancer (hereinafter referred to as breast cancer survivors) are at increased risk for subsequent chronic diseases, but the long-term changes in peripheral leukocyte composition following a breast cancer diagnosis and treatment remain unknown.

Objective

To examine longitudinal changes in peripheral leukocyte composition in women who did and did not develop breast cancer and identify whether differences in breast cancer survivors were associated with specific treatments.

Design, Setting, and Participants

In this prospective cohort study, paired blood samples were collected from 2315 women enrolled in The Sister Study, a US-nationwide prospective cohort study of 50 884 women, at baseline (July 2003 to March 2009) and follow-up (October 2013 to March 2015) home visits, with a mean (SD) follow-up interval of 7.6 (1.4) years. By design, approximately half of the included women had been diagnosed and treated for breast cancer after enrollment and before the second blood draw. A total of 410 women were included in the present study, including 185 breast cancer survivors and 225 who remained free of breast cancer over a comparable follow-up period. Data were analyzed from April 21 to September 9, 2022.

Exposures

Breast cancer status and, among breast cancer survivors, cancer treatment type (chemotherapy, radiotherapy, endocrine therapy, or surgery).

Main Outcomes and Measures

Blood DNA methylation data were generated in 2019 using a genome-wide methylation screening tool and deconvolved to estimate percentages of 12 circulating leukocyte subsets.

Results

Of the 410 women included in the analysis, the mean (SD) age at enrollment was 56 (9) years. Compared with breast cancer-free women, breast cancer survivors had decreased percentages of circulating eosinophils (-0.45% [95% CI, -0.87% to -0.03%]; P = .03), total CD4+ helper T cells (-1.50% [95% CI, -2.56% to -0.44%]; P = .01), and memory B cells (-0.22% [95% CI, -0.34% to -0.09%]; P = .001) and increased percentages of circulating naive B cells (0.46% [95% CI, 0.17%-0.75%]; P = .002). In breast cancer survivor-only analyses, radiotherapy was associated with decreases in total CD4+ T cell levels, whereas chemotherapy was associated with increases in naive B cell levels. Surgery and endocrine therapy were not meaningfully associated with leukocyte changes.

Conclusions and Relevance

In this cohort study of 410 women, breast cancer survivors experienced lasting changes in peripheral leukocyte composition compared with women who remained free of breast cancer. These changes may be related to treatment with chemotherapy or radiotherapy and could influence future chronic disease risk.

Changes in methylation-based aging in women who do and do not develop breast cancer

BACKGROUND

Breast cancer survivors have increased incidence of age-related diseases, suggesting that some survivors may experience faster biological aging.

METHODS

Among 417 women enrolled in the prospective Sister Study cohort, DNA methylation data were generated on paired blood samples collected an average of 7.7 years apart and used to calculate 3 epigenetic metrics of biological aging (PhenoAgeAccel, GrimAgeAccel, and Dunedin Pace of Aging Calculated from the Epigenome [DunedinPACE]). Approximately half (n = 190) the women sampled were diagnosed and treated for breast cancer between blood draws, whereas the other half (n = 227) remained breast cancer-free. Breast tumor characteristics and treatment information were abstracted from medical records.

RESULTS

Among women who developed breast cancer, diagnoses occurred an average of 3.5 years after the initial blood draw and 4 years before the second draw. After accounting for covariates and biological aging metrics measured at baseline, women diagnosed and treated for breast cancer had higher biological aging at the second blood draw than women who remained cancer-free as measured by PhenoAgeAccel (standardized mean difference [β] = 0.13, 95% confidence interval [CI) = 0.00 to 0.26), GrimAgeAccel (β = 0.14, 95% CI = 0.03 to 0.25), and DunedinPACE (β = 0.37, 95% CI = 0.24 to 0.50). In case-only analyses assessing associations with different breast cancer therapies, radiation had strong positive associations with biological aging (PhenoAgeAccel: β = 0.39, 95% CI = 0.19 to 0.59; GrimAgeAccel: β = 0.29, 95% CI = 0.10 to 0.47; DunedinPACE: β = 0.25, 95% CI = 0.02 to 0.48).

CONCLUSIONS

Biological aging is accelerated following a breast cancer diagnosis and treatment. Breast cancer treatment modalities appear to differentially contribute to biological aging.

Differences in epigenetic age by HIV status among patients with a non-AIDS defining cancer

OBJECTIVE

People with HIV (PWH) are living longer and experiencing higher numbers of non-AIDS-defining cancers (NADC). Epigenetic aging biomarkers have been linked to cancer risk, and cancer is now a leading cause of death in PWH, but these biomarkers have not been investigated in PWH and cancer.

DESIGN

In order to compare epigenetic age by HIV status, HIV-uninfected participants were matched to PWH by reported age, tumor site, tumor sequence number, and cancer treatment status.

METHODS

DNA from blood was assayed using Illumina MethylationEPIC BeadChip, and we estimated immune cell composition and aging from three epigenetic clocks: Horvath, GrimAge, and epiTOC2. Age acceleration by clock was computed as the residual from the expected value, calculated using linear regression, for each study participant. Comparisons across HIV status used the Wilcoxon rank sum test. Hazard ratios and 95% confidence intervals for the association between age acceleration and survival in PWH were estimated with Cox regression.

RESULTS

Among 65 NADC participants with HIV and 64 without, biological age from epiTOC2 ( P  < 0.0001) and GrimAge ( P  = 0.017) was significantly higher in PWH. Biological age acceleration was significantly higher in PWH using epiTOC2 ( P  < 0.01) and GrimAge ( P  < 0.0001), with the difference in GrimAge remaining statistically significant after adjustment for immune cell composition. Among PWH, GrimAge acceleration was significantly associated with increased risk of death (hazard ratio 1.11; 95% confidence interval (CI) 1.04-1.18).

CONCLUSION

We observed a higher epigenetic age in PWH with a NADC diagnosis compared with their HIV-uninfected counterparts, as well as a significant association between this accelerated biological aging and survival for patients diagnosed with a NADC.

Air pollution and epigenetic aging among Black and White women in the US

BACKGROUND

DNA methylation-based measures of biological aging have been associated with air pollution and may link pollutant exposures to aging-related health outcomes. However, evidence is inconsistent and there is little information for Black women.

OBJECTIVE

We examined associations of ambient particulate matter <2.5 μm and <10 μm in diameter (PM2.5 and PM10) and nitrogen dioxide (NO2) with DNA methylation, including epigenetic aging and individual CpG sites, and evaluated whether associations differ between Black and non-Hispanic White (NHW) women.

METHODS

Validated models were used to estimate annual average outdoor residential exposure to PM2.5, PM10, and NO2 in a sample of self-identified Black (n=633) and NHW (n=3493) women residing in the contiguous US. We used sampling-weighted generalized linear regression to examine the effects of pollutants on six epigenetic aging measures (primary: DunedinPACE, GrimAgeAccel, and PhenoAgeAccel; secondary: Horvath intrinsic epigenetic age acceleration [EAA], Hannum extrinsic EAA, and skin & blood EAA) and epigenome-wide associations for individual CpG sites. Wald tests of nested models with and without interaction terms were used to examine effect measure modification by race/ethnicity.

RESULTS

Black participants had higher median air pollution exposure than NHW participants. GrimAgeAccel was associated with both PM10 and NO2 among Black participants, (Q4 versus Q1, PM10: β=1.09, 95% CI: 0.16-2.03; NO2: β=1.01, 95% CI 0.08-1.94) but not NHW participants (p-for-heterogeneity: PM10=0.10, NO2=0.20). In Black participants, we also observed a monotonic exposure-response relationship between NO2 and DunedinPACE (Q4 versus Q1, NO2: β=0.029, 95% CI: 0.004-0.055; p-for-trend=0.03), which was not observed in NHW participants (p-for-heterogeneity=0.09). In the EWAS, pollutants were significantly associated with differential methylation at 19 CpG sites in Black women and one in NHW women.

CONCLUSIONS

In a US-wide cohort study, our findings suggest that air pollution is associated with DNA methylation alterations consistent with higher epigenetic aging among Black, but not NHW, women.

Abstract 5757: Breast cancer diagnosis and treatment associated with acceleration of biological aging over time in a racially diverse cohort of women

Leukocyte DNA methylation (DNAm) at individual sites across the genome can be used to construct measures of biological age. Positive age acceleration—when biological age is older than chronological age—is associated with higher risk of age-associated diseases. Recent adjuvant therapy is reported to increase age acceleration, but the longer-term effects of a breast cancer diagnosis and treatment on age acceleration remain unknown. Here, we use blood samples collected at two timepoints to examine changes in age acceleration over time comparing women who did and did not develop breast cancer. Paired whole blood samples were drawn an average of 8 years apart (range: 5-11 years) in a sample of non-Hispanic White and Black (Hispanic and non-Hispanic) women. DNAm was profiled using Infinium MethylationEPIC BeadChips. Approximately half the women were diagnosed and treated for breast cancer between blood draws (cases; n= 190, baseline mean age= 57) whereas the other half remained breast cancer-free (controls; n= 227, baseline mean age= 56). Longitudinal changes in three age acceleration metrics were compared to determine whether an intervening breast cancer diagnosis and treatment was associated with trajectories in biological aging. On average, the cases were diagnosed with breast cancer 3.5 years after the initial blood draw and 4 years before the second blood draw. Among the cases, 36% were treated with chemotherapy, 65% with radiation therapy, and 70% with hormonal therapies; 45% of the cases received two types of therapy, and 13% received all three. Compared to women who remained cancer-free, women diagnosed and treated for breast cancer had increases in age acceleration over time as measured by PhenoAgeAccel (adjusted standardized mean difference (β)= 0.13, 95% CI: 0.00, 0.26), GrimAgeAccel (β= 0.13, 95% CI: 0.03, 0.24), and DunedinPACE (β= 0.35, 95% CI: 0.23, 0.48). The associations did not vary by timing of diagnosis between the blood draws or race; however, women diagnosed with estrogen receptor (ER) negative tumors appeared to experience faster increases in age acceleration than women diagnosed with ER positive tumors (GrimAgeAccel; ER negative β= 0.27, 95% CI: 0.07, 0.47; ER positive β= 0.10, 95% CI: -0.01, 0.21; P-interaction= 0.14). To investigate the impact of different types of breast cancer therapies, associations were examined using a case-only design. In models that simultaneously included chemotherapy, radiation therapy and hormone therapy, radiation therapy had the strongest associations with accelerated biological aging as measured by PhenoAgeAccel (β= 0.38, 95% CI: 0.18, 0.58), GrimAgeAccel (β= 0.27, 95% CI: 0.09, 0.45), and DunedinPACE (β= 0.25, 95% CI: 0.03, 0.47). We find that years after the initial diagnosis, breast cancer survivors have significantly accelerated biological aging; treatment modalities may differentially influence these rates.

Citation Format: Jacob K. Kresovich, Katie M. O'Brien, Zongli Xu, Clarice R. Weinberg, Dale P. Sandler, Jack A. Taylor. Breast cancer diagnosis and treatment associated with acceleration of biological aging over time in a racially diverse cohort of women. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5757.

Methylation-Based Biological Age and Hypertension Prevalence and Incidence

BACKGROUND

Hypertension is common in older individuals and is a major risk factor for cardiovascular disease. Blood DNA methylation profiles have been used to derive metrics of biological age that capture age-related physiological change, disease risk, and mortality. The relationships between hypertension and DNA methylation-based biological age metrics have yet to be carefully described.

METHODS

Among 4419 women enrolled in the prospective Sister Study cohort, DNA methylation data generated from whole blood samples collected at baseline were used to calculate 3 biological age metrics (PhenoAgeAccel, GrimAgeAccel, DunedinPACE). Women were classified as hypertensive at baseline if they had high blood pressure (systolic blood pressure ≥140 mm Hg or diastolic blood pressure ≥90 mm Hg) or reported current use of antihypertensive medication. New incident cases of hypertension during follow-up were identified via self-report on annual health questionnaires.

RESULTS

All 3 DNA methylation metrics of biological age were positively associated with prevalent hypertension at baseline (per 1-SD increase; PhenoAgeAccel, adjusted odds ratio, 1.16 [95% CI, 1.05-1.28]; GrimAgeAccel, adjusted odds ratio, 1.28 [95% CI, 1.14-1.45]; DunedinPACE, adjusted odds ratio, 1.16 [95% CI, 1.03-1.30]). Among 2610 women who were normotensive at baseline, women with higher biological age were more likely to be diagnosed with incident hypertension (per 1-SD increase; PhenoAgeAccel, adjusted hazard ratio, 1.09 [95% CI, 0.97-1.23]; GrimAgeAccel, adjusted hazard ratio, 1.16 [95% CI, 0.99-1.36]; DunedinPACE, adjusted hazard ratio, 1.16 [95% CI, 1.01-1.33]).

CONCLUSIONS

Methylation-based biological age metrics increase before a hypertension diagnosis and appear to remain elevated in the years after clinical diagnosis and treatment.

Peripheral Immune Cell Composition is Altered in Women Before and After a Hypertension Diagnosis

BACKGROUND

The development and consequences of hypertension involve multiple biological systems that may include changes in immune profiles. Whether hypertension is related to peripheral immune cell composition has not been examined in large human cohorts.

METHODS

We estimated circulating proportions of 12 leukocyte subsets from the lymphoid and myeloid lineages by deconvolving cell-type-specific DNA methylation data from 4124 women. Hypertension status at baseline was defined by current use of antihypertensive medication and blood pressure measurements while new incident cases were identified during follow-up via annual health questionnaires.

RESULTS

Among hypertension-free women at baseline, higher B cell and lower naïve CD4+ helper T cell proportions were associated with subsequent increased hazard of hypertension incidence (B cells; adjusted HR: 1.17 [95% CI: 1.02-1.35]; P=0.03; naïve CD4+ T cell, adjusted HR: 0.88 [95% CI: 0.78-0.99]; P=0.04). Blood pressure measurements at baseline were similarly positively associated with B cells and inversely associated with naïve CD4+ helper T cells. Compared to normotensive women, women with hypertension had higher circulating proportions of neutrophils (adjusted odds ratio: 1.18 [95% CI: 1.07-1.31]; P=0.001) and lower proportions of CD4+ helper T cells (adjusted odds ratio: 0.90 [95% CI: 0.81-1.00] P=0.05), natural killers (adjusted odds ratio: 0.82 [95% CI: 0.74-0.91]; P<0.001), and B cells (adjusted odds ratio: 0.84 [95% CI: 0.74-0.96]; P=0.01).

CONCLUSIONS

These observations suggest that shifts in lymphocyte subsets occur before hypertension development, followed by later changes to neutrophils and additional lymphocytes.

Healthy eating patterns and epigenetic measures of biological age

BACKGROUND

Healthy eating is associated with lower risks of disease and mortality, but the mechanisms underlying these associations are unclear. Age is strongly related to health outcomes, and biological age can be estimated using the blood methylome.

OBJECTIVES

To determine whether healthy eating patterns are associated with methylation-based measures of biological age.

METHODS

Among women in the Sister Study, we calculated scores on 4 recommendation-based healthy eating indexes [Dietary Approaches to Stop Hypertension diet, Healthy Eating Index-2015, Alternative Healthy Eating Index (aHEI-2010), and the Alternative Mediterranean diet] using a validated 110-item Block FFQ completed at enrollment. Genome-wide DNA methylation data were generated using the HumanMethylation450 BeadChip on whole blood samples collected at enrollment from a case-cohort sample of 2694 women and were used to calculate 4 measures of epigenetic age acceleration (Hannum AgeAccel, Horvath AgeAccel, PhenoAgeAccel, and GrimAgeAccel). Linear regression models, adjusted for covariates and cohort sampling weights, were used to examine cross-sectional associations between eating patterns and measures of biological age.

RESULTS

All 4 healthy eating indexes had inverse associations with epigenetic age acceleration, most notably with PhenoAgeAccel and GrimAgeAccel. Of these, the strongest associations were for aHEI-2010 [per 1-SD increase in diet quality, PhenoAgeAccel β = -0.5 y (95% CI: -0.8 to -0.2 y) and GrimAgeAccel β = -0.4 y (95% CI: -0.6 to -0.3 y)]. Although effect modification was not observed for most lifestyle factors, in analyses stratified by physical activity, the benefits of a healthy diet on epigenetic age acceleration were more pronounced among women who did not meet physical activity guidelines (reporting <2.5 h/wk of exercise).

CONCLUSIONS

Higher diet quality is inversely associated with methylation-based measures of biological age. Improving diet could have the most benefits in lowering biological age among women with lower levels of physical activity. This trial was registered at clinicaltrials.gov as NCT00047970.

Low serum klotho associated with all-cause mortality among a nationally representative sample of American adults

α-Klotho (klotho) is a protein involved in suppressing oxidative stress and inflammation. In animal models, it is reported to underlie numerous aging phenotypes and longevity. Among a nationally representative sample of adults aged 40 to 79 in the United States, we investigated whether circulating concentrations of klotho is a marker of mortality risk. Serum klotho was measured by ELISA on 10,069 individuals enrolled in the National Health and Nutrition Examination Survey between 2007-2014. Mortality follow-up data based on the National Death Index were available through December 31, 2015. After a mean follow-up of 58 months (range: 1-108), 616 incident deaths occurred. Using survey-weighted Cox regression models adjusted for age, sex and survey cycle, low serum klotho concentration (< 666 pg/mL) was associated with a 31% higher risk of death (compared to klotho concentration > 985 pg/mL, HR: 1.31, 95% CI: 1.00, 1.71, P= 0.05). Associations were consistent for mortality caused by heart disease or cancer. Associations of klotho with all-cause mortality did not appear to differ by most participant characteristics. However, we observed effect modification by physical activity, such that low levels of serum klotho were more strongly associated with mortality among individuals who did not meet recommendation-based physical activity guidelines. Our findings suggest that, among the general population of American adults, circulating levels of klotho may serve as a marker of mortality risk.

Blood DNA methylation profiles improve breast cancer prediction

Although blood DNA methylation (DNAm) profiles are reported to be associated with breast cancer incidence, they have not been widely used in breast cancer risk assessment. Among a breast cancer case–cohort of 2774 women (1551 cases) in the Sister Study, we used candidate CpGs and DNAm estimators of physiologic characteristics to derive a methylation‐based breast cancer risk score, mBCRS. Overall, 19 CpGs and five DNAm estimators were selected using elastic net regularization to comprise mBCRS. In a test set, higher mBCRS was positively associated with breast cancer incidence, showing similar strength to the polygenic risk score (PRS) based on 313 single nucleotide polymorphisms (313 SNPs). Area under the curve for breast cancer prediction was 0.60 for self‐reported risk factors (RFs), 0.63 for PRS, and 0.63 for mBCRS. Adding mBCRS to PRS and RFs improved breast cancer prediction from 0.66 to 0.71. mBCRS findings were replicated in a nested case–control study within the EPIC‐Italy cohort. These results suggest that mBCRS, a risk score derived using blood DNAm, can be used to enhance breast cancer prediction.

Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging

BACKGROUND

Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field.

RESULTS

Leveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels.

CONCLUSION

This study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.

Associations of Body Composition and Physical Activity Level With Multiple Measures of Epigenetic Age Acceleration

Epigenetic clocks use DNA methylation to estimate biological age. Whether body composition and physical activity are associated with these clocks is not well understood. Using blood samples collected at enrollment (2003-2009) from 2,758 women in the US nationwide Sister Study, we calculated 6 epigenetic age acceleration metrics using 4 epigenetic clocks (Hannum, Horvath, PhenoAge, GrimAge). Recreational physical activity was self-reported, and adiposity measures were assessed by trained medical examiners (body mass index (BMI), waist-to-hip ratio (WtH), waist circumference). In cross-sectional analyses, all adiposity measures were associated with epigenetic age acceleration. The strongest association was for BMI and PhenoAge, a measure of biological age that correlates with chronic disease (BMI of ≥35.0 vs. 18.5-24.9, β = 3.15 years, 95% confidence interval (CI): 2.41, 3.90; P for trend < 0.001). In a mutual-adjustment model, both were associated with PhenoAge age acceleration (BMI of ≥35.0 vs. 18.5-24.9, β = 2.69 years, 95% CI: 1.90, 3.48; P for trend < 0.001; quartile 4 vs.1 WtH, β = 1.00 years, 95% CI: 0.34, 1.65; P for trend < 0.008). After adjustment, physical activity was associated only with GrimAge (quartile 4 vs. 1, β = -0.42 years, 95% CI: -0.70, -0.14; P for trend = 0.001). Physical activity attenuated the waist circumference associations with PhenoAge and GrimAge. Excess adiposity was associated with epigenetic age acceleration; physical activity might attenuate associations with waist circumference.

Alcohol consumption and methylation-based measures of biological age

Epigenetic age acceleration is considered a measure of biological aging based on genome-wide patterns of DNA methylation. Although age acceleration has been associated with incidence of diseases and death, less is known about how it is related to lifestyle behaviors. Among 2,316 women, we evaluate associations between self-reported alcohol consumption and various metrics of epigenetic age acceleration. Recent average alcohol consumption was defined as the mean number of drinks consumed per week within the past year; lifetime average consumption was estimated as the mean number of drinks per year drinking. Whole blood genome-wide DNA methylation was measured with HumanMethylation450 BeadChips and used to assess four epigenetic clocks (Hannum, Horvath, PhenoAge, GrimAge) and their corresponding metrics of epigenetic age acceleration (Hannum AgeAccel, Horvath AgeAccel, PhenoAgeAccel, GrimAgeAccel). Although alcohol consumption showed little association with most age acceleration metrics, both lifetime and recent average consumption measures were positively associated with GrimAgeAccel (lifetime, per additional 135 drinks/year: β=0.30 years, 95% CI: 0.11, 0.48, p=0.002; recent, per additional 5 drinks/week: β=0.19 years, 95% CI: 0.01, 0.37, p=0.04). In a mutually adjusted model, only average lifetime alcohol consumption remained associated with GrimAgeAccel (lifetime, per additional 135 drinks/year: β=0.27 years, 95% CI: 0.04, 0.50, p=0.02; recent, per 5 additional drinks/week: β=0.05 years, 95% CI: -0.16, 0.26, p=0.64). Although alcohol use does not appear to be strongly associated with biological age measured by most epigenetic clocks, lifetime average consumption is associated with higher biological age assessed by the GrimAge epigenetic clock.

Association of Neighborhood Deprivation With Epigenetic Aging Using 4 Clock Metrics

IMPORTANCE

Neighborhood deprivation is associated with age-related disease, mortality, and reduced life expectancy. However, biological pathways underlying these associations are not well understood.

OBJECTIVE

To evaluate the association between neighborhood deprivation and epigenetic measures of age acceleration and genome-wide methylation.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study used data from the Sister Study, a prospective cohort study comprising 50 884 women living in the US and Puerto Rico aged 35 to 74 years at enrollment who had a sister with breast cancer but had not had breast cancer themselves. Cohort enrollment occurred between July 2003 and March 2009. Participants completed a computer-assisted telephone interview on demographic, socioeconomic, lifestyle, and residential factors and provided anthropometric measures and peripheral blood samples at a home examination. DNA methylation data obtained for 2630 non-Hispanic White women selected for a case-cohort study in 2014 were used in this cross-sectional analysis. DNA methylation was measured using the HumanMethylation450 BeadChips in whole blood samples collected at baseline. Data analysis for this study was performed from October 17, 2019, to August 27, 2020.

EXPOSURES

Each participants' primary address was linked to an established index of neighborhood deprivation.

MAIN OUTCOMES AND MEASURES

Epigenetic age was estimated using 4 epigenetic clocks (Horvath, Hannum, PhenoAge, and GrimAge). Age acceleration was determined using residuals from regressing chronologic age on each of the 4 epigenetic age metrics. Linear regression was used to estimate associations between neighborhood deprivation and epigenetic age acceleration as well as DNA methylation at individual cytosine-guanine sites across the genome.

RESULTS

Mean (SD) age of the 2630 participants was 56.9 (8.7) years. Those with the greatest (>75th percentile) vs least (≤25th percentile) neighborhood deprivation had higher epigenetic age acceleration estimated by Hannum (β = 0.23; 95% CI, 0.01-0.45), PhenoAge (β = 0.28; 95% CI, 0.06-.50), and GrimAge (β = 0.37; 95% CI, 0.12-0.62). Increasing US quartiles of neighborhood deprivation exhibited a trend with Hannum, PhenoAge, and GrimAge. For example, GrimAge showed a significant dose-response (P test for trend <.001) as follows: level 2 vs level 1 (β = 0.30; 95% CI, 0.17-0.42), level 3 vs level 1 (β = 0.35; 95% CI, 0.19-0.50), and level 4 vs level 1 (β = 0.37; 95% CI, 0.12-0.62). Neighborhood deprivation was found to be associated with 3 cytosine-phosphate-guanine sites, with 1 of these annotated to a known gene MAOB (P = 9.71 × 10-08).

CONCLUSIONS AND RELEVANCE

The findings of this study suggest that residing in a neighborhood with a higher deprivation index appears to be reflected by methylation-based markers of aging.

Reproduction, DNA methylation and biological age

STUDY QUESTION

Are reproductive characteristics associated with genome-wide DNA methylation and epigenetic age?

SUMMARY ANSWER

Our data suggest that increasing parity is associated with differences in blood DNA methylation and small increases in epigenetic age.

WHAT IS KNOWN ALREADY

A study of 397 young Filipino women (ages 20-22) observed increasing epigenetic age with an increasing number of pregnancies.

STUDY DESIGN, SIZE, DURATION

We used data from 2356 non-Hispanic white women (ages 35-74) enrolled in the Sister Study cohort.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Data on reproductive history were ascertained via questionnaire. Of the 2356 women, 1897 (81%) reported at least one live birth. Among parous women, 487 (26%) women reported ever experiencing a pregnancy complication. Three epigenetic clocks (i.e. Hannum, Horvath and Levine) and genome-wide methylation were measured in DNA from whole blood using Illumina's HumanMethylation450 BeadChip. We estimated association β-values and 95% CIs using linear regression.

MAIN RESULTS AND THE ROLE OF CHANCE

All three epigenetic clocks showed weak associations between number of births and epigenetic age (per live birth; Hannum: β = 0.16, 95% CI = 0.02, 0.29, P = 0.03; Horvath: β = 0.12, 95% CI = -0.04, 0.27, P = 0.14; Levine: β = 0.27, 95% CI = 0.08, 0.45, P = 0.01); however, additional adjustment for current BMI attenuated the associations. Among parous women, a history of abnormal glucose tolerance during pregnancy was associated with increased epigenetic age by the Hannum clock (β = 0.96; 95% CI = 0.10, 1.81; P = 0.03) and Levine clocks (β = 1.69; 95% CI = 0.54, 2.84; P < 0.01). In epigenome-wide analysis, increasing parity was associated with methylation differences at 17 CpG sites (Bonferroni corrected P≤ 1.0 × 10-7).

LIMITATIONS, REASONS FOR CAUTION

We relied on retrospective recall to ascertain reproductive history and pregnancy complications.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings suggest that parity is associated with small increases in epigenetic age and with DNA methylation at multiple sites in the genome.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by the Intramural Research program of the NIH, National Institute of Environmental Health Sciences (Z01-ES049033, Z01-ES049032 and Z01-ES044055). None of the authors have a conflict of interest.

TRIAL REGISTRATION NUMBER

Not applicable.

Methylation-Based Biological Age and Breast Cancer Risk

BACKGROUND

Age is one of the strongest predictors of cancer, chronic disease, and mortality, but biological responses to aging differ among people. Epigenetic DNA modifications have been used to estimate "biological age," which may be a useful predictor of disease risk. We tested this hypothesis for breast cancer.

METHODS

Using a case-cohort approach, we measured baseline blood DNA methylation of 2764 women enrolled in the Sister Study, 1566 of whom subsequently developed breast cancer after an average of 6 years. Using three previously established methylation-based "clocks" (Hannum, Horvath, and Levine), we defined biological age acceleration for each woman by comparing her estimated biological age with her chronological age. Hazard ratios and 95% confidence intervals for breast cancer risk were estimated using Cox regression models. All statistical tests were two-sided.

RESULTS

Each of the three clocks showed that biological age acceleration was statistically significantly associated with increased risk of developing breast cancer (5-year age acceleration, Hannum's clock: hazard ratio [HR] = 1.10, 95% confidence interval [CI] = 1.00 to 1.21, P = .04; Horvath's clock: HR = 1.08, 95% CI = 1.00 to 1.17, P = .04; Levine's clock: HR = 1.15, 95% CI = 1.07 to 1.23, P < .001). For Levine's clock, each 5-year acceleration in biological age corresponded with a 15% increase in breast cancer risk. Although biological age may accelerate with menopausal transition, age acceleration in premenopausal women independently predicted breast cancer. Case-only analysis suggested that, among women who develop breast cancer, increased age acceleration is associated with invasive cancer (odds ratio for invasive = 1.09, 95% CI = 0.98 to 1.22, P = .10).

CONCLUSIONS

DNA methylation-based measures of biological age may be important predictors of breast cancer risk.

Shift work, DNA methylation and epigenetic age

BACKGROUND

Shift work has been associated with increased risk of age-related morbidity and mortality. Biological age, estimated using DNA methylation (DNAm), may quantify the biological consequences of shift work on the risk of age-related disease. We examined whether prior employment in shift-working occupations was associated with epigenetic age acceleration.

METHODS

In a sample of non-Hispanic White women aged 35-74 (n = 2574), we measured DNAm using the Illumina Infinium Human450 BeadChip and calculated DNAm age using three established epigenetic clocks. Age-acceleration metrics were derived by regressing DNAm age on chronological age and predicting the residuals. Using linear regression, we estimated associations between shift work history and age acceleration. We also conducted an epigenome-wide association study using robust linear-regression models corrected with false discovery rate (FDR) q-values.

RESULTS

Approximately 7% of women reported any shift work. Higher age acceleration was observed for a 1-year increase in overall [β = 0.11, 95% confidence interval (CI): 0.02-0.21] and night-specific shift work (β = 0.12, 95% CI: 0.03-0.21). The association was strongest for ≥10 years of night shift work (β = 3.16, 95% CI: 1.17-5.15). From the epigenome-wide association study, years of overall and night shift work were associated with DNAm at 66 and 85 CpG sites (FDR < 0.05), respectively. Years of night shift work was associated with lower methylation of a CpG in the gene body of ZFHX3 (cg04994202, q = 0.04), a gene related to circadian rhythm.

CONCLUSIONS

Shift work was associated with differential CpG site methylation and with differential DNAm patterns, measured by epigenetic age acceleration, consistent with long-term negative health effects.

Prediagnostic Immune Cell Profiles and Breast Cancer

IMPORTANCE

Higher overall leukocyte counts in women may be associated with increased risk of breast cancer, but the association of specific leukocyte subtypes with breast cancer risk remains unknown.

OBJECTIVE

To determine associations between circulating leukocyte subtypes and risk of breast cancer.

DESIGN, SETTING, AND PARTICIPANTS

Between 2003 and 2009, the Sister Study enrolled 50 884 women who had a sister previously diagnosed with breast cancer but were themselves breast cancer free. A case-cohort subsample was selected in July 2014 from the full Sister Study cohort. Blood samples were obtained at baseline, and women were followed up through October 2016. Data analysis was performed in April 2019.

MAIN OUTCOMES AND MEASURES

The main outcome was the development of breast cancer in women. Whole-blood DNA methylation was measured, and methylation values were deconvoluted using the Houseman method to estimate proportions of 6 leukocyte subtypes (B cells, natural killer cells, CD8+ and CD4+ T cells, monocytes, and granulocytes). Leukocyte subtype proportions were dichotomized at their population median value, and Cox proportional hazard models were used to estimate associations with breast cancer.

RESULTS

Among 2774 non-Hispanic white women included in the analysis (mean [SD] age at enrollment, 56.6 [8.8] years), 1295 women were randomly selected from the full cohort (of whom 91 developed breast cancer) along with an additional 1479 women who developed breast cancer during follow-up (mean [SD] time to diagnosis, 3.9 [2.2] years). Circulating proportions of B cells were positively associated with later breast cancer (hazard ratio [HR], 1.17; 95% CI, 1.01-1.36; P = .04). Among women who were premenopausal at blood collection, the association between B cells and breast cancer was significant (HR, 1.38; 95% CI, 1.05-1.82; P = .02), and an inverse association for circulating proportions of monocytes was found (HR, 0.75; 95% CI, 0.57-0.99; P = .05). Among all women, associations between leukocyte subtypes and breast cancer were time dependent: higher monocyte proportions were associated with decreased near-term risk (within 1 year of blood collection, HR, 0.62; 95% CI, 0.43-0.89; P = .01), whereas higher B cell proportions were associated with increased risk 4 or more years after blood collection (HR, 1.38; 95% CI, 1.15-1.67; P = .001).

CONCLUSIONS AND RELEVANCE

Circulating leukocyte profiles may be altered before clinical diagnoses of breast cancer and may be time-dependent markers for breast cancer risk, particularly among premenopausal women.

Epigenetic mortality predictors and incidence of breast cancer

Measures derived using blood DNA methylation are increasingly under investigation as indicators of disease and mortality risk. Three existing epigenetic age measures or “epigenetic clocks” appear associated with breast cancer. Two newly-developed epigenetic mortality predictors may be related to all-cancer incidence, but associations with specific cancers have not been examined in large studies. Using HumanMethylation450 BeadChips to measure blood DNA methylation in 2,773 cancer-free women enrolled in the Sister Study, we calculated two epigenetic mortality predictors: ‘GrimAgeAccel’ and the ‘mortality score’ (MS). Using Cox proportional hazard models, neither GrimAgeAccel nor the MS were associated with overall breast cancer incidence (GrimAgeAccel hazard ratio [HR]: 1.06, 95% confidence interval [CI]: 0.98-1.14, P=0.17; MS HR: 0.99, 95% CI: 0.92-1.07, P=0.85); however, a weak, positive association was observed for GrimAgeAccel and invasive breast cancer (HR: 1.08, 95% CI: 0.99-1.17, P=0.08). Stratification of invasive cancers by menopause status at diagnoses revealed the association was predominantly observed for postmenopausal breast cancer (HR: 1.10, 95% CI: 1.01, 1.20, P=0.04). Although the MS was unrelated to breast cancer risk, we find evidence that GrimAgeAccel may be weakly associated with invasive breast cancer, particularly for women diagnosed after menopause.

Reproductive history and blood cell telomere length

Telomeres are repetitive nucleotide sequences that protect against chromosomal shortening. They are replenished by telomerase, an enzyme that may be activated by estrogen. Women have longer telomeres than men; this difference might be due to estrogen exposure. We hypothesized that reproductive histories reflecting greater estrogen exposure will be associated with longer blood cell telomeres. Among women in the Sister Study (n= 1,048), we examined telomere length in relation to self-reported data on reproductive history. The difference between age at menarche and last menstrual period was used to approximate the reproductive period. Relative telomere length (rTL) was measured using qPCR. After adjustment, rTL decreased with longer reproductive period (β= -0.019, 95% CI: -0.04, -0.00, p= 0.03). Premenopausal women had shorter rTL than postmenopausal women (β= -0.051, 95% CI: -0.12, 0.01, p= 0.13). Longer breastfeeding duration was associated with longer rTL (β= 0.027, 95% CI: 0.01, 0.05, p=0.01); increasing parity was associated with shorter rTL (β = -0.016, 95% CI: -0.03, 0.00, p=0.07). Duration of exogenous hormone use was not associated with rTL. Reproductive histories reflecting greater endogenous estrogen exposure were associated with shorter rTL. Our findings suggest that longer telomeres in women are unlikely to be explained by greater estrogen exposure.

Air pollution, particulate matter composition and methylation-based biologic age

BACKGROUND

Epigenetic age, as defined by DNA methylation, may be influenced by air pollution exposure.

OBJECTIVE

To evaluate the relationship between NO₂, particulate matter (PM), PM components and accelerated epigenetic age.

METHODS

In a sample of non-Hispanic white women living in the contiguous U.S. (n = 2747), we estimated residential exposure to PM_2.5, PM₁₀ and NO₂ using a model incorporating land-use regression and kriging. Predictive k-means was used to assign participants to clusters representing different PM_2.5 component profiles. We measured DNA methylation (DNAm) in blood using the Illumina's Infinium HumanMethylation450 BeadChip and calculated DNAm age using the Hannum, Horvath and Levine epigenetic clocks. Age acceleration was defined based on residuals after regressing DNAm age on chronological age. We estimated associations between interquartile range (IQR) increases in pollutants and age acceleration using linear regression. For PM_2.5, we stratified by cluster membership. We examined epigenome-wide associations using robust linear regression models corrected with false discovery rate q-values.

RESULTS

NO₂ was inversely associated with age acceleration using the Hannum clock (β = -0.24, 95% CI: -0.47, -0.02). No associations were observed for PM₁₀. For PM_2.5, the association with age acceleration varied by PM_2.5 component cluster. For example, with the Levine clock, an IQR increase in PM_2.5 was associated with an over 6-year age acceleration in a cluster that has relatively high fractions of crustal elements relative to overall PM_2.5 (β = 6.57, 95% CI: 2.68, 10.47), and an almost 2-year acceleration in a cluster characterized by relatively low sulfur fractions (β = 1.88, 95% CI: 0.51, 3.25). In a cluster distinguished by lower relative nitrate concentrations, PM_2.5 was inversely associated with age acceleration (β = -1.33, 95% CI: -2.43, -0.23). Across the epigenome, NO₂ was associated with methylation at 2 CpG sites.

CONCLUSION

Air pollution was associated with epigenetic age, a marker of mortality and disease risk, among certain PM_2.5 component profiles.

Metallic air pollutants and breast cancer heterogeneity

BACKGROUND

Emerging evidence suggests airborne metals may be associated with breast cancer risk. However, breast cancer is heterogenous and associations with heavy metals vary by subtype. Heavy metals possess both carcinogenic and xenoestrogenic properties which may be related to different tumor etiologies. Therefore, we tested for etiologic heterogeneity, using a case-series approach, to determine whether associations between residential airborne metal concentrations and breast cancer differed by tumor subtype.

METHODS

Between 2005 and 2008, we enrolled incident breast cancer cases into the Breast Cancer Care in Chicago study. Tumor estrogen and progesterone receptors status was determined by medical record abstraction and confirmed immunohistochemically (N = 696; 147 ER/PR-negative). The 2002 USEPA's National Air Toxics Assessment census-tract estimates of metal concentrations (antimony, arsenic, beryllium, cadmium, chromium, cobalt, lead, manganese, mercury, nickel and selenium) were matched to participants' residences of the same year. Adjusted logistic regression models were used to examine whether the airborne heavy metal associations differed by tumor ER/PR status. Principal component analysis was performed to assess associations by metal co-exposures.

RESULTS

Comparing the highest and lowest quintiles, higher concentrations of antimony (odds ratio[OR]: 1.8, 95% confidence interval[CI]: 0.9, 3.7, P-trend: 0.05), cadmium (OR: 2.3, 95% CI: 1.2, 4.4, P-trend: 0.04) and cobalt (OR: 2.0, 95% CI: 0.9, 4.4, P-trend: 0.04) were associated with ER/PR-negative breast cancer. Mixture analysis using principal components suggested co-exposures to multiple airborne heavy metals may drive associations with tumor receptor status.

CONCLUSIONS

Among women diagnosed with breast cancer, metallic air pollutants were associated with increased odds of developing ER/PR-negative breast cancer.

Promoter methylation of PGC1A and PGC1B predicts cancer incidence in a veteran cohort

AIM

Previous studies suggest telomere shortening represses PGC1A and PGC1B expression leading to mitochondrial dysfunction. Methylation of CpG sites within these genes may interact with these factors to affect cancer risk.

MATERIALS & METHODS

Among 385 men, we identified 84 incidents of cancers (predominantly prostate and nonmelanoma skin). We examined associations between leukocyte DNA methylation of 41 CpGs from PGC1A and PGC1B with telomere length, mitochondrial 8-OHdG lesions, mitochondrial abundance and cancer incidence.

RESULTS

Methylation of five and eight CpG sites were significantly associated with telomere length and mitochondrial abundance at p < 0.05. Two CpG sites were independently associated with cancer risk: cg27514608 (PGC1A, TSS1500; HR: 1.55, 95% CI: 1.19-2.03, FDR = 0.02), and cg15219393 (PGC1B, first exon/5'UTR; HR: 3.71, 95% CI: 1.82-7.58, FDR < 0.01). Associations with cg15219393 were observed primarily among men with shorter leukocyte telomeres.

CONCLUSION

PGC1A and PGC1B methylation may serve as early biomarkers of cancer risk.

The Inflammatory Potential of Dietary Manganese in a Cohort of Elderly Men

Manganese is an essential nutrient that may play a role in the production of inflammatory biomarkers. We examined associations between estimated dietary manganese intake from food/beverages and supplements with circulating biomarkers of inflammation. We further explored whether estimated dietary manganese intake affects DNA methylation of selected genes involved in the production of these biomarkers. We analyzed 1023 repeated measures of estimated dietary manganese intakes and circulating blood inflammatory biomarkers from 633 participants in the Normative Aging Study. Using mixed-effect linear regression models adjusted for covariates, we observed positive linear trends between estimated dietary manganese intakes and three circulating interleukin proteins. Relative to the lowest quartile of estimated intake, concentrations of IL-1β were 46% greater (95% CI - 5, 126), IL-6 52% greater (95% CI - 9, 156). and IL-8 32% greater (95% CI 2, 71) in the highest quartiles of estimated intake. Estimated dietary manganese intake was additionally associated with changes in DNA methylation of inflammatory biomarker-producing genes. Higher estimated intake was associated with higher methylation of NF-κβ member activator NKAP (Q4 vs Q1: β = 3.32, 95% CI - 0.6, 7.3). When stratified by regulatory function, higher manganese intake was associated with higher gene body methylation of NF-κβ member activators NKAP (Q4 vs Q1: β = 10.10, 95% CI - 0.8, 21) and NKAPP1 (Q4 vs Q1: β = 8.14, 95% CI 1.1, 15). While needed at trace amounts for various physiologic functions, our results suggest estimated dietary intakes of manganese at levels slightly above nutritional adequacy contribute to inflammatory biomarker production.

Candidate gene DNA methylation associations with breast cancer characteristics and tumor progression

AIM

We examined methylation patterns with aggressive tumor phenotypes and investigated demographic, socioeconomic and reproductive predictors of gene methylation.

MATERIALS & METHODS

Pyrosequencing quantified methylation of BRCA1, EGFR, GSTM2, RASSF1, TFF1 and Sat 2. We used quantile regression models to calculate adjusted median methylation values by estrogen and progesterone receptor (ER/PR) status. Bivariate associations between participant characteristics and methylation were examined.

RESULTS

Higher percent methylation of GSTM2 was observed in ER/PR-negative compared with ER/PR-positive tumors in ductal carcinoma in situ (14 vs 2%) and invasive (35 vs 3%) tissue components. Trends in aberrant GSTM2 methylation across tissue components were stronger among ER/PR-negative tumors (p-interaction <0.001). Black women were more likely to have ER/PR-negative tumors (p = 0.01) and show hypermethylation of GSTM2 compared with other women (p = 0.05).

CONCLUSION

GSTM2 promoter hypermethylation may serve as a potential biomarker of aggressive tumor development and a mechanism for ER/PR-negative tumor progression.

Retinal Oximetry and Vessel Diameter Measurements With a Commercially Available Scanning Laser Ophthalmoscope in Diabetic Retinopathy

Purpose

To test the hypothesis that retinal vascular diameter and hemoglobin oxygen saturation alterations, according to stages of diabetic retinopathy (DR), are discernible with a commercially available scanning laser ophthalmoscope (SLO).

Methods

One hundred eighty-one subjects with no diabetes (No DM), diabetes with no DR (No DR), nonproliferative DR (NPDR), or proliferative DR (PDR, all had photocoagulation) underwent imaging with an SLO with dual lasers (532 nm and 633 nm). Customized image analysis software determined the diameters of retinal arteries and veins (DA and DV) and central retinal artery and vein equivalents (CRAE and CRVE). Oxygen saturations of hemoglobin in arteries and veins (SO2A and SO2V) were estimated from optical densities of vessels on images at the two wavelengths. Statistical models were generated by adjusting for effects of sex, race, age, eye, and fundus pigmentation.

Results

DA, CRAE, and CRVE were reduced in PDR compared to No DM (P ≤ 0.03). DV and CRVE were similar between No DM and No DR, but they were higher in NPDR than No DR (P ≤ 0.01). Effect of stage of disease on SO2A differed by race, being increased relative to No DM in NPDR and PDR in Hispanic participants only (P ≤ 0.02). Relative to No DM, SO2V was increased in NPDR and PDR (P ≤ 0.05).

Conclusions

Alterations in retinal vascular diameters and SO2 by diabetic retinopathy stage can be detected with a widely available SLO, and covariates such as race can influence the results.

Cord blood DNA methylation and adiposity measures in early and mid-childhood

Background

Excess adiposity in childhood is associated with numerous adverse health outcomes. As this condition is difficult to treat once present, identification of risk early in life can help inform and implement strategies to prevent the onset of the condition. We performed an epigenome-wide association study to prospectively investigate the relationship between cord blood DNA methylation and adiposity measurements in childhood.

Methods

We measured genome-wide DNA methylation from 478 children in cord blood and measured overall and central adiposity via skinfold caliper measurements in early (range 3.1–3.3 years) and mid-childhood (age range 7.3–8.3 years) and via dual X-ray absorptiometry (DXA) in mid-childhood. Final models were adjusted for maternal age at enrollment, pre-pregnancy body mass index, education, folate intake during pregnancy, smoking during pregnancy, and gestational weight gain, and child sex, race/ethnicity, current age, and cord blood cell composition.

Results

We identified four promoter proximal CpG sites that were associated with adiposity as measured by subscapular (SS) and triceps (TR) ratio (SS:TR) in early childhood, in the genes KPRP, SCL9A10, MYLK2, and PRLHR. We additionally identified one gene body CpG site associated with early childhood SS + TR on PPAPDC1A; this site was nominally associated with SS + TR in mid-childhood. Higher methylation at one promoter proximal CpG site in MMP25 was also associated with SS:TR in mid-childhood. In regional analyses, methylation at an exonal region of GFPT2 was positively associated with SS:TR in early childhood. Finally, we identified regions of two long, non-coding RNAs which were associated with SS:TR (LOC100049716) and fat-free mass index (LOC102723493) in mid-childhood.

Conclusion

This analysis identified novel CpG loci associated with adiposity outcomes. However, our results suggest little consistency across the various adiposity outcomes tested, particularly among the more accurate DXA measurements of body composition. We recommend using caution when interpreting these associations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-017-0384-9) contains supplementary material, which is available to authorized users.

Histone 3 modifications and blood pressure in the Beijing Truck Driver Air Pollution Study

CONTEXT

Histone modifications regulate gene expression; dysregulation has been linked with cardiovascular diseases. Associations between histone modification levels and blood pressure in humans are unclear.

OBJECTIVE

We examine the relationship between global histone concentrations and various markers of blood pressure.

MATERIALS AND METHODS

Using the Beijing Truck Driver Air Pollution Study, we investigated global peripheral white blood cell histone modifications (H3K9ac, H3K9me3, H3K27me3, and H3K36me3) associations with pre- and post-work measurements of systolic (SBP) and diastolic (DBP) blood pressure, mean arterial pressure (MAP), and pulse pressure (PP) using multivariable mixed-effect models.

RESULTS

H3K9ac was negatively associated with pre-work SBP and MAP; H3K9me3 was negatively associated with pre-work SBP, DBP, and MAP; and H3K27me3 was negatively associated with pre-work SBP. Among office workers, H3K9me3 was negatively associated with pre-work SBP, DBP, and MAP. Among truck drivers, H3K9ac and H3K27me were negatively associated with pre-work SBP, and H3K27me3 was positively associated with post-work PP.

DISCUSSION AND CONCLUSION

Epigenome-wide H3K9ac, H3K9me3, and H3K27me3 were negatively associated with multiple pre-work blood pressure measures. These associations substantially changed during the day, suggesting an influence of daily activities. Blood-based histone modification biomarkers are potential candidates for studies requiring estimations of morning/pre-work blood pressure.

Abstract 4251: DNA methylation of mitochondrial biogenesis regulating genes: A possible link between telomeres, mitochondria, and cancer incidence

Background: PGC1A and PGC1B encode transcriptional factors that regulate mitochondrial biogenesis and have been implicated as a link between telomeric and mitochondrial functions. Telomere dysfunction is associated with impaired mitochondrial biogenesis and increased generation of reactive oxygen species. Animal studies have also shown that loss of PGC1A protects against cancer as mitochondrial function is required for transformation and tumor growth. No human studies have examined the role of these genes in relation to cancer incidence. Our objective was to examine associations between PGC1A and PGC1B methylation in relation to cancer incidence.

Methods: We studied 491 Normative Aging Study participants who had blood drawn 1-4 times from 1999 through 2012. After median 10.2-year follow-up, there were 125 incident cancers including 36 prostate. PGC1A and PGC1B methylation was measured at 30 and 27 sites, respectively, using the HumanMethylation450k assay. We used Cox proportional hazards models to examine associations between CpG methylation and cancer incidence measured at first blood draw as well as in time-dependent associations. All models adjusted for age, race, smoking status and pack-years, alcohol consumption, blood cell composition, and processing batch.

Results: In single-site adjusted time-dependent models, we identified 13 instances of 11 individual loci (10 from PGC1A and 1 from PGC1B) significantly associated with all-cancer and prostate cancer incidence. In multi-site adjusted models, we showed cg0677257 from the 3’ UTR of PGC1A was inversely associated with first-visit (HR: 0.41; 95% CI: 0.21, 0.79) and time-dependent all-cancer incidence (HR: 0.42; 95% CI: 0.22, 0.81). Similarly, we showed cg0942771 and cg03281309 from the gene body of PGC1A were inversely associated with time-dependent all-cancer incidence (HR: 0.51; 95% CI: 0.30, 0.88; HR: 0.74; 95% CI: 0.56, 0.98, respectively). Finally, we found that cg1521939 from the 5’ UTR region of PGC1B was positively associated with time-dependent all-cancer incidence (HR: 3.27; 95% CI: 1.55, 6.90).

Conclusion: This is the first study in humans to show site-specific PGC1A and PGC1B methylation is a significant predictor of cancer incidence. These findings point to a possible interplay between telomere and mitochondrial dysfunction, and epigenetics in carcinogenesis. Additional studies should also examine these associations in larger cohorts with greater racial/ethnic, gender, and socioeconomic diversity to validate these findings.

Citation Format: Jacob K. Kresovich, Tao Gao, Brian T. Joyce, Pantel Vokonas, Joel Schwartz, Andrea A. Baccarelli, Lifang Hou. DNA methylation of mitochondrial biogenesis regulating genes: A possible link between telomeres, mitochondria, and cancer incidence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4251. doi:10.1158/1538-7445.AM2017-4251

Abstract 2305: Residential airborne heavy metal concentrations and breast cancer characteristics

Background: Ambient air metal concentrations have recently been implicated in the etiology of breast cancer. Previous studies have shown airborne concentrations of arsenic and cadmium are associated with the development of estrogen receptor-negative tumors. This study aims to replicate these findings and examine the role of other toxic and essential heavy metals.

Methods: Participants were women who were diagnosed with breast cancer in Chicago between 2005 and 2008. We examined estrogen and progesterone receptor-negative (ER-/PR-) and high-grade tumors as markers of aggressive breast cancer, and estimated 15-year markers of exposure of 11 heavy metals. Exposures were calculated using census tract-level airborne concentrations from the National-scale Air Toxics Assessment and participants’ residential histories. We adjusted all models for socioeconomic status and reproductive factors.

Results: We found that prevalent ER-/PR- tumors were associated with increased residential exposure to airborne concentrations of antimony (Q4 vs Q1: OR= 1.81; 95% CI: 0.95, 3.44; Ptrend= 0.04), cobalt (Q4 vs Q1: OR= 2.37; 95% CI: 1.26, 4.45; Ptrend &lt; 0.01), manganese (Q4 vs Q1: OR= 2.55; 95% CI: 1.24, 5.24; Ptrend= 0.04), and selenium (Q4 vs Q1: OR= 1.85; 95% CI: 1.03, 3.29; Ptrend= 0.05), and also identified marginally significant trends for arsenic (Ptrend= 0.06), chromium (Ptrend= 0.08), lead (Ptrend= 0.08), and mercury (Ptrend= 0.07). We did not identify any overall associations with high-grade tumors, however when stratifying by menopausal status we found that antimony (Q4 vs Q1: OR= 6.97, 95% CI: 1.61-30.19) and arsenic (Q4 vs Q1: OR= 6.97, 95% CI: 1.61-30.19) were associated with prevalent high-grade tumors in premenopausal women only.

Discussion: This study found further support for a role of airborne arsenic concentrations, and novel evidence implicating other airborne estrogen-pathway disrupting metal concentrations, in the development of aggressive breast cancer subtypes. Additionally, this is the first study to implicate heavy metal exposure in the etiology of high-grade tumors. These results suggest that long-term, low-dose exposures to certain heavy metals play a role in the etiology of aggressive breast cancer characteristics. Airborne exposures have the ability to affect large populations and findings from this and similar studies have large public health implications.

Citation Format: Jacob K. Kresovich, Serap Erdal, Maria Argos, Hua Yun Chen, Peter H. Gann, Garth H. Rauscher. Residential airborne heavy metal concentrations and breast cancer characteristics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2305. doi:10.1158/1538-7445.AM2017-2305

Traffic-derived particulate matter exposure and histone H3 modification: A repeated measures study

BACKGROUND

Airborne particulate matter (PM) may induce epigenetic changes that potentially lead to chronic diseases. Histone modifications regulate gene expression by influencing chromatin structure that can change gene expression status. We evaluated whether traffic-derived PM exposure is associated with four types of environmentally inducible global histone H3 modifications.

METHODS

The Beijing Truck Driver Air Pollution Study included 60 truck drivers and 60 office workers examined twice, 1-2 weeks apart, for ambient PM₁₀ (both day-of and 14-day average exposures), personal PM_2.5, black carbon (BC), and elemental components (potassium, sulfur, iron, silicon, aluminum, zinc, calcium, and titanium). For both PM₁₀ measures, we obtained hourly ambient PM₁₀ data for the study period from the Beijing Municipal Environmental Bureau's 27 representatively distributed monitoring stations. We then calculated a 24h average for each examination day and a moving average of ambient PM₁₀ measured in the 14 days prior to each examination. Examinations measured global levels of H3 lysine 9 acetylation (H3K9ac), H3 lysine 9 tri-methylation (H3K9me3), H3 lysine 27 tri-methylation (H3K27me3), and H3 lysine 36 tri-methylation (H3K36me3) in blood leukocytes collected after work. We used adjusted linear mixed-effect models to examine percent changes in histone modifications per each μg/m³ increase in PM exposure.

RESULTS

In all participants each μg/m³ increase in 14-day average ambient PM₁₀ exposure was associated with lower H3K27me3 (β=-1.1%, 95% CI: -1.6, -0.6) and H3K36me3 levels (β=-0.8%, 95% CI: -1.4, -0.1). Occupation-stratified analyses showed associations between BC and both H3K9ac and H3K36me3 that were stronger in office workers (β=4.6%, 95% CI: 0.9, 8.4; and β=4.1%, 95% CI: 1.3; 7.0 respectively) than in truck drivers (β=0.1%, 95% CI: -1.3, 1.5; and β=0.9%, 95% CI: -0.9, 2.7, respectively; both p_interaction <0.05). Sex-stratified analyses showed associations between examination-day PM₁₀ and H3K9ac, and between BC and H3K9me3, were stronger in women (β=10.7%, 95% CI: 5.4, 16.2; and β=7.5%, 95% CI: 1.2, 14.2, respectively) than in men (β=1.4%, 95% CI: -0.9, 3.7; and β=0.9%, 95% CI: -0.9, 2.7, respectively; both p_interaction <0.05). We observed no associations between personal PM_2.5 or elemental components and histone modifications.

CONCLUSIONS

Our results suggest a possible role of global histone H3 modifications in effects of traffic-derived PM exposures, particularly BC exposure. Future studies should assess the roles of these modifications in human diseases and as potential mediators of air pollution-induced disease, in particular BC exposure.

Abstract B51: Exploring the role of reproductive factors and DNA methylation in ethnic disparities in breast cancer tumor aggressiveness

Purpose: Non-Hispanic (nH) Black and Hispanic (or minority) breast cancer patients tend to be diagnosed with more aggressive forms of breast cancer compared to their nH White counterparts. Prior research as well as analyses from the current study has identified hormonal and reproductive factors associated with breast cancer aggressiveness subtypes. We explored the potential role of hormonal and reproductive factors, and the potential contribution of DNA methylation, in explaining the racial/ethnic disparity in tumor aggressiveness in a population based study of breast cancer disparities.

Methods: The breast Cancer Care in Chicago (BCCC) study included 989 recently diagnosed nH White, nH Black and Hispanic patients with first primary breast cancer. Analyses include a subset of 286 patients with available tumor immunohistochemistry (IHC) data on estrogen and progesterone receptor (ER/PR), HER2, p53 and Ki67 status. A tumor aggressiveness score (TAS) with a high internal reliability coefficient (Chronbach's alpha=0.76) was created from tumor grade and IHC data on ER, PR, HER2, p53 and Ki67. Values were standardized to have a mean of 0 and standard deviation of 1, then summed together and re-standardized to create the score. Pyrosequencing assays for DNA methylation were conducted on a set of DNA sequences identified based on prior literature, ENCODE data for DNA methylation, and transcription for normal vs. cancer cell lines from the UCSC genome browser. Of the 286 patients with tumor aggressiveness data, 214 had available methylation data for BRCA1, GSTM2, EGFR, RASSF1, Sat2 and TFF1 genes. Multivariable linear regression models were estimated with standardized aggressiveness score as the dependent variable and using nested models to conduct likelihood ratio tests for both forward (type 1) and backwards (type 3) analyses. A method of rescaled-coefficients was then used to estimate an average controlled direct effect representing the ethnic disparity in breast cancer tumor aggressiveness and the extent to which the disparity might be explained by patient reproductive factors and tumor DNA methylation. Because stage at diagnosis is downstream of, and strongly influenced by, tumor aggressiveness, it was excluded from our analyses.

Results: Factors significantly associated with having a higher TAS (p&lt; 0.05) included: nH black or Hispanic race/ethnicity; younger age at first birth; nulliparity; positive family history (FH) of breast cancer, longer use of oral contraceptives; higher pathologic stage; and higher mean BRCA1, GSTM2 and TFF2 methylation levels. In multivariable modeling, variables retained for further analysis included: FH, nulliparity, and methylation of BRCA1, GSTM2, TFF1 and Sat2. In forwards (type 1) analysis of nested models, both nulliparity (p= 0.034) and DNA methylation variables (p&lt; 0.001) were retained. In backwards (type 3) analyses, DNA methylation variables (p&lt; 0.001) but not nulliparity (p= 0.261) were retained. As independent domains, DNA methylation variables explained 46% of the ethnic disparity in TAS (p= 0.054), whereas nulliparity explained 38% (p= 0.058), and family history did not explain any of the disparity. Further, the combination of DNA methylation variables and nulliparity together explained 63% of the disparity (p= 0.033).

Conclusions: Our findings suggest that DNA methylation of specific genes may influence breast cancer tumor aggressiveness and may help to explain the preponderance of aggressive subtypes diagnosed in ethnic minority women. DNA methylation may represent a promising avenue for biomarker development for early detection for biologically aggressive tumor types in vulnerable populations. These findings require replication and validation in other studies.

Citation Format: Keith A. Dookeran, Abeer M. Mahmoud, Matthew Poulin, Liying Yan, Melanie Ehrlich, Jacob K. Kresovich, Virgilia Macias, Andre Kajdacsy-Balla, Elizabeth Wiley, Garth H. Rauscher. Exploring the role of reproductive factors and DNA methylation in ethnic disparities in breast cancer tumor aggressiveness. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr B51.

Associations of lead and cadmium with sex hormones in adult males

Heavy metal exposures are ubiquitous in the environment and their relation to sex hormones is not well understood. This paper investigates the associations between selected heavy metals (lead and cadmium) and sex hormones (testosterone, free testosterone, estradiol, free estradiol) as well as other major molecules in the steroid biosynthesis pathway (androstanedione glucuronide and sex-hormone binding globulin (SHBG)). Blood lead and cadmium were selected as biomarkers of exposure, and tested for associations in males using National Health and Nutritional Examination Survey (NHANES) data from 1999-2004. After adjustment for age, race, body mass index, smoking status, diabetes and alcohol intake, blood lead was positively associated with testosterone and SHBG while blood cadmium was positively associated with SHBG. After controlling for additional heavy metal exposure, the associations between lead and testosterone as well as cadmium and SHBG remained significant. Furthermore, the association between blood lead and testosterone was modified by smoking status (P for interaction=0.011), diabetes (P for interaction=0.021) and blood cadmium (P for interaction=0.029). The association between blood cadmium and SHBG levels was modified by blood lead (P for interaction=0.004). This study is the most comprehensive investigation to date regarding the association between heavy metals and sex hormones in males.

Abstract 2774: Androgen receptor is an independent prognostic marker of breast cancer in ethnically diverse women from Chicago

Androgen receptor (AR) has been demonstrated to be a prognostic marker in invasive breast cancer; higher expression levels of AR is associated with better prognosis among breast cancer patients. The goal of this analysis was to examine the extent to which AR was associated with specific breast cancer subtypes, and whether it could serve as an additional prognostic marker above and beyond breast cancer subtype, in an ethnically diverse sample of 287 patients (86 Non-Hispanic White, 84 Hispanic and 116 African American). Immunohistochemical analysis was performed on tissue microarrays constructed from invasive breast cancer samples obtained from the Breast Cancer Care in Chicago study. Tissue samples were tested for the expression of estrogen receptor (ER), progesterone receptor (PR), HER2. From these results, breast cancers were classified as Luminal A (ER+/PR+/HER2-), Luminal B (ER+/PR+/HER2+), HER2 enriched (ER-/PR-/HER2+), and triple negative (TN) (ER-/PR-/HER2-). Tumor tissues were also analyzed for the expression of other proliferative and apopototic markers (i.e. Ki67, P53 and bcl2) as well as BRCA1 protein expression. AR expression was evaluated based on the percentage of positive tumor cells and staining intensity using the H-score. The H score is a product of the percentage of cells (0-100%) in each intensity category (0, 1+, 2+ and 3+). The final score is on a continuous scale between 0 and 300. AR expression was then classified as low (&lt;60%) or high (≥60%) using the mean of the AR score as a cutoff. Among the 287 breast cancer cases, 59% were expressing low levels of AR while 41% were expressing high AR. The percentage of tumor samples with high AR expression was much higher for luminal A (52%) than for luminal B, HER2, and TN subtypes (43, 29, and 9%, respectively(P&lt;0.0001). High AR expression significantly correlated with early stage (P = 0.01), lower nuclear grade (P&lt;0.0001), ER and PR positivity (P&lt;0.0001), bcl2 positivity(P&lt;0.0001), higher levels of BRCA1 expression (P&lt;0.0001), lower Ki67 index (P&lt;0.0001), and lower P53 expression (P&lt;0.0001). A hormone receptor expression score (HRES) with a high internal reliability (Cronbach's alpha = 0.7035) was created based on standardized variables for ER, PR and AR expression. Using an ordinal logistic regression model, the HRES was a highly significant predictor of tumor grade (P&lt;0.0001). In conclusion, in this multi-ethnic sample of breast cancer patients, we found that AR was a significant independent predictor of less aggressive, lower grade disease, even after accounting for molecular subtype. AR might serve as a useful additional marker for the classification of breast cancer into molecular subtypes.

Citation Format: Abeer M. Mahmoud, Umaima Al-alem, Virgilia Macias, Jacob K. Kresovich, Andre Kajdacsy-Balla, Elizabeth L. Wiley, Garth H. Rauscher. Androgen receptor is an independent prognostic marker of breast cancer in ethnically diverse women from Chicago. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2774. doi:10.1158/1538-7445.AM2015-2774

Abstract LB-274: Mode of breast cancer detection: Do markers of tumor aggressiveness predict which tumors are “missed” at screening

Screening mammography reduces breast cancer stage at diagnosis by detecting it early before symptoms develop. Nonetheless, a breast cancer can arise as a lump despite a recent prior negative screen (“missed detection”). In the Breast Cancer Care in Chicago study, Non-Hispanic (nH) Black and Hispanic women were more likely than their nH White counterparts to report a missed detection despite a recent prior screening mammogram. We examined whether breast cancer subtype and immunohistochemical (IHC) markers of tumor aggressiveness predicted missed detection and whether they could explain racial/ethnic disparities in missed detection, in a subsample of 198 patients with a recent prior screening mammogram (63 Non-Hispanic White, 78 Hispanic and 57 African American).

Missed detection was defined as symptomatic awareness despite a negative screen in the prior 24 months. IHC analyses were conducted for estrogen receptor (ER), progesterone receptor (PR), HER2, EGFR and CK5/6, Ki67 and p53 expression. Breast cancers were classified as Luminal A (ER+/PR+/HER2-), Luminal B (ER+/PR+/HER2+), HER2 enriched (ER-/PR-/HER2+), and triple negative (TN) (ER-/PR-/HER2-).

Missed detection was highest for more aggressive TN and HER2 enriched subtypes (61% and 60%) and lowest for luminal A and B tumors (37% and 38%). Greater Ki67, EGFR and p53 expression were each associated with missed detection (p&lt;0.02 for all), while PR and CK5/6 were marginally associated with missed detection. Before accounting for tumor characteristics, missed detection was twice as likely for minority than for nH white patients (47% vs. 24%, p=0.002); and the disparity in missed detected remained nearly the same after adjustment for tumor aggressiveness markers (47% vs. 27%, p=0.013)

In this multi-ethnic sample of breast cancer patients, markers of tumor aggressiveness were strongly associated with missed detection at screening but they did not explain racial/ethnic disparities in missed detection.

Citation Format: Abeer Mostafa Mahmoud, Virgilia Macias, Jacob K. Kresovich, Andre Kajdacsy-Balla, Elizabeth L. Wiley, Garth H. Rauscher. Mode of breast cancer detection: Do markers of tumor aggressiveness predict which tumors are “missed” at screening. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-274. doi:10.1158/1538-7445.AM2014-LB-274

Abstract 5569: Ki67 is an independent prognostic marker in breast cancer even after accounting for molecular subtype

Ki67 labeling index (LI) has been demonstrated to be a prognostic marker in invasive breast cancer; a high Ki67 LI is associated with poorer survival among breast cancer patients. The goal of these analyses was to examine the extent to which Ki67 was associated with specific breast cancer subtypes, and whether it could serve as an additional prognostic marker above and beyond breast cancer subtype, in an ethnically diverse sample of 287 patients (86 Non-Hispanic White, 84 Hispanic and 116 African American).

IHC analysis was performed on tissue microarrays constructed from invasive breast cancer samples obtained from the Breast Cancer Care in Chicago study (patients diagnosed between 2005-2008). Tissue samples were tested for the expression of estrogen receptor (ER), progesterone receptor (PR), HER2, EGFR and CK5/6. From these results, breast cancers were classified as Luminal A (ER+/PR+/HER2-), Luminal B (ER+/PR+/HER2+), HER2 enriched (ER-/PR-/HER2+), and triple negative (TN) (ER-/PR-/HER2-). TN tumors were subclassified into basal like (BL) if they expressed either EGFR or CK5/6 or otherwise classified as unspecified (US) if negative for both EGFR and CK5/6. Ki67 LI was classified as low (&lt;14%) or high (≥14%). We used multivariable logistic regression to examine associations between Ki67, breast cancer subtype, and histological grade, controlling for race/ethnicity and age at diagnosis in all models.

In adjusted models, the proportion of tumors with a high Ki67 LI was much lower for luminal A (28%) than for luminal B, HER2, TN-US, and TN-BL subtypes (91,66, 77 and 89%, respectively, p&lt;0.0001). The proportion of tumors that were high histologic grade was also much lower for luminal A (29%) than for luminal B, HER2, TN-US, and TN-BL subtypes (85, 86, 94 and 68%, respectively, p&lt;0.0001). Before accounting for subtype, 68% of high Ki67 tumors were high grade, compared with only 26% of low Ki67 tumors (p&lt;0.0001); after controlling for breast cancer subtype these percentages were 58% and 37%, respectively, p=0.001).

In this multi-ethnic sample of breast cancer patients, we found that Ki67 was a significant independent predictor of more aggressive, higher grade disease, even after accounting for molecular subtype. Ki67 might serve as a useful additional marker for the classification of breast cancer into molecular subtypes.

Citation Format: Abeer M. Mahmoud, Virgilia Macias, Umaima Al-alem, Jacob K. Kresovich, Galina Khramtsova, Andre Kajdacsy-Balla, Elizabeth L. Wiley, Garth H. Rauscher. Ki67 is an independent prognostic marker in breast cancer even after accounting for molecular subtype. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5569. doi:10.1158/1538-7445.AM2014-5569

Prenatal nutrition, epigenetics and schizophrenia risk: can we test causal effects?

We posit that maternal prenatal nutrition can influence offspring schizophrenia risk via epigenetic effects. In this article, we consider evidence that prenatal nutrition is linked to epigenetic outcomes in offspring and schizophrenia in offspring, and that schizophrenia is associated with epigenetic changes. We focus upon one-carbon metabolism as a mediator of the pathway between perturbed prenatal nutrition and the subsequent risk of schizophrenia. Although post-mortem human studies demonstrate DNA methylation changes in brains of people with schizophrenia, such studies cannot establish causality. We suggest a testable hypothesis that utilizes a novel two-step Mendelian randomization approach, to test the component parts of the proposed causal pathway leading from prenatal nutritional exposure to schizophrenia. Applied here to a specific example, such an approach is applicable for wider use to strengthen causal inference of the mediating role of epigenetic factors linking exposures to health outcomes in population-based studies.