Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities

We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.

Differences in polygenic score distributions in European ancestry populations: implications for breast cancer risk prediction

The 313-variant polygenic risk score (PRS313) provides a promising tool for breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Here, we explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 225,105 female participants from the UK Biobank. The mean PRS313 differed markedly across European countries, being highest in south-eastern Europe and lowest in north-western Europe. Using the overall European PRS313 distribution to categorise individuals leads to overestimation and underestimation of risk in some individuals from south-eastern and north-western countries, respectively. Adjustment for principal components explained most of the observed heterogeneity in mean PRS. Country-specific PRS distributions may be used to calibrate risk categories in individuals from different countries.

A population-level digital histologic biomarker for enhanced prognosis of invasive breast cancer

Breast cancer is a heterogeneous disease with variable survival outcomes. Pathologists grade the microscopic appearance of breast tissue using the Nottingham criteria, which are qualitative and do not account for noncancerous elements within the tumor microenvironment. Here we present the Histomic Prognostic Signature (HiPS), a comprehensive, interpretable scoring of the survival risk incurred by breast tumor microenvironment morphology. HiPS uses deep learning to accurately map cellular and tissue structures to measure epithelial, stromal, immune, and spatial interaction features. It was developed using a population-level cohort from the Cancer Prevention Study-II and validated using data from three independent cohorts, including the Prostate, Lung, Colorectal, and Ovarian Cancer trial, Cancer Prevention Study-3, and The Cancer Genome Atlas. HiPS consistently outperformed pathologists in predicting survival outcomes, independent of tumor-node-metastasis stage and pertinent variables. This was largely driven by stromal and immune features. In conclusion, HiPS is a robustly validated biomarker to support pathologists and improve patient prognosis.

Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel

BACKGROUND

Polygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women.

METHODS

We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel.

RESULTS

In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28).

CONCLUSIONS

Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.

In utero exposure to diethylstilbestrol and blood DNA methylation in adult women: Results from a meta-analysis of two cohort studies

BACKGROUND

Prenatal exposure to diethylstilbestrol (DES) is associated with several adverse health outcomes. Animal studies have shown associations between prenatal DES exposure and DNA methylation.

OBJECTIVE

The aim of this study was to explore blood DNA methylation in women exposed and unexposed to DES in utero.

METHODS

Sixty women (40 exposed and 20 unexposed) in the National Cancer Institute's Combined DES Cohort Study and 199 women (99 exposed and 100 unexposed women) in the Sister Study Cohort were included in this analysis. Within each study, robust linear regression models were used to assess associations between DES exposure and blood DNA methylation. Study-specific associations were combined using fixed-effect meta-analysis with inverse variance weights. Our analysis focused on CpG sites located within nine candidate genes identified in animal models. We further explored whether in utero DES exposure was associated with age acceleration.

RESULTS

Blood DNA methylation levels at 10 CpG sites in six of the nine candidate genes were statistically significantly associated with prenatal DES exposure (P < 0.05) in this meta-analysis. Genes included EGF, EMB, EGFR, WNT11, FOS, and TGFB1, which are related to cell proliferation and differentiation. The most statistically significant CpG site was cg19830739 in gene EGF, and it was associated with lower methylation levels in women prenatally exposed to DES compared with those not exposed (P < 0.0001; false discovery rate<0.05). The association between prenatal DES exposure in utero and age acceleration was not statistically significant (P = 0.07 for meta-analyzed results).

CONCLUSIONS

There are few opportunities to investigate the effects of prenatal DES exposure. These findings suggest that in utero DES exposure may be associated with differential blood DNA methylation levels, which could mediate the increased risk of several adverse health outcomes observed in exposed women. Our findings need further evaluation using larger data sets.

A population-level computational histologic signature for invasive breast cancer prognosis

Breast cancer is a heterogeneous disease with variable survival outcomes. Pathologists grade the microscopic appearance of breast tissue using the Nottingham criteria, which is qualitative and does not account for non-cancerous elements within the tumor microenvironment (TME). We present the Histomic Prognostic Signature (HiPS), a comprehensive, interpretable scoring of the survival risk incurred by breast TME morphology. HiPS uses deep learning to accurately map cellular and tissue structures in order to measure epithelial, stromal, immune, and spatial interaction features. It was developed using a population-level cohort from the Cancer Prevention Study (CPS)-II and validated using data from three independent cohorts, including the PLCO trial, CPS-3, and The Cancer Genome Atlas. HiPS consistently outperformed pathologists' performance in predicting survival outcomes, independent of TNM stage and pertinent variables. This was largely driven by stromal and immune features. In conclusion, HiPS is a robustly validated biomarker to support pathologists and improve prognosis.

Risk of second primary cancer among women in the Kaiser Permanente Breast Cancer Survivors Cohort

BACKGROUND

Breast cancer survivors are living longer due to early detection and advances in treatment and are at increased risk for second primary cancers. Comprehensive evaluation of second cancer risk among patients treated in recent decades is lacking.

METHODS

We identified 16,004 females diagnosed with a first primary stage I-III breast cancer between 1990 and 2016 (followed through 2017) and survived ≥ 1 year at Kaiser Permanente (KP) Colorado, Northwest, and Washington. Second cancer was defined as an invasive primary cancer diagnosed ≥ 12 months after the first primary breast cancer. Second cancer risk was evaluated for all cancers (excluding ipsilateral breast cancer) using standardized incidence ratios (SIRs), and a competing risk approach for cumulative incidence and hazard ratios (HRs) adjusted for KP center, treatment, age, and year of first cancer diagnosis.

RESULTS

Over a median follow-up of 6.2 years, 1,562 women developed second cancer. Breast cancer survivors had a 70% higher risk of any cancer (95%CI = 1.62-1.79) and 45% higher risk of non-breast cancer (95%CI = 1.37-1.54) compared with the general population. SIRs were highest for malignancies of the peritoneum (SIR = 3.44, 95%CI = 1.65-6.33), soft tissue (SIR = 3.32, 95%CI = 2.51-4.30), contralateral breast (SIR = 3.10, 95%CI = 2.82-3.40), and acute myeloid leukemia (SIR = 2.11, 95%CI = 1.18-3.48)/myelodysplastic syndrome (SIR = 3.25, 95%CI = 1.89-5.20). Women also had elevated risks for oral, colon, pancreas, lung, and uterine corpus cancer, melanoma, and non-Hodgkin lymphoma (SIR range = 1.31-1.97). Radiotherapy was associated with increased risk for all second cancers (HR = 1.13, 95%CI = 1.01-1.25) and soft tissue sarcoma (HR = 2.36, 95%CI = 1.17-4.78), chemotherapy with decreased risk for all second cancers (HR = 0.87, 95%CI = 0.78-0.98) and increased myelodysplastic syndrome risk (HR = 3.01, 95%CI = 1.01-8.94), and endocrine therapy with lower contralateral breast cancer risk (HR = 0.48, 95%CI = 0.38-0.60). Approximately 1 in 9 women who survived ≥ 1 year developed second cancer, 1 in 13 developed second non-breast cancer, and 1 in 30 developed contralateral breast cancer by 10 years. Trends in cumulative incidence declined for contralateral breast cancer but not for second non-breast cancers.

CONCLUSIONS

Elevated risks of second cancer among breast cancer survivors treated in recent decades suggests that heightened surveillance is warranted and continued efforts to reduce second cancers are needed.

DNA methylation age in paired tumor and adjacent normal breast tissue in Chinese women with breast cancer

BACKGROUND

Few studies have examined epigenetic age acceleration (AA), the difference between DNA methylation (DNAm) predicted age and chronological age, in relation to somatic genomic features in paired cancer and normal tissue, with less work done in non-European populations. In this study, we aimed to examine DNAm age and its associations with breast cancer risk factors, subtypes, somatic genomic profiles including mutation and copy number alterations and other aging markers in breast tissue of Chinese breast cancer (BC) patients from Hong Kong.

METHODS

We performed genome-wide DNA methylation profiling of 196 tumor and 188 paired adjacent normal tissue collected from Chinese BC patients in Hong Kong (HKBC) using Illumina MethylationEPIC array. The DNAm age was calculated using Horvath's pan-tissue clock model. Somatic genomic features were based on data from RNA sequencing (RNASeq), whole-exome sequencing (WES), and whole-genome sequencing (WGS). Pearson's correlation (r), Kruskal-Wallis test, and regression models were used to estimate associations of DNAm AA with somatic features and breast cancer risk factors.

RESULTS

DNAm age showed a stronger correlation with chronological age in normal (Pearson r = 0.78, P < 2.2e-16) than in tumor tissue (Pearson r = 0.31, P = 7.8e-06). Although overall DNAm age or AA did not vary significantly by tissue within the same individual, luminal A tumors exhibited increased DNAm AA (P = 0.004) while HER2-enriched/basal-like tumors exhibited markedly lower DNAm AA (P = < .0001) compared with paired normal tissue. Consistent with the subtype association, tumor DNAm AA was positively correlated with ESR1 (Pearson r = 0.39, P = 6.3e-06) and PGR (Pearson r = 0.36, P = 2.4e-05) gene expression. In line with this, we found that increasing DNAm AA was associated with higher body mass index (P = 0.039) and earlier age at menarche (P = 0.035), factors that are related to cumulative exposure to estrogen. In contrast, variables indicating extensive genomic instability, such as TP53 somatic mutations, high tumor mutation/copy number alteration burden, and homologous repair deficiency were associated with lower DNAm AA.

CONCLUSIONS

Our findings provide additional insights into the complexity of breast tissue aging that is associated with the interaction of hormonal, genomic, and epigenetic mechanisms in an East Asian population.

Treatment-related thoracic soft tissue sarcomas in US breast cancer survivors: a retrospective cohort study

BACKGROUND

Soft tissue sarcoma is a rare but serious side-effect of radiotherapy to treat breast cancer, and rates are increasing in the USA. We evaluated potential co-factors in two complimentary cohorts of US breast cancer survivors.

METHODS

In this retrospective cohort study, we sourced data from the Kaiser Permanente (KP) cohort and the Surveillance, Epidemiology, and End Results (SEER) 13 registries cohort, both in the USA. The KP cohort included 15 940 women diagnosed with breast cancer from Jan 1, 1990, to Dec 31, 2016, in KP Colorado, KP Northwest (which serves Oregon and Southwest Washington state), or KP Washington, with detailed treatment data and comorbidities (including hypertension and diabetes at or before breast cancer diagnosis) from electronic medical records. The SEER cohort included 457 300 women diagnosed with breast cancer from Jan 1, 1992, to Dec 31, 2016, within the 13 SEER registries across the USA, with initial treatment data (yes vs no or unknown). Eligibility criteria in both cohorts were female breast cancer survivors (stage I-III) aged 20-84 years at diagnosis who had breast cancer surgery, and had survived at least 1 year after breast cancer diagnosis. The outcome of interest was any second thoracic soft tissue sarcoma (angiosarcomas and other subtypes) that developed at least 1 year after breast cancer diagnosis. Risk factors for thoracic soft tissue sarcoma were assessed using multivariable Poisson regression models.

FINDINGS

In the KP cohort, median follow-up was 9·3 years (IQR 5·7-13·9) and 19 (0·1%) of 15 940 eligible, evaluable women developed a thoracic soft tissue sarcoma (11 angiosarcomas, eight other subtypes). Most (94·7%; 18 of 19) thoracic soft tissue sarcomas occurred in women treated with radiotherapy; thus, radiotherapy was associated with a significantly increased risk of developing a thoracic soft tissue sarcoma (relative risk [RR] 8·1 [95% CI 1·1-60·4]; p=0·0052), but there was no association with prescribed dose, fractionation, or boost. The RR of angiosarcoma after anthracyclines was 3·6 (95% CI 1·0-13·3; p=0·058). Alkylating agents were associated with an increased risk of developing other sarcomas (RR 7·7 [95% CI 1·2-150·8]; p=0·026). History of hypertension (RR 4·8 [95% CI 1·3-17·6]; p=0·017) and diabetes (5·3 [1·4-20·8]; p=0·036) were each associated with around a five-times increased risk of angiosarcoma. In the SEER cohort, 430 (0·1%) of 457 300 patients had subsequent thoracic soft tissue sarcomas (268 angiosarcomas and 162 other subtypes) after a median follow-up of 8·3 years (IQR 4·3-13·9). Most (77·9%; 335 of 430) cases occurred after radiotherapy; thus, radiotherapy was associated with a significantly increased risk of developing a thoracic soft tissue sarcoma (RR 3·0 [95% CI 2·4-3·8]; p<0·0001) and, for angiosarcomas, the RR for breast-conserving surgery plus radiotherapy versus mastectomy plus radiotherapy was 1·9 (1·1-3·3; p=0·012). By 10 years after radiotherapy, the cumulative incidence of thoracic soft tissue sarcoma was 0·21% (95% CI 0·12-0·34) in the KP cohort and 0·15% (95% CI 0·13-0·17) in SEER.

INTERPRETATION

Radiotherapy was the strongest risk factor for thoracic soft tissue sarcoma in both cohorts. This finding, along with the novel findings for diabetes and hypertension as potential risk factors for angiosarcomas, warrant further investigation as potential targets for prevention strategies and increased surveillance.

FUNDING

US National Cancer Institute and National Institutes of Health.

Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies

BACKGROUND

DNA methylation in blood may reflect adverse exposures accumulated over the lifetime and could therefore provide potential improvements in the prediction of cancer risk. A substantial body of research has shown associations between epigenetic aging and risk of disease, including cancer. Here we aimed to study epigenetic measures of aging and lifestyle-related factors in association with risk of breast cancer.

METHODS

Using data from four prospective case-control studies nested in three cohorts of European ancestry participants, including a total of 1,655 breast cancer cases, we calculated three methylation-based measures of lifestyle factors (body mass index [BMI], tobacco smoking and alcohol consumption) and seven measures of epigenetic aging (Horvath-based, Hannum-based, PhenoAge and GrimAge). All measures were regression-adjusted for their respective risk factors and expressed per standard deviation (SD). Odds ratios (OR) and 95% confidence intervals (CI) were calculated using conditional or unconditional logistic regression and pooled using fixed-effects meta-analysis. Subgroup analyses were conducted by age at blood draw, time from blood sample to diagnosis, oestrogen receptor-positivity status and tumour stage.

RESULTS

None of the measures of epigenetic aging were associated with risk of breast cancer in the pooled analysis: Horvath 'age acceleration' (AA): OR per SD = 1.02, 95%CI: 0.95-1.10; AA-Hannum: OR = 1.03, 95%CI:0.95-1.12; PhenoAge: OR = 1.01, 95%CI: 0.94-1.09 and GrimAge: OR = 1.03, 95%CI: 0.94-1.12, in models adjusting for white blood cell proportions, body mass index, smoking and alcohol consumption. The BMI-adjusted predictor of BMI was associated with breast cancer risk, OR per SD = 1.09, 95%CI: 1.01-1.17. The results for the alcohol and smoking methylation-based predictors were consistent with a null association. Risk did not appear to substantially vary by age at blood draw, time to diagnosis or tumour characteristics.

CONCLUSION

We found no evidence that methylation-based measures of aging, smoking or alcohol consumption were associated with risk of breast cancer. A methylation-based marker of BMI was associated with risk and may provide insights into the underlying associations between BMI and breast cancer.

Mammographic Density Decline, Tamoxifen Response, and Prognosis by Molecular Characteristics of Estrogen Receptor-Positive Breast Cancer

BACKGROUND

Mammographic breast density (MBD) decline post-tamoxifen initiation is a favorable prognostic factor in estrogen receptor (ER)-positive breast cancer (BC) and has potential utility as a biomarker of tamoxifen response. However, the prognostic value of MBD decline may vary by molecular characteristics among ER-positive patients.

METHODS

We investigated associations between MBD decline (≥10% vs <10%) and breast cancer-specific mortality (BCSM) among ER-positive breast cancer patients aged 36-87 years at diagnosis treated with tamoxifen at Kaiser Permanente Northwest (1990-2008). Patients who died of BC (case patients; n = 62) were compared with those who did not (control patients; n = 215) overall and by tumor molecular characteristics (immunohistochemistry [IHC]-based subtype [luminal A-like: ER-positive/progesterone receptor [PR]-positive/HER2-negative/low Ki67; luminal B-like: ER-positive and 1 or more of PR-negative, HER2-positive, high Ki67] and modified IHC [mIHC]-based recurrence score of ER/PR/Ki67). Percent MBD was measured in the unaffected breast at baseline mammogram (mean = 6 months before tamoxifen initiation) and follow-up (mean = 12 months post-tamoxifen initiation). Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were computed from logistic regression models. All statistical tests were 2-sided.

RESULTS

MBD decline was statistically significantly associated with reduced risk of BCSM overall (OR = 0.38, 95% CI = 0.15 to 0.92). This association was, however, stronger among women with aggressive tumor characteristics including luminal B-like (OR = 0.17, 95% CI = 0.04 to 0.73) vs A-like (OR = 0.74, 95% CI = 0.19 to 2.92); large (OR = 0.26, 95% CI = 0.08 to 0.78) vs small (OR = 0.41, 95% CI = 0.04 to 3.79) tumors; PR-negative (OR = 0.02, 95% CI = 0.001 to 0.37) vs PR-positive (OR = 0.50, 95% CI = 0.18 to 1.40) disease; and high (OR = 0.25, 95% CI = 0.07 to 0.93) vs low (OR = 0.44, 95% CI = 0.10 to 2.09) mIHC3 score.

CONCLUSION

The findings support MBD decline as a prognostic marker of tamoxifen response among patients with aggressive ER-positive BC phenotypes, for whom understanding treatment effectiveness is critical.

Mammary collagen architecture and its association with mammographic density and lesion severity among women undergoing image-guided breast biopsy

Background

Elevated mammographic breast density is a strong breast cancer risk factor with poorly understood etiology. Increased deposition of collagen, one of the main fibrous proteins present in breast stroma, has been associated with increased mammographic density. Collagen fiber architecture has been linked to poor outcomes in breast cancer. However, relationships of quantitative collagen fiber features assessed in diagnostic biopsies with mammographic density and lesion severity are not well-established.

Methods

Clinically indicated breast biopsies from 65 in situ or invasive breast cancer cases and 73 frequency matched-controls with a benign biopsy result were used to measure collagen fiber features (length, straightness, width, alignment, orientation and density (fibers/µm²)) using second harmonic generation microscopy in up to three regions of interest (ROIs) per biopsy: normal, benign breast disease, and cancer. Local and global mammographic density volumes were quantified in the ipsilateral breast in pre-biopsy full-field digital mammograms. Associations of fibrillar collagen features with mammographic density and severity of biopsy diagnosis were evaluated using generalized estimating equation models with an independent correlation structure to account for multiple ROIs within each biopsy section.

Results

Collagen fiber density was positively associated with the proportion of stroma on the biopsy slide (p < 0.001) and with local percent mammographic density volume at both the biopsy target (p = 0.035) and within a 2 mm perilesional ring (p = 0.02), but not with global mammographic density measures. As severity of the breast biopsy diagnosis increased at the ROI level, collagen fibers tended to be less dense, shorter, straighter, thinner, and more aligned with one another (p < 0.05).

Conclusions

Collagen fiber density was positively associated with local, but not global, mammographic density, suggesting that collagen microarchitecture may not translate into macroscopic mammographic features. However, collagen fiber features may be markers of cancer risk and/or progression among women referred for biopsy based on abnormal breast imaging.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-021-01482-z.

Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies candidate susceptibility genes for breast and ovarian cancer

Familial, sequencing, and genome-wide association studies (GWASs) and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWASs) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through application of a pleiotropy-guided conditional/conjunction false discovery rate (FDR) approach in the setting of a TWASs. This identified 14 candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were >1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. The 22 genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.

Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident

Effects of radiation exposure from the Chernobyl nuclear accident remain a topic of interest. We investigated germline de novo mutations (DNMs) in children born to parents employed as cleanup workers or exposed to occupational and environmental ionizing radiation after the accident. Whole-genome sequencing of 130 children (born 1987-2002) and their parents did not reveal an increase in the rates, distributions, or types of DNMs relative to the results of previous studies. We find no elevation in total DNMs, regardless of cumulative preconception gonadal paternal [mean = 365 milligrays (mGy), range = 0 to 4080 mGy] or maternal (mean = 19 mGy, range = 0 to 550 mGy) exposure to ionizing radiation. Thus, we conclude that, over this exposure range, evidence is lacking for a substantial effect on germline DNMs in humans, suggesting minimal impact from transgenerational genetic effects.

Risk factors for contralateral breast cancer in postmenopausal breast cancer survivors in the NIH-AARP Diet and Health Study

PURPOSE

The role of established breast cancer risk factors and clinical characteristics of the first breast cancer in the development of contralateral breast cancer (CBC) among postmenopausal women is unclear.

METHODS

We identified 10,934 postmenopausal women diagnosed with a first primary breast cancer between 1995 and 2011 in the NIH-AARP Diet and Health Study. CBC was defined as a second primary breast cancer diagnosed in the contralateral breast ≥ 3 months after the first breast cancer. Exposures included pre-diagnosis risk factors (lifestyle, reproductive, family history) and clinical characteristics of the first breast cancer. We used multivariable Cox proportional hazards regression to estimate hazard ratios (HRs) and 95% confidence intervals (CIs).

RESULTS

Over a median follow-up of 6.8 years, 436 women developed CBC. We observed an increasing trend in CBC risk by age (p-trend = 0.002) and decreasing trend by year of diagnosis (p-trend = 0.001) of the first breast cancer. Additional risk factor associations were most pronounced for endocrine therapy (HR 0.68, 95% CI 0.53-0.87) and family history of breast cancer (HR 1.38, 95% CI 1.06-1.80, restricted to invasive first breast cancer). No associations were found for lifestyle (body mass index, physical activity, smoking, alcohol) or reproductive factors (age at menarche, parity, age at first birth, age at menopause).

CONCLUSIONS

This study suggests that clinical characteristics of the first breast cancer and family history of breast cancer, but not pre-diagnosis lifestyle and reproductive factors, are strongly associated with CBC risk among postmenopausal women. Future studies are needed to understand how these factors contribute to CBC etiology and to identify further opportunities for prevention.

Body Mass Index and Risk of Second Cancer Among Women With Breast Cancer

BACKGROUND

Breast cancer survivors are at increased risk for developing second primary cancers compared with the general population. Little is known about whether body mass index (BMI) increases this risk. We examined the association between BMI and second cancers among women with incident invasive breast cancer.

METHODS

This retrospective cohort included 6481 patients from Kaiser Permanente Colorado and Washington of whom 822 (12.7%) developed a second cancer (mean follow-up was 88.0 months). BMI at the first cancer was extracted from the medical record. Outcomes included: 1) all second cancers, 2) obesity-related second cancers, 3) any second breast cancer, and 4) estrogen receptor-positive second breast cancers. Multivariable Poisson regression models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs) for second cancers associated with BMI adjusted for site, diagnosis year, treatment, demographic, and tumor characteristics.

RESULTS

The mean age at initial breast cancer diagnosis was 61.2 (SD = 11.8) years. Most cases were overweight (33.4%) or obese (33.8%) and diagnosed at stage I (62.0%). In multivariable models, for every 5 kg/m2 increase in BMI, the risk of any second cancer diagnosis increased by 7% (RR = 1.07, 95% CI = 1.01 to 1.14); 13% (RR = 1.13, 95% CI = 1.05 to 1.21) for obesity-related cancers, 11% (RR = 1.11, 95% CI = 1.02 to 1.21) for a second breast cancer, and 15% (RR = 1.15, 95% CI = 1.04 to 1.27) for a second estrogen receptor-positive breast cancer.

CONCLUSIONS

We observed a statistically significant increased risk of second cancers associated with increasing BMI. These findings have important public health implications given the prevalence of overweight and obesity in breast cancer survivors and underscore the need for effective prevention strategies.

Cross-Cancer Genome-Wide Association Study of Endometrial Cancer and Epithelial Ovarian Cancer Identifies Genetic Risk Regions Associated with Risk of Both Cancers

BACKGROUND

Accumulating evidence suggests a relationship between endometrial cancer and ovarian cancer. Independent genome-wide association studies (GWAS) for endometrial cancer and ovarian cancer have identified 16 and 27 risk regions, respectively, four of which overlap between the two cancers. We aimed to identify joint endometrial and ovarian cancer risk loci by performing a meta-analysis of GWAS summary statistics from these two cancers.

METHODS

Using LDScore regression, we explored the genetic correlation between endometrial cancer and ovarian cancer. To identify loci associated with the risk of both cancers, we implemented a pipeline of statistical genetic analyses (i.e., inverse-variance meta-analysis, colocalization, and M-values) and performed analyses stratified by subtype. Candidate target genes were then prioritized using functional genomic data.

RESULTS

Genetic correlation analysis revealed significant genetic correlation between the two cancers (rG = 0.43, P = 2.66 × 10-5). We found seven loci associated with risk for both cancers (P Bonferroni < 2.4 × 10-9). In addition, four novel subgenome-wide regions at 7p22.2, 7q22.1, 9p12, and 11q13.3 were identified (P < 5 × 10-7). Promoter-associated HiChIP chromatin loops from immortalized endometrium and ovarian cell lines and expression quantitative trait loci data highlighted candidate target genes for further investigation.

CONCLUSIONS

Using cross-cancer GWAS meta-analysis, we have identified several joint endometrial and ovarian cancer risk loci and candidate target genes for future functional analysis.

IMPACT

Our research highlights the shared genetic relationship between endometrial cancer and ovarian cancer. Further studies in larger sample sets are required to confirm our findings.

Field Study of the Possible Effect of Parental Irradiation on the Germline of Children Born to Cleanup Workers and Evacuees of the Chornobyl Nuclear Accident

Although transgenerational effects of exposure to ionizing radiation have long been a concern, human research to date has been confined to studies of disease phenotypes in groups exposed to high doses and high dose rates, such as the Japanese atomic bomb survivors. Transgenerational effects of parental irradiation can be addressed using powerful new genomic technologies. In collaboration with the Ukrainian National Research Center for Radiation Medicine, the US National Cancer Institute, in 2014-2018, initiated a genomic alterations study among children born in selected regions of Ukraine to cleanup workers and/or evacuees exposed to low-dose-rate radiation after the 1986 Chornobyl (Chernobyl) nuclear accident. To investigate whether parental radiation exposure is associated with germline mutations and genomic alterations in the offspring, we are collecting biospecimens from father-mother-offspring constellations to study de novo mutations, minisatellite mutations, copy-number changes, structural variants, genomic insertions and deletions, methylation profiles, and telomere length. Genomic alterations are being examined in relation to parental gonadal dose, reconstructed using questionnaire and measurement data. Subjects are being recruited in exposure categories that will allow examination of parental origin, duration, and timing of exposure in relation to conception. Here we describe the study methodology and recruitment results and provide descriptive information on the first 150 families (mother-father-child(ren)) enrolled.

Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)

PURPOSE

Gene expression-based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features.

EXPERIMENTAL DESIGN

Adopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting.

RESULTS

Gene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations.

CONCLUSIONS

We validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications.See related commentary by McMullen et al., p. 5271.

Polygenic risk score for the prediction of breast cancer is related to lesser terminal duct lobular unit involution of the breast

Terminal duct lobular units (TDLUs) are the predominant anatomical structures where breast cancers originate. Having lesser degrees of age-related TDLU involution, measured as higher TDLUs counts or more epithelial TDLU substructures (acini), is related to increased breast cancer risk among women with benign breast disease (BBD). We evaluated whether a recently developed polygenic risk score (PRS) based on 313-common variants for breast cancer prediction is related to TDLU involution in the background, normal breast tissue, as this could provide mechanistic clues on the genetic predisposition to breast cancer. Among 1398 women without breast cancer, higher values of the PRS were significantly associated with higher TDLU counts (P = 0.004), but not with acini counts (P = 0.808), in histologically normal tissue samples from donors and diagnostic BBD biopsies. Mediation analysis indicated that TDLU counts may explain a modest proportion (≤10%) of the association of the 313-variant PRS with breast cancer risk. These findings suggest that TDLU involution might be an intermediate step in the association between common genetic variation and breast cancer risk.

Prognostic gene expression signature for high-grade serous ovarian cancer

BACKGROUND

Median overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is ∼4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC.

PATIENTS AND METHODS

Expression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies.

RESULTS

Expression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years.

CONCLUSION

The OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.

Abstract 3495: Associations between circulating estrogens and estrogens metabolites and blood DNA methylation

Background. Endogenous estrogen and its metabolites have widespread physiological actions and have been associated with several conditions and diseases, including bone density, atherosclerosis, and different cancers. The two parent estrogens, estrone and estradiol, are irreversibly hydroxylated at the C-2, C-4, and C-16 positions of the steroid ring, leading to a cascade of metabolites with potentially different effects on disease risk. Little is known about the relation between estrogen metabolism and DNA methylation, although different estrogen metabolites may alter DNA methylation, which could ultimately result in expression changes in genes affecting hormonally related diseases. Here, we analyze the relationship between circulating parent estrogens and estrogen metabolites and blood DNA methylation.

Methods. Estrone, estradiol (total and unconjugated) and 13 estrogen metabolites (five metabolites in the 2-hydroxylation pathway, three in the 4-pathway, and five in the 16-pathway) were measured using highly sensitive liquid chromatography-tandem mass spectrometry in serum from 260 postmenopausal women from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial who were not currently taking exogenous hormones at the time of blood collection. Using the same blood draw, DNA methylation was measured in 638,586 CpG sites using the Ilumina MethylationEPIC BeadChip array. Associations between estrogens and estrogen metabolites and methylation were estimated using linear regression, adjusting for age, BMI, smoking, and alcohol intake. The Bonferroni correction at the 5% level was used to account for multiple testing. The relationships between estrogens and estrogen metabolites and previously derived methylation measures of age acceleration were also investigated.

Results. Median age at blood collection was 63 years. We identified 235 statistically significant associations between different parent estrogens and estrogen metabolites and CpG sites at the Bonferroni level. Approximately 60-70% of these sites, depending on the estrogen/estrogen metabolite, lie in the promoter or the body of a gene. Genes included GPR180 and SDK1, which are related to vascular function and fat metabolism. Approximately 40% of the CpG sites associated with the 2- and 4-hydroxylation pathways lie in enhancer regions. The Horvath measure of age acceleration was inversely associated with 4-hydroxyestrone (P=0.02) and the overall 4-hydroxylation pathway (P=0.04).

Conclusions. Circulating estrogens and estrogen metabolites were statistically significantly associated with blood DNA methylation at several hormonally related genes, which could partially explain mechanisms underlying associations between estrogen and hormonally related cancers and other conditions. Work is ongoing to validate these findings.

Citation Format: Clara Bodelon. Associations between circulating estrogens and estrogens metabolites and blood DNA methylation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3495.

Differences in Genome-wide DNA Methylation Profiles in Breast Milk by Race and Lactation Duration

Black women in the United States are disproportionately affected by early-onset, triple-negative breast cancer. DNA methylation has shown differences by race in healthy and tumor breast tissues. We examined associations between genome-wide DNA methylation levels in breast milk and breast cancer risk factors, including race, to explain how this reproductive stage influences a woman's risk for, and potentially contributes to racial disparities in, breast cancer. Breast milk samples and demographic, behavioral, and reproductive data, were obtained from cancer-free, uniparous, and lactating U.S. black (n = 57) and white (n = 82) women, ages 19-44. Genome-wide DNA methylation analysis was performed on extracted breast milk DNA using the Infinium HumanMethylation450 BeadChip. Statistically significant associations between breast cancer risk factors and DNA methylation beta values, adjusting for potential confounders, were determined using linear regression followed by Bonferroni Correction (P < 1.63 × 10^-7). Epigenetic analysis in breast milk revealed statistically significant associations with race and lactation duration. Of the 284 CpG sites associated with race, 242 were hypermethylated in black women. All 227 CpG sites associated with lactation duration were hypomethylated in women who lactated longer. Ingenuity Pathway Analysis of differentially methylated promoter region CpGs by race and lactation duration revealed enrichment for networks implicated in carcinogenesis. Associations between DNA methylation and lactation duration may offer insight on its role in lowering breast cancer risk. Epigenetic associations with race may mediate social, behavioral, or other factors related to breast cancer and may provide insight into potential mechanisms underlying racial disparities in breast cancer incidence.

Molecular Classification of Epithelial Ovarian Cancer Based on Methylation Profiling: Evidence for Survival Heterogeneity

PURPOSE

Ovarian cancer is a heterogeneous disease that can be divided into multiple subtypes with variable etiology, pathogenesis, and prognosis. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes, copy number variation, RNA expression data, and outcomes.

EXPERIMENTAL DESIGN

A total of 162 paraffin-embedded ovarian epithelial tumor tissues, including the five major epithelial ovarian tumor subtypes (high- and low-grade serous, endometrioid, mucinous, and clear cell) and tumors of low malignant potential were selected from two different sources: The Polish Ovarian Cancer study, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR). Analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. For 45 tumors array copy number data were available. NanoString gene expression data for 39 genes were available for 61 high-grade serous carcinomas (HGSC).

RESULTS

Consensus nonnegative matrix factorization clustering of the 1,000 most variable CpG sites showed four major clusters among all epithelial ovarian cancers. We observed statistically significant differences in survival (log-rank test, P = 9.1 × 10^-7) and genomic instability across these clusters. Within HGSC, clustering showed three subgroups with survival differences (log-rank test, P = 0.002). Comparing models with and without methylation subgroups in addition to previously identified gene expression subtypes suggested that the methylation subgroups added significant survival information (P = 0.007).

CONCLUSIONS

DNA methylation profiling of ovarian cancer identified novel molecular subgroups that had significant survival difference and provided insights into the molecular underpinnings of ovarian cancer.See related commentary by Ishak et al., p. 5729.

Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies

BACKGROUND

Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date.

METHODS

We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing.

RESULTS

The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98).

CONCLUSIONS

Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.

Abstract P6-10-07: Differences in genome-wide DNA methylation levels in breast milk by race and lactation duration

Introduction: Identifying biomarkers of breast cancer risk among young women would have value in developing effective screening and prevention strategies at early ages. We have proposed that DNA methylation analysis of breast milk may provide breast cancer risk information among young women, and could possibly provide etiologic clues related to the higher rates of early onset cancers among African American as compared with White women in the US.

Objective: The purpose of this project was to identify associations between genome-wide DNA methylation levels in breast milk and race adjusted for other breast cancer risk factors.

Study Population: Cancer-free, lactating U.S. Black (n=57) and White (n=82) women, ages 19 to 44, provided frozen breast milk samples, as well as demographic, behavioral, and reproductive data, to the Breastmilk Laboratory at University of Massachusetts Amherst. Women were uniparous and did not have a personal history of breast cancer at the time of milk donation.

Methods: DNA was extracted from breast milk samples using the phenol-chloroform method. Genome-wide methylation analysis was performed on breast milk samples using the Infinium HumanMethylation450 BeadChip. Probes with 50% or more missing data, cross-reactive probes, as well as probes with minor allelic frequency greater than 0.05 in European- or African-Americans were removed, leaving 379,042 CpG sites for analysis. Multivariate generalized linear regression models were used to examine associations between race and other breast cancer risk factors and methylation beta values, adjusting for potential confounding factors. P-values less than 1E-7 were considered statistically significant.

Results: Black women in this study were more likely to be never smokers, to not have used over-the-counter pain medication in the past week, and to breastfeed longer. After adjustment by age, BMI, smoking status, and batch number, race was significantly associated with differential methylation at 1143 CpG sites, including 1024 at which Black women demonstrated increased methylation levels. Additionally, breastfeeding duration was associated with 269 CpG sites, with 268 showing a significant inverse relationship with methylation. Methylation sites significantly associated with Black race and lactation duration were located within tumor suppressor and promoter genes as well as in genes implicated in obesity and diabetes.

Conclusion: This preliminarily analysis of DNA methylation in breast milk suggests that Black women have increased methylation and longer breastfeeding is associated with reduced methylation. Further research to understand how etiologic factors related to breast cancer may alter DNA methylation patterns in normal breast may lead to improved understanding of breast cancer risk at a young age and potentially causes of racial disparities in breast cancer incidence between White and Black women.

Citation Format: Davis Lynn BC, Bodelon C, Pfeiffer RM, Yang HP, Yang H, Lee M, Laird PW, Campan M, Weisenberger DJ, Murphy J, Sherman ME, Browne EP, Anderton DL, Arcaro KF, Gierach GL. Differences in genome-wide DNA methylation levels in breast milk by race and lactation duration [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-10-07.

Abstract LB-154: Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous

Background. Ovarian cancer is a heterogeneous disease that is divisible into multiple subtypes with variable pathogenesis, etiology and biological behavior. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes and prognosis.

Methods. A total of 176 paraffin embedded ovarian epithelial tumor tissues, including the four major epithelial ovarian tumor subtypes (serous, endometrioid, mucinous and clear cell) and tumors of low malignant potential (LMP) were selected from two different sources: The Polish Ovarian Cancer study, an incident population-based case-control study conducted from 2001-2004, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR), which included ovarian tumors blocks collected between 1994 and 2004 from the Iowa and Hawaii SEER registries. The distributions of tumor histologic subtypes and grades from the studies were similar. All analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. Analyses were restricted to the 22 autosomal chromosomes and non-SNP probes. Fourteen samples that did not pass quality control were excluded from the analysis.

Results. Among 162 samples, 32 were from the Polish study and 130 were from the SEER RTR. Unsupervised hierarchical clustering of the 5,000 most variable CpG sites showed 4 major clusters: Cluster 1 with 79% invasive serous and 14% endometrioid carcinomas, including the majority of high grade carcinomas; cluster 2 with 77% either endometrioid or clear cell carcinomas; cluster 3 with 71% serous LMP; and cluster 4 with 73% mucinous carcinomas. We observed significant survival differences across these clusters (long-rank test P= 4.27×10-6), similar to differences observed for histologic subtypes. Within high grade (HG) serous carcinomas, clustering showed three subgroups with prognostic significance (long-rank test P= 0.008).

Conclusions. Our results suggest that methylation-based subtypes provide a classification of ovarian tumors that are in agreement with morphologic subtypes and probable mechanisms of origin. Unsupervised clustering analysis of HG serous carcinomas showed subtypes within HG serous with significance survival difference. Ongoing analyses are comparing performance of the methylation subgroups with gene expression subgroups of ovarian cancer.

Citation Format: Clara Bodelon. Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous [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 LB-154. doi:10.1158/1538-7445.AM2017-LB-154

Abstract IS01: METHYLATION PROFILING OF OVARIAN CANCER TO STUDY ETIOLOGIC AND PROGNOSTIC HETEROGENEITY AND TO DEVELOP A MOLECULAR CLASSIFIER

BACKGROUND. Ovarian cancer is a heterogeneous disease that is divisible into multiple subtypes with variable pathogenesis, etiology and biological behavior. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes and prognosis. Additionally, we developed a molecular classifier for classification of ovarian tumors in epidemiologic studies.

METHODS. A total of 176 paraffin embedded ovarian epithelial tumor tissues, including the four major epithelial ovarian tumor subtypes (serous, endometrioid, mucinous and clear cell) and tumors of low malignant potential (LMP) were selected from two different sources: The Polish Ovarian Cancer study, an incident population–based case–control study conducted from 2001–2004, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR), which included ovarian tumors blocks collected between 1994 and 2004 from the Iowa and Hawaii SEER registries. The distributions of tumor histologic subtypes and grades from the studies were similar. All analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. Analyses were restricted to the 22 autosomal chromosomes and non–SNP probes. Fourteen samples that did not pass quality control were excluded from the analysis.

RESULTS. Among 162 samples, 32 were from the Polish study and 130 were from the SEER RTR. Unsupervised hierarchical clustering of the 5,000 most variable CpG sites showed 4 major clusters: Cluster 1 with 79% invasive serous and 14% endometrioid carcinomas, including the majority of high grade carcinomas; cluster 2 with 77% either endometrioid or clear cell carcinomas; cluster 3 with 71% serous LMP; and cluster 4 with 73% mucinous carcinomas. We observed significant survival differences across these clusters (long–rank test P= 4.27×10–6), similar to differences observed for histologic subtypes. Within high grade (HG) serous carcinomas, clustering showed three subgroups with prognostic significance (long–rank test P= 0.008).

CONCLUSIONS. Our results suggest that methylation–based subtypes provide a classification of ovarian tumors that are in agreement with morphologic subtypes and probable mechanisms of origin. Unsupervised clustering analysis of HG serous carcinomas showed subtypes within HG serous with significance survival difference. Ongoing analyses will compare performance of the methylation classifier with histologic subtype in relation to risk factors and prognosis.

Citation Format: Clara Bodelon, J. Keith Killian, Joshua N. Sampson, Holly Stevenson, William F. Anderson, Rayna Matsuno, Louise A. Brinton, Jolanta Lissowska, Mark E. Sherman, Nicolas Wentzensen. METHYLATION PROFILING OF OVARIAN CANCER TO STUDY ETIOLOGIC AND PROGNOSTIC HETEROGENEITY AND TO DEVELOP A MOLECULAR CLASSIFIER [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr IS01.

Discovery and validation of candidate host DNA methylation markers for detection of cervical precancer and cancer

Human papillomavirus (HPV) testing has been recently introduced as an alternative to cytology for cervical cancer screening. However, since most HPV infections clear without causing clinically relevant lesions, additional triage tests are required to identify women who are at high risk of developing cancer. We performed DNA methylation profiling on formalin-fixed, paraffin-embedded tissue specimens from women with benign HPV16 infection and histologically confirmed cervical intraepithelial neoplasia grade 3, and cancer using a bead-based microarray covering 1,500 CpG sites in over 800 genes. Methylation levels in individual CpG sites were compared using a t-test, and results were summarized by computing p-values. A total of 12 candidate genes (ADCYAP1, ASCL1, ATP10, CADM1, DCC, DBC1, HS3ST2, MOS, MYOD1, SOX1, SOX17 and TMEFF2) identified by DNA methylation profiling, plus an additional three genes identified from the literature (EPB41L3, MAL and miR-124) were chosen for validation in an independent set of 167 liquid-based cytology specimens using pyrosequencing and targeted, next-generation bisulfite sequencing. Of the 15 candidate gene markers, 10 had an area under the curve (AUC) of ≥ 0.75 for discrimination of high grade squamous intraepithelial lesions or worse (HSIL+) from <HSIL cytology using at least one assay. Overall, SOX1, DCC, and EPB41L3 showed the best discrimination with AUC values of ≥0.80, irrespective of methylation detection assay. In addition to verifying candidate markers from the literature (e.g., SOX1 and EPB41L3), we identified novel markers that may be considered for detection of cervical precancer and cancer and warrant further validation in prospective studies.

Abstract A27: Timing of pregnancies and oral contraceptive use and risk of ovarian cancer

Background: Parity and use of oral contraceptive (OC) are associated with reduced risk of ovarian cancer. However, it is not clear whether these exposures have similar risk effects during different periods of life. In a large consortial analysis, we seek to evaluate the risk reductions associated with pregnancy and with OC use in different periods during the lifetime of a woman.

Methods: We combined data from 17 population-based case-control studies of ovarian cancer that are part of the Ovarian Cancer Association Consortium (OCAC). Odds ratios (ORs) and 95% confidence intervals (CI) for associations between age of pregnancies and duration of OC use were estimated in individual studies using logistic regression and combined using random effects meta-analysis. Analyses were adjusted for age, duration of OC use, number of pregnancies, and race (Caucasian, Black, Asian and other). Studies that matched on ethnicity were additionally adjusted for Hispanic ethnicity (yes/no). All tests were two-sided and P-values less than 0.05 were considered statistically significant.

Results: The analysis included 15,033 ovarian cancer cases and 25,312 controls. The median age for cases was 57 (interquantile range: 50-65) and 56 for controls (interquantile range: 48-64). Approximately 83.4% of cases and 88.5% of controls reported at least one pregnancy and 55.4% of cases and 61.7% of controls reported OCs use for at least one month. On average, each pregnancy was associated with a 17% reduced risk of ovarian cancer (OR=0.83, 95% CI: 0.8-0.85) while each year of OC use was associated with a 6% reduced risk (OR=0.94, CI 0.92-0.95). Among women who reported having at least one pregnancy, older age at last pregnancy was associated with lower risk of ovarian cancer (P&lt;0.0001). Specifically, compared to women whose last pregnancy was before the age of 25, women who had their last pregnancy between the ages of 25-30 had a 15% reduced risk of ovarian cancer (OR=0.85, 95% CI: 0.78-0.93), women who had their last pregnancy between the ages of 30-35 had a 18% reduced risk of ovarian cancer (OR=0.82, 95% CI: 0.74-0.90) and women who had their last pregnancy after the age of 35 had a 21% reduced risk of ovarian cancer (OR=0.79, 95% CI: 0.70-0.90). Similar findings were observed when analyses were stratified by increasing number of pregnancies. With respect to OC use, compared to women who reported the age at last used before the age of 25, those who reported the age at last use to be between the ages of 25-30 had a 15% lower risk of ovarian cancer (OR=0.85, 95% CI: 0.73-0.98) and those who reported the age of last use was after the age of 30 had a 18% reduced risk of ovarian cancer (OR=0.82, 95% CI: 0.66-1.03 for age at last used between 30-35; OR=0.82, 95% CI: 0.63-1.07 for age at last older than 35), but the trend was not significant.

Conclusions: In summary, older age at last pregnancy was significantly associated with reduced risk of ovarian cancer. There was a suggestion that older age at last used of OCs was associated with lower risk of ovarian cancer. These findings suggest that use of OCs to later ages in life can reduce ovarian cancer risk. A joint evaluation of life periods with pregnancies and OC use and ovarian cancer risk is under way.

Citation Format: Clara Bodelon, Harvey Risch, Francesmary Modugno, Penelope Webb, Celeste Leigh Pearce, Malcolm Pike, Nicolas Wentzensen. Timing of pregnancies and oral contraceptive use and risk of ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference: Improving Cancer Risk Prediction for Prevention and Early Detection; Nov 16-19, 2016; Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(5 Suppl):Abstract nr A27.

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer

To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.

Association between breast cancer genetic susceptibility variants and terminal duct lobular unit involution of the breast

Terminal duct lobular units (TDLUs) are the predominant source of future breast cancers, and lack of TDLU involution (higher TDLU counts, higher acini count per TDLU and the product of the two) is a breast cancer risk factor. Numerous breast cancer susceptibility single nucleotide polymorphisms (SNPs) have been identified, but whether they are associated with TDLU involution is unknown. In a pooled analysis of 872 women from two studies, we investigated 62 established breast cancer SNPs and relationships with TDLU involution. Poisson regression models with robust variance were used to calculate adjusted per-allele relative risks (with the non-breast cancer risk allele as the referent) and 95% confidence intervals between TDLU measures and each SNP. All statistical tests were two-sided; P < 0.05 was considered statistically significant. Overall, 36 SNPs (58.1%) were related to higher TDLU counts although this was not statistically significant (p = 0.25). Six of the 62 SNPs (9.7%) were nominally associated with at least one TDLU measure: rs616488 (PEX14), rs11242675 (FOXQ1) and rs6001930 (MKL1) were associated with higher TDLU count (p = 0.047, 0.045 and 0.031, respectively); rs1353747 (PDE4D) and rs6472903 (8q21.11) were associated with higher acini count per TDLU (p = 0.007 and 0.027, respectively); and rs1353747 (PDE4D) and rs204247 (RANBP9) were associated with the product of TDLU and acini counts (p = 0.024 and 0.017, respectively). Our findings suggest breast cancer SNPs may not strongly influence TDLU involution. Agnostic genome-wide association studies of TDLU involution may provide new insights on its biologic underpinnings and breast cancer susceptibility.

Genomic characterization of viral integration sites in HPV-related cancers

Persistent infection with carcinogenic human papillomaviruses (HPV) causes the majority of anogenital cancers and a subset of head and neck cancers. The HPV genome is frequently found integrated into the host genome of invasive cancers. The mechanisms of how it may promote disease progression are not well understood. Thoroughly characterizing integration events can provide insights into HPV carcinogenesis. Individual studies have reported limited number of integration sites in cell lines and human samples. We performed a systematic review of published integration sites in HPV-related cancers and conducted a pooled analysis to formally test for integration hotspots and genomic features enriched in integration events using data from the Encyclopedia of DNA Elements (ENCODE). Over 1,500 integration sites were reported in the literature, of which 90.8% (N = 1,407) were in human tissues. We found 10 cytobands enriched for integration events, three previously reported ones (3q28, 8q24.21 and 13q22.1) and seven additional ones (2q22.3, 3p14.2, 8q24.22, 14q24.1, 17p11.1, 17q23.1 and 17q23.2). Cervical infections with HPV18 were more likely to have breakpoints in 8q24.21 (p = 7.68 × 10(-4) ) than those with HPV16. Overall, integration sites were more likely to be in gene regions than expected by chance (p = 6.93 × 10(-9) ). They were also significantly closer to CpG regions, fragile sites, transcriptionally active regions and enhancers. Few integration events occurred within 50 Kb of known cervical cancer driver genes. This suggests that HPV integrates in accessible regions of the genome, preferentially genes and enhancers, which may affect the expression of target genes.

Ages at menarche- and menopause-related genetic variants in relation to terminal duct lobular unit involution in normal breast tissue

Reduced levels of terminal duct lobular unit (TDLU) involution, as reflected by higher numbers of TDLUs and acini per TDLU, have been associated with higher breast cancer risk. Younger age at menarche and older age at menopause have been previously related to lower levels of TDLU involution. To determine a possible genetic link, we examined whether single-nucleotide polymorphisms (SNPs) previously established in genome-wide association studies (GWAS) for ages at menarche and menopause are associated with TDLU involution. We conducted a pooled analysis of 862 women from two studies. H&E tissue sections were assessed for numbers of TDLUs and acini/TDLU. Poisson regression models were used to estimate associations of 36 menarche- and 21 menopause-SNPs with TDLU counts, acini counts/TDLU, and the product of these two measures, adjusting for age and study site. Fourteen percent of evaluated SNPs (eight SNPs) were associated with TDLU counts at p < 0.05, suggesting an enrichment of associations with TDLU counts. However, only menopause-SNPs had >50 % that were either significantly or nonsignificantly associated with TDLU measures in the directions consistent with their relationships shown in GWAS. Among ten SNPs that were statistically significantly associated with at least one TDLU involution measure (p < 0.05), seven SNPs (rs466639: RXRG; rs2243803: SLC14A2; rs2292573: GAB2; rs6438424: 3q13.32; rs7606918: METAP1D; rs11668344: TMEM150B; rs1635501: EXO1) were associated in the consistent directions. Our data suggest that the loci associated with ages at menarche and menopause may influence TDLU involution, suggesting some shared genetic mechanisms. However, larger studies are needed to confirm the results.

Abstract B41: Methylation profiling of ovarian cancer to study etiologic and prognostic heterogeneity and to develop a molecular classifier

Background: Ovarian cancer is a heterogeneous disease that is divisible into multiple subtypes with variable pathogenesis, etiology and biological behavior. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes and prognosis. Additionally, we developed a molecular classifier in relation to standard histologic subtype for classification of ovarian tumors in epidemiologic studies.

Methods: A total of 180 paraffin embedded ovarian epithelial tumor tissues, including the four major epithelial ovarian tumor subtypes (serous, endometrioid, mucinous and clear cell) and tumors of low malignant potential (LMP) were selected from two different sources: The Polish Ovarian Cancer study, an incident population-based case-control study conducted from 2001-2004, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR), which included ovarian tumors blocks collected between 1994 and 2004 from the Iowa and Hawaii SEER registries. The distributions of tumor histologic subtypes and grades from the studies were similar. All analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. Analyses were restricted to the 22 autosomal chromosomes and non-SNP probes. Fourteen samples did not pass quality control and were excluded from the analysis. Of the 166 evaluable samples, 29 cases (17.5%) had their histologic subtype recoded after expert review. In order to compute and validate our histological signatures, the samples were divided into a training set (N=110) and a validation set (N=56). In addition, 10 high grade serous cases with 450K methylation data from the ovarian TCGA effort were included for replication. Signatures were computed using a LASSO logistic regression.

Results: Among 166 samples, 32 (19%) were from the Polish study and 134 (81%) were from the SEER RTR. Unsupervised hierarchical clustering of the 5,000 most variable CpG sites showed 4 major clusters: Cluster 1 with 79% invasive serous and 14% endometrioid carcinomas, including the majority of high grade carcinomas; cluster 2 with 77% either endometrioid or clear cell carcinomas; cluster 3 with 71% serous LMP; and cluster 4 with 73% mucinous carcinomas. We observed significant survival differences across these clusters (long-rank test P= 4.64×10-6), similar to differences observed for histologic subtypes. We used the training set to determine a parsimonious classifier based on methylation markers for histologic subtypes. We applied these signatures to an independent validation set from the Polish Study, SEER RTR, and the ovarian TCGA and found that 77% of the samples were correctly classified. Among the cases for which the histology was recoded after expert review, the methylation signatures correctly classified the histology subtype in 76% of the cases.

Conclusions: Unsupervised analysis of DNA methylation profiling identified 4 distinct clusters of ovarian carcinomas, consistent with data indicating that ovarian cancer is heterogeneous with respect to cells of origin, carcinogenic pathways and histology. High grade serous carcinomas were grouped with high grade endometrioid cancers, while the remaining endometrioid carcinomas clustered with clear cell carcinomas, consistent with a common origin for a subset of these tumors from orthotopic or ectopic endometrial tissue. Our results suggest that methylation signatures provide a classification of ovarian tumors that overlaps with histologic subtypes and probable mechanisms of origin. Ongoing analyses will compare performance of the methylation classifier with histologic subtype in relation to risk factors and prognosis.

Citation Format: Clara Bodelon, Keith Killian, Joshua Sampson, Holly Stevenson, William Anderson, Rayna Matsuno, Louise Brinton, Jolanta Lissowska, Mark Sherman, Nicolas Wentzensen. Methylation profiling of ovarian cancer to study etiologic and prognostic heterogeneity and to develop a molecular classifier. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B41.

Leukocyte telomere length and its association with mammographic density and proliferative diagnosis among women undergoing diagnostic image-guided breast biopsy

Background

Elevated mammographic density (MD) is a strong breast cancer risk factor but the mechanisms underlying the association are poorly understood. High MD and breast cancer risk may reflect cumulative exposures to factors that promote epithelial cell division. One marker of cellular replicative history is telomere length, but its association with MD is unknown. We investigated the relation of telomere length, a marker of cellular replicative history, with MD and biopsy diagnosis.

Methods

One hundred and ninety-five women, ages 40–65, were clinically referred for image-guided breast biopsies at an academic facility in Vermont. Relative peripheral blood leukocyte telomere length (LTL) was measured using quantitative polymerase chain reaction. MD volume was quantified in cranio-caudal views of the breast contralateral to the primary diagnosis in digital mammograms using a breast density phantom, while MD area (cm²) was measured using thresholding software. Associations between log-transformed LTL and continuous MD measurements (volume and area) were evaluated using linear regression models adjusted for age and body mass index. Analyses were stratified by biopsy diagnosis: proliferative (hyperplasia, in-situ or invasive carcinoma) or non-proliferative (benign or other non-proliferative benign diagnoses).

Results

Mean relative LTL in women with proliferative disease (n = 141) was 1.6 (SD = 0.9) vs. 1.2 (SD = 0.6) in those with non-proliferative diagnoses (n = 54) (P = 0.002). Mean percent MD volume did not differ by diagnosis (P = 0.69). LTL was not associated with MD in women with proliferative (P = 0.89) or non-proliferative (P = 0.48) diagnoses. However, LTL was associated with a significant increased risk of proliferative diagnosis (adjusted OR = 2.46, 95 % CI: 1.47, 4.42).

Conclusions

Our analysis of LTL did not find an association with MD. However, our findings suggest that LTL may be a marker of risk for proliferative pathology among women referred for biopsy based on breast imaging.

p16/Ki-67 Dual Stain Cytology for Detection of Cervical Precancer in HPV-Positive Women

BACKGROUND

Human papillomavirus (HPV)-based cervical cancer screening requires triage markers to decide who should be referred to colposcopy. p16/Ki-67 dual stain cytology has been proposed as a biomarker for cervical precancers. We evaluated the dual stain in a large population of HPV-positive women.

METHODS

One thousand five hundred and nine HPV-positive women screened with HPV/cytology cotesting at Kaiser Permanente California were enrolled into a prospective observational study in 2012. Dual stain cytology was performed on residual Surepath material, and slides were evaluated for dual stain-positive cells. Disease endpoints were ascertained from the clinical database at KPNC. We evaluated the clinical performance of the assay among all HPV-positive women and among HPV-positive, cytology-negative women. We used internal benchmarks for clinical management to evaluate the clinical relevance of the dual stain assay. We evaluated sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the dual stain compared with Pap cytology. All statistical tests were two-sided.

RESULTS

The dual stain had lower positivity (45.9%) compared with cytology at an ASC-US threshold (53.4%). For detection of CIN2+, the dual stain had similar sensitivity (83.4% vs 76.6%, P = .1), and statistically higher specificity (58.9% vs 49.6%, P < .001), PPV (21.0% vs 16.6%, P < .001), and NPV (96.4% vs 94.2%, P = .01) compared with cytology. Similar patterns were observed for CIN3+. Women with a positive test had high enough risk for referral to colposcopy, while the risk for women with negative tests was below a one-year return threshold based on current US management guidelines.

CONCLUSION

Dual stain cytology showed good risk stratification for all HPV-positive women and for HPV-positive women with normal cytology. Additional follow-up is needed to determine how long dual stain negative women remain at low risk of precancer.

Abstract 3700: Incidence trends of breast, endometrial, and ovarian cancer among US women in relation to changing patterns of menopausal hormone therapy

Background: Menopausal hormone therapy (MHT) increases risk of breast, endometrial, and ovarian cancer. Following the Women's Health Initiative (WHI) report in 2002 linking MHT to increased breast cancer risk, both MHT use and breast cancer rates declined sharply in the US. Subsequently, we reported an accelerated decline in ovarian cancer rates after 2002 using age-period-cohort (APC) modeling to estimate period changes independent of age and birth cohort effects. Given links between MHT and risks for breast, ovarian and endometrial cancer, we compared changes in rates of these tumors following the WHI announcement in 2002 by applying a comparative APC modeling approach.

Methods: Using the North American Association of Central Cancer Registries (NAACCR) database (1995-2010), we created three analytic files for women ages 50 to 84 years (surrogate for menopause): breast (ICD-0-3 codes C500-509; n = 1,597,409), endometrial (C540-549, C559; 340,498), and ovarian (C569; 174,755) cancers. We applied standard (SEER*STAT, joinpoint regression) and APC models to estimate cancer incidence rate changes pre- (1995-2002) and post- (2003-2010) WHI report, to assess temporal changes associated with the decline in MHT prescriptions.

Results: Although age-standardized breast cancer incidence was heterogeneous before and after WHI-report, APC models demonstrated a decline in rates after 2002. Age-standardized endometrial cancer rates declined 0.82%/year (95% CI: -1.44 to -0.19%/year) pre-WHI, after which the rates increased 1.03%/year (95% CI: 0.59 to 1.47%/year). APC models confirmed the increase for endometrial cancer post-WHI. Age-standardized ovarian cancer incidence declined 1.02%/year (95% CI: -1.55 to -0.48%/year) pre-WHI, after which the rates declined 2.36%/year (95% CI: -3.00 to -1.70%/year). APC models showed an accelerated decline in ovarian cancer incidence post-WHI.

Conclusion: Following a marked reduction in MHT use circa 2002, incidence rate trends changed somewhat differently for breast, endometrial and ovarian cancer. Specifically, rising breast cancer rates fell, decreasing endometrial cancer rates increased, and decreasing ovarian cancer rates fell more rapidly. Further analysis by age, race and histological subtype may provide insights into complex etiological differences between these hormone-related tumors.

Citation Format: Hannah P. Yang, William F. Anderson, Britton Trabert, Philip S. Rosenberg, Gretchen L. Gierach, Clara Bodelon, Nicolas Wentzensen, Kathleen A. Cronin, Mark E. Sherman. Incidence trends of breast, endometrial, and ovarian cancer among US women in relation to changing patterns of menopausal hormone therapy. [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 3700. doi:10.1158/1538-7445.AM2015-3700

Abstract 5580: Characterization of HPV integration sites in the human genome

Background. Persistent infection with carcinogenic human papillomaviruses (HPV) is known to be cause of the majority of anogenital cancers as well as some head and neck cancers. With the progression of the disease, the HPV genome is commonly integrated within the host DNA, although the mechanism by which integration may promote the progression of the disease is not well-understood. We performed a systematic review of integration events in HPV-related cancers and analyzed the genomic regions where these events occur.

Methods. A PubMed search was performed to collect all published data on integration loci. A total of 29 articles were eligible for the analysis. Determination of genomic integration sites for papers that provided exact nucleotide sequences of integration sites or viral fusion regions was done by using the Basic Local Alignment Search Tool (BLAST, http://blast.ncbi.nlm.nih.gov/Blast.cgi) for the GRCh37/hg19 build. We used the Encyclopedia of DNA Elements (ENCODE) data to investigate if certain genetic features clustered with integrations sites. The Wilcoxon rank sum test was computed to compare the observed and expected distributions of minimal distances from the integration sites with known nucleotide positions to the different genetic features.

Results. As of November 2014, approximately 1,200 integration events were reported in the literature from both tumors and cell lines. The majority of integrations sites (53%) were reported in cervical tumors, 9% in head and neck tumors, 4% of oropharyngeal tumors and 23% in cell lines,. Six percent and 2% of the integration sites were found in high-grade and low-grade cervical lesions, respectively. The majority of reported integration events (77%) were related to HPV16. We found that integration sites from tumors were closer to known genes (p &lt;10−14) and CpG islands (p &lt;10−9) than expected by chance. Among repetitive elements, long terminal repeats (LTR) were enriched in integration sites (P = 0.001). Open chromatin based on the FAIRE-seq peaks showed significant enrichment in integration sites (p &lt;10−11).

Conclusions. In summary, integration sites occur in genomic regions with enrichment for genetic elements, such as gene-rich regions, CpG sites, repetitive elements and open chromatin regions. This corroborates that accessible regions of the genome are preferentially targeted by integration and suggests that host genes may be functionally altered in development of HPV-related cancers.

Citation Format: Clara Bodelon, Micahel Untereiner, Svetlana Vinokurova, Mitchell J. Machiela, Nicolas Wentzensen. Characterization of HPV integration sites in the human genome. [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 5580. doi:10.1158/1538-7445.AM2015-5580

Analysis of serial ovarian volume measurements and incidence of ovarian cancer: implications for pathogenesis

BACKGROUND

Accumulating evidence suggests that many ovarian cancers represent metastases from occult fallopian tube carcinomas or tumors arising within ovarian endometriosis. We hypothesized that small ovarian volumes, as reflected in nonvisualization by transvaginal ultrasound (TVU), would be a marker of lower ovarian cancer risk, whereas enlargement on serial examinations would indicate higher risk.

METHODS

To address these hypotheses, we analyzed serial ovarian volume measurements determined by TVU for 29321 women (102787 scans) performed in the ovarian cancer screening arm of the Prostate, Lung, Colorectal, and Ovarian (PLCO) trial. Cox models were used to compute hazard ratios (HRs) and 95% confidence intervals (CIs) as measures of association between TVU results and ovarian cancer. We assessed whether increasing ovarian volume preceded diagnosis of ovarian cancer in a nested case-control analysis comparing case patients and control patients matched on age, center, and screening year (1:4 ratio). All statistical tests were two-sided.

RESULTS

Visualization of normal-appearing ovaries at the last TVU scan was associated with marginally higher ovarian cancer risk compared with nonvisualization of the ovaries (HR = 1.42, 95% CI = 1.00 to 2.01). Ovarian volume increased statistically significantly in ovarian cancer case patients one to two years before diagnosis (P < .001), but not in matched control patients.

CONCLUSION

Our analysis of TVU data suggests that increasing ovarian volume is associated with greater ovarian cancer risk, but it is only detectable one to two years before diagnosis.

Common sequence variants in chemokine-related genes and risk of breast cancer in post-menopausal women

Chemokines are small molecules that when secreted by tissues under pathological conditions such as inflammation are believed to be involved in carcinogenesis. Recent reports have found that the genetic variation in chemokine encoding genes are associated with risk of breast cancer.

METHODS

Using data from a population-based case-control study of 845 invasive breast cases and 807 controls, we genotyped 34 single nucleotide polymorphisms (SNPs) in 8 chemokine candidate genes (CCL3, CCL4, CCL5, CCL20, CCR5, CCR6, CXCL12 and CXCR4). Associations with breast cancer were computed for individual SNPs, groups of SNPs within genes, and in a gene-set analysis. We also performed a meta-analysis of CXCL12 rs1801157 and a haplotype analysis for two SNPs: CXCR4 rs2228014 and CXCL12 rs1801157.

RESULTS

We found no significant associations between the risk of breast cancer and any individual SNPs, single genes, or combined gene sets. Some individual variants were marginally associated with some histologic subtypes, but these associations were not significant after adjustment for multiple comparisons. In the meta-analysis of five studies of European ancestry, CXCL12 rs1801157 was marginally associated with breast cancer risk (OR=1.14, 95% CI: 1.00, 1.30).

CONCLUSIONS

Our findings suggest that genetic variants in the 8 candidate genes coding for chemotactic cytokines have little influence in the risk of breast cancer in postmenopausal women. Additional examination of the relationship between CXCL12 rs1801157 and breast cancer risk is warranted.

Genetic variation in the TLR and NF-κB pathways and cervical and vulvar cancer risk: a population-based case-control study

Genital infection with the oncogenic human papillomavirus is the necessary cause of cervical cancer and of a large fraction of vulvar cancers. The toll-like receptor and the nuclear factor κB (NF-κB) signaling pathways have been implicated in inflammation, autoimmune disease and cancer, but whether common nucleotide variation in these pathways is associated with the risk of cervical and vulvar cancers has received little study. Using data from a population-based case-control study of cervical and vulvar cancers, we genotyped 205 single nucleotide polymorphisms (SNPs) in and around 32 candidate gene regions within these pathways. Gene-based analyses were used to estimate the associations between individual gene regions and the risk of cervical and vulvar cancers. Odds ratio (OR) and 95% confidence intervals (CI) were calculated to assess the risk of cervical and vulvar cancers for each SNP. p-Values were adjusted for multiple testing. A total of 876 cervical cancer cases, 517 vulvar cancer cases and 1,100 controls were included in the analysis. The TNF region was significantly associated with the risks of cervical cancer (gene-based p-value: 2.0 × 10(-4) ) and vulvar cancer (gene-based p-value: 1.0 × 10(-4) ). The rare allele (A) of SNP rs2239704 in the 5' UTR of the LTA gene was significantly associated with increased risks of cervical cancer (OR=1.31, 95% CI: 1.15-1.50; adjusted p-value: 0.013) and vulvar cancer (OR=1.51, 95% CI: 1.30-1.75; adjusted p-value: 1.9 × 10(-5) ). These findings add to the evidence of the importance of the immune system in the etiology of cervical and vulvar cancers.

Circulating levels of immune and inflammatory markers and long versus short survival in early-stage lung cancer

BACKGROUND

Some patients diagnosed with early-stage lung cancer and treated according to standard care survive for only a short period of time, while others survive for years for reasons that are not well understood. Associations between markers of inflammation and survival from lung cancer have been observed.

MATERIALS AND METHODS

Here, we investigate whether circulating levels of 77 inflammatory markers are associated with long versus short survival in stage I and II lung cancer. Patients who had survived either <79 weeks (~1.5 years) (short survivors, SS) or >156 weeks (3 years) (long survivors, LS) were selected from a retrospective population-based study. Logistic regression was used to calculate adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs). The false discovery rate was calculated to adjust for multiple testing.

RESULTS

A total of 157 LS and 84 SS were included in this analysis. Thirteen markers had adjusted OR on the order of 2- to 5-fold when comparing the upper and lower quartiles with regard to the odds of short survival versus long. Chemokine CCL15 [chemokine (C-C motif) ligand 15] was the most significant marker associated with increased odds of short survival (ORs = 4.93; 95% CI 1.90-12.8; q-value: 0.042). Smoking and chronic obstructive pulmonary disease were not associated with marker levels.

CONCLUSIONS

Our results provide some evidence that deregulation of inflammatory responses may play a role in the survival of early-stage lung cancer. These findings will require confirmation in future studies.

Abstract 150: Ovarian visualization in transvaginal ultrasound scans and risk of ovarian cancer

Background. Ovarian cancer is typically diagnosed at an advanced stage, resulting in poor survival. Detection of ovarian cancer at an early curable stage could reduce mortality; however, annual screening with transvaginal ultrasound (TVU) and CA-125 serum levels using predetermined cutpoints did not lower mortality in the Prostate, Lung, Colorectal and Ovarian (PLCO) trial. In this trial, approximately 40% of TVU scans resulted in non-visualization of the ovaries. Currently, TVU studies consider non-visualization of the ovaries as having normal ovaries, even though this may confer risk information. Accordingly, we assessed risk of ovarian cancer among women with non-visualization of the ovaries by TVU in the PLCO trial.

Methods. Study participants were women from the ovarian screening arm of the PLCO trial. Briefly, women aged 55-74 years were recruited at ten US clinical centers between 1993 and 2001. Those with a previous diagnosis of ovarian cancer were excluded from enrollment. Subjects with at least one ovary underwent a TVU at baseline and annually for 3 additional years and were followed-up for up to 13 years. Individuals were excluded from the current analysis if they did not complete the baseline questionnaire or did not have at least one adequate screening (i.e., visualization of the iliac vessels). Ovaries were considered not visualized if they were not seen after a search of at least 5 minutes. Associations between participant characteristics and ovarian visualization were estimated using logistic regression models adjusted for age and calendar year. Hazard ratios (HR) and 95% confidence intervals (CI) were computed to estimate the risk of ovarian cancer with TVU visualization using Cox proportional hazard models. Age was the time metric and models were adjusted for calendar year, body mass index (BMI), race, parity and oral contraceptive (OC) use.

Results. Our analysis included 29,329 women, with 98.6% of them having two or more TVUs. Two hundred and five women were diagnosed with invasive ovarian cancer during follow-up. Lack of visualization of the ovaries by TVU was associated with older age, non-White race, greater BMI, ever use of OC and ever having children. However, ovarian visualization was not associated with risk of ovarian cancer (HR=1.17; 95% CI: 0.86-1.59). Moreover, women with visualized ovaries but negative TVUs were not at elevated ovarian cancer risk compared to women with non-visualized ovaries (HR=1.06; 95% CI: 0.77-1.45).

Conclusions. Women with non-visualization of the ovaries by TVU and those with visualization and a negative result do not have a different risk of ovarian cancer, suggesting that data for these women may be combined. Ongoing analysis will examine serial measurements of ovarian volume by TVU and ovarian cancer risk.

Citation Format: Clara Bodelon, Amanda Black, Ruth M. Pfeiffer, Mark E. Sherman. Ovarian visualization in transvaginal ultrasound scans and risk of ovarian cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 150. doi:10.1158/1538-7445.AM2013-150

On the interplay of telomeres, nevi and the risk of melanoma

The relationship between telomeres, nevi and melanoma is complex. Shorter telomeres have been found to be associated with many cancers and with number of nevi, a known risk factor for melanoma. However, shorter telomeres have also been found to decrease melanoma risk. We performed a systematic analysis of telomere-related genes and tagSNPs within these genes, in relation to the risk of melanoma, dysplastic nevi, and nevus count combining data from four studies conducted in Italy. In addition, we examined whether telomere length measured in peripheral blood leukocytes is related to the risk of melanoma, dysplastic nevi, number of nevi, or telomere-related SNPs. A total of 796 cases and 770 controls were genotyped for 517 SNPs in 39 telomere-related genes genotyped with a custom-made array. Replication of the top SNPs was conducted in two American populations consisting of 488 subjects from 53 melanoma-prone families and 1,086 cases and 1,024 controls from a case-control study. We estimated odds ratios for associations with SNPs and combined SNP P-values to compute gene region-specific, functional group-specific, and overall P-value using an adaptive rank-truncated product algorithm. In the Mediterranean population, we found suggestive evidence that RECQL4, a gene involved in genome stability, RTEL1, a gene regulating telomere elongation, and TERF2, a gene implicated in the protection of telomeres, were associated with melanoma, the presence of dysplastic nevi and number of nevi, respectively. However, these associations were not found in the American samples, suggesting variable melanoma susceptibility for these genes across populations or chance findings in our discovery sample. Larger studies across different populations are necessary to clarify these associations.

Sun exposure and risk of epithelial ovarian cancer

PURPOSE

Associations between sun exposure (a primary source of vitamin D) and risk of ovarian cancer have been inconsistent. Furthermore, studies have not investigated whether sun exposure at different periods in the lifetime of a person results in differences in risk associations, and little is known about differences according to histological subtype.

METHODS

Using a population-based case-control study of 1,334 non-Hispanic white women diagnosed with epithelial ovarian cancer in western Washington State between 2002 and 2009 and 1,679 non-Hispanic white controls, we assessed the relation of epithelial ovarian cancer with constitutional pigmentation characteristics, sun exposure behaviors, and an index of ultraviolet (UV) exposure based on residential history. Information was collected through in-person interviews. Logistic regression was used to compute odds ratios, 95 % confidence intervals, and trend p values (P(trend)).

RESULTS

We noted no association with residence-based measures of UV exposure or self-reported sun exposure, either over the lifetime or within specific age intervals. Also, we observed little evidence of association between constitutional pigmentation characteristics and risk, save for a suggestion of increased risk among women who reported increased ability to suntan upon prolonged sun exposure (P(trend) = 0.03).

CONCLUSIONS

Results from this study suggest that sun exposure has little influence on the risk of epithelial ovarian cancer. Additional studies in populations with a wider gradient of sun exposure may yet be warranted.