Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants

The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.

Image analysis with deep learning to predict breast cancer grade, ER status, histologic subtype, and intrinsic subtype

RNA-based, multi-gene molecular assays are available and widely used for patients with ER-positive/HER2-negative breast cancers. However, RNA-based genomic tests can be costly and are not available in many countries. Methods for inferring molecular subtype from histologic images may identify patients most likely to benefit from further genomic testing. To identify patients who could benefit from molecular testing based on H&E stained histologic images, we developed an image analysis approach using deep learning. A training set of 571 breast tumors was used to create image-based classifiers for tumor grade, ER status, PAM50 intrinsic subtype, histologic subtype, and risk of recurrence score (ROR-PT). The resulting classifiers were applied to an independent test set (n = 288), and accuracy, sensitivity, and specificity of each was assessed on the test set. Histologic image analysis with deep learning distinguished low-intermediate vs. high tumor grade (82% accuracy), ER status (84% accuracy), Basal-like vs. non-Basal-like (77% accuracy), Ductal vs. Lobular (94% accuracy), and high vs. low-medium ROR-PT score (75% accuracy). Sampling considerations in the training set minimized bias in the test set. Incorrect classification of ER status was significantly more common for Luminal B tumors. These data provide proof of principle that molecular marker status, including a critical clinical biomarker (i.e., ER status), can be predicted with accuracy >75% based on H&E features. Image-based methods could be promising for identifying patients with a greater need for further genomic testing, or in place of classically scored variables typically accomplished using human-based scoring.

TP53 protein levels, RNA-based pathway assessment, and race among invasive breast cancer cases

Mutations in tumor suppressor TP53 have been inconsistently linked to breast cancer risk factors and survival. Immunohistochemistry (IHC) staining, a primary clinical means of TP53 mutation determination, only detects mutations that facilitate protein accumulation (e.g., missense mutations). RNA-based pathway methods capture functional status and may aid in understanding the role of TP53 function in racial disparities of breast cancer. TP53 status was assessed among invasive breast cancer cases from the Carolina Breast Cancer Study (CBCS) (2008–2013) using IHC and an established RNA-based TP53 signature (CBCS and The Cancer Genome Atlas (TCGA)). Frequency of TP53 status (IHC, RNA-based) was estimated in association with tumor characteristics, PAM50 intrinsic subtype, age, and race using relative frequency differences (RFDs) and 95% confidence intervals (95% CI) as the measure of association. Approximately 60% of basal-like tumors were TP53 protein positive (IHC), while nearly 100% were TP53 mutant-like (RNA). Luminal A tumors had low frequency of TP53 positivity (IHC: 7.9%) and mutant-like status (RNA: 1.7%). Mutant-like TP53 (RNA) was strongly associated with age ≤50 years, high tumor grade, advanced stage of disease, large tumor size, and basal-like and HER2 intrinsic subtypes. Black race was strongly associated with TP53 mutant-like status (RNA) (RFD: 24.8%, 95% CI: 20.5, 29.0) even after adjusting for age, grade, stage (RFD: 11.3%; 95% CI: 7.6, 15.0). Associations were attenuated and non-significant when measured by IHC. IHC-based TP53 status is an insensitive measurement of TP53 functional status. RNA-based methods suggest a role for TP53 in tumor prognostic features and racial disparities.

RNA-based assays offer a more sensitive and clinically informative measure of mutations in the tumor suppressor TP53 among women with invasive breast cancer than do immunohistochemistry techniques that can only detect altered proteins. Using tumor samples from more than 1000 women enrolled in the Carolina Breast Cancer Study (CBCS), Melissa Troester from the University of North Carolina at Chapel Hill, USA, and coworkers assessed the functional status of TP53 via both classical immunohistochemistry methods and an RNA-based test of expression levels among 52 TP53-dependent genes. The results of the RNA analysis were strongly associated with younger age-of-onset, higher grade tumors, more advanced stage disease, larger tumor size, aggressive cancer subtypes and race—with more black women harboring TP53 mutant-like tumors than white women. By comparison, these associations were weaker or non-significant when using immunohistochemistry-based tests.

Age/race differences in HER2 testing and in incidence rates for breast cancer triple subtypes: a population-based study and first report

BACKGROUND

Although US year 2000 guidelines recommended characterizing breast cancers by human epidermal growth factor receptor 2 (HER2), national cancer registries do not collect HER2, rendering a population-based understanding of HER2 and clinical "triple subtypes" (estrogen receptor [ER] / progesterone receptor [PR] / HER2) largely unknown. We document the population-based prevalence of HER2 testing / status, triple subtypes and present the first report of subtype incidence rates.

METHODS

Medical records were searched for HER2 on 1842 metropolitan Atlanta females diagnosed with breast cancer during 2003-2004. HER2 testing/status and triple subtypes were analyzed by age, race/ethnicity, tumor factors, socioeconomic status, and treatment. Age-adjusted incidence rates were calculated.

RESULTS

Over 90% of cases received HER2 testing: 12.6% were positive, 71.7% negative, and 15.7% unknown. HER2 testing compliance was significantly better for women who were younger, of Caucasian or African-American descent, or diagnosed with early stage disease. Incidence rates (per 100,000) were 21.1 for HER2+ tumors and 27.8 for triple-negative tumors, the latter differing by race (36.3 and 19.4 for black and white women, respectively).

CONCLUSIONS

HER2 recommendations are not uniformly adhered to. Incidence rates for breast cancer triple subtypes differ by age/race. As biologic knowledge is translated into the clinical setting eg, HER2 as a biomarker, it will be incumbent upon national cancer registries to report this information. Incidence rates cautiously extrapolate to an annual burden of 3000 and 17,000 HER2+ tumors for black and white women, respectively, and triple-negative tumors among 5000 and 16,000 respectively. Testing, rate, and burden variations warrant population-based in-depth exploration and clinical translation.

Triple negative breast cancer confers higher recurrence rates after breast conserving therapy

Abstract #5127

Purpose
 There has been a recent surge of information regarding the treatment outcomes for women with estrogen receptor (ER) negative, progesterone receptor (PR) negative, and human epidermal growth factor receptor 2 (HER2) negative breast cancer; known as the triple negative (TN) subtype. The purpose of this study is to evaluate the impact of these receptor expressions on local, regional and distant recurrences, and overall survival (OS) in patients undergoing breast conserving therapy (BCT).
 Patients and Methods
 The study population included 475 primary invasive female breast cancer patients (excluding Stage IV); who were residents of Fulton-Dekalb counties in Atlanta when diagnosed in 2003-2004 and treated within the Emory University affiliated hospitals. Data was obtained from the SEER cancer registry and augmented with medical record abstraction. Median follow-up was 3.4 years. The endpoints of the study were local, regional and distant recurrences, and OS. Tumors were subgrouped as: ER-/PR-/HER2- (TN), ER+/PR+/HER2-, ER+/PR+/HER2+, ER+/PR+/HER2-. Chi-square and Fisher exact tests were employed.
 Results
 For the entire population, median age was 58 years. TN tumors accounted for 17% of the cases. Of the TN patients, 78% were African-American (p<0.01) and 40% had BCT. The majority of TN tumors were high grade (71%), p< 0.01. Total recurrence was 33% among the TN patients vs. 14% in the combined non-TN patient group, p< 0.01. Death occurred among 29% of TN vs. 14% of non-TN, p< 0.01.
 For the patients that were treated with BCT, 94% of TN patients completed their adjuvant radiation therapy and 73% received chemotherapy. Of those receiving BCT, recurrence was 28% for TN patients and 6% for non-TN patients (p<0.01). Local recurrence was 9% and 4% for TN and non-TN patients, respectively and distant metastatic rate was 16% versus 2% respectively (p< 0.01). There were no regional recurrences in the BCT group. Time to recurrence, OS, time to death, and breast cancer specific death did not differ between the two groups.
 Conclusion
 A significant increase in local recurrence and distant metastatic rates were observed after BCT among patients diagnosed with TN breast cancers; however there was not a significant short-term survival difference between the TN and non-TN receptor groups. The complexity of this patient population within the conventional treatment algorithm warrants further investigation to reduce local and distant recurrences.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5127.

High prevalence of triple-negative tumors in an urban cancer center

BACKGROUND

A disparate proportion of breast cancer deaths occur among young women, those of African-American (AA) ancestry, and particularly young AA women. Estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor-2 (HER-2) are key clinically informative biomarkers. The triple-negative (ER-/PR-/HER-2-) tumor subgroup is intrinsically resistant to treatment and portends a poor prognosis. Age, race, and socioeconomic status have been associated with triple-negative tumors (TNT). In the current study, the authors investigated breast cancer subgroups among patients in an urban cancer center serving a multiracial, low socioeconomic population.

METHODS

This case series analyzed female invasive breast cancers diagnosed and/or treated between 2003 and 2004 in the AVON Comprehensive Breast Center at Grady Hospital in Atlanta, Georgia. Data were obtained from the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program, and augmented by the hospital registry and pathology reports. Statistical analyses utilized frequency distributions and logistic regression.

RESULTS

Of 190 breast cancers; 167 (88%) were diagnosed among AA and 23 (12%) were diagnosed among non-AA women. The median age at diagnosis in the 2 groups was 58 years and 57 years, respectively. TNT prevalence was found to differ by race (29.3% among AA women and 13.0% among non-AA women; P = .010). Differences persisted after adjustment for age and stage (odds ratio [OR] of 3.1; 95%confidence interval [95% CI], 0.8-11.6). The majority of recurrences (40.0%) occurred among women with TNT, who were also most likely to experience a fatal event (OR of 3.7; 95%CI, 1.1-13.0).

CONCLUSIONS

Despite a similarity in their age at diagnosis, AA women in our urban cancer center presented with a higher prevalence of TNT and TNT was found to predict the poorest outcomes. Institutional interactive breast conferences and intervention/navigation programs could help to dispel breast cancer disparities and improve outcomes.

HEPES may stimulate cultured endothelial cells to make growth-retarding oxygen metabolites

Zwitterion buffers are often used to modulate the pH of cell culture medium but their effect on cultured cells is controversial. We found that addition of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) caused superoxide dismutase (SOD) inhibitable increases in nitroblue tetrazolium dye reduction and SOD and catalase inhibitable decreases in the growth of cultured bovine pulmonary artery endothelial cells. The findings suggest that HEPES stimulates endothelial cells to make toxic oxygen metabolites that contribute to decreased cell growth.

Hyperoxia damages cultured endothelial cells causing increased neutrophil adherence

Exposure of cultured bovine pulmonary artery endothelial cells to hyperoxia (95% O2) caused cellular injury manifested by decreased growth rates and release of cytoplasmic lactic dehydrogenase (LDH). In addition, a greater number of polymorphonuclear leukocytes (PMN) adhered to endothelial cells that had been exposed to hyperoxia for 24 or 48 h than to control endothelial cells that had been exposed to normoxia (15% O2). Direct endothelial cell injury from hyperoxia may contribute to vascular damage and the increased PMN accumulation seen in lungs of animals exposed to hyperoxia.