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.

Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients

Age-related DNA methylation is a potential mechanism contributing to breast cancer development. Studies of primarily Caucasian women have identified many CpG sites of age-related methylation in non-diseased breast tissue possibly driving cancer development over time. There is a paucity of studies involving Asian women whose ages at breast cancer onset are usually younger than Caucasians. We identified the 181 most consistent age-related methylation events in non-diseased breast tissue across published studies. Age-related methylation events were measured in adjacent normal and breast tumour tissue in an exclusively Asian population at the previously identified age-related methylation sites. Age-related methylation was found in 118 probes in adjacent normal breast tissue. Methylation of 99% of these sites was increased with age and predominantly located on CpG islands in promoter regions. To ascertain biological relevance to breast cancer, we focused on the 37 sites with overall higher methylation in tumour compared to adjacent normal samples. Some sites positively related to age, including AQP5 and CORO6, inversely correlated with gene expression. Several others have known involvement in suppression of carcinogenesis including GPC5 and SST, suggesting that perturbation of epigenetic regulation at these sites due to ageing may contribute to the progression of carcinogenesis. This study highlights an age-related methylation landscape in non-tumour tissue, consistent not just across studies, but also across different populations. We present candidate age-related methylation sites warranting further investigation as potential epigenetic drivers of breast cancer. They may serve as potential targets of site-specific demethylation intervention strategies for the prevention of age-related breast cancer.

Abstract 146: DNA methylation age of paired tumor-normal breast tissue in Chinese women with breast cancer

Background: Epigenetic age, captured by DNA methylation changes, is thought to be more informative with respect to disease risk and progression, than chronological age. A few studies have associated epigenetic age acceleration (EAA), the difference between DNA methylation age (DNAm age) and chronological age, with BC risk and subtypes. However, most of these studies were conducted in Western populations. In this study, we examined EAA in an Asian population, in which BC incidence rate is lower and age at BC onset is younger compared to most Western populations.

Methods: We performed genome-wide DNA methylation profiling of 97 tumor and 89 paired distant normal tissue samples collected from BC patients in Hong Kong (HK) using an Illumina MethylationEPIC array. Two independent datasets were used to compare results: The Cancer Genome Atlas (TCGA, n=525 tumor and n=88 adjacent normal) and healthy women from the Komen tissue bank (n=59). DNAm age was calculated using Horvath's model based on 353 CpGs. The significance of EAA was tested using a simple linear regression model. We also used a multivariate regression model to test for equality of slopes (EAA rates) among different BC subtypes or datasets, considering interaction terms between age and subtype/dataset.

Results: The average age at BC diagnosis was 58 years old (range: 33-81) and the distribution of the molecular subtype based on PAM50 was 43.0%, 29.1%, and 27.9% for luminal A, luminal B, and HER2-enriched/basal tumors, respectively. As expected, DNAm age showed a stronger correlation with chronological age in normal tissue (r=0.78, p&lt;.0001) than in tumor tissue (r=0.27, p=0.0075). The average EAAs in normal and tumor samples were 9.43 and 6.02 years, respectively. Among different BC subtypes, EAA in normal tissue did not vary by subtypes. However, in tumor samples, luminal patients showed positive EAA (average 10/13 years in luminal A/B, respectively), while HER2-enriched/basal patients showed a negative EAA (average -8 years), although the rate of EAA did not vary significantly by subtype. Analyses on TCGA data produced consistent results. When comparing the rate of DNAm acceleration in normal tissue of HK, TCGA, and Komen, HK patients had a significantly different rate (βHK=0.46) compared to TCGA (βTCGA=0.65, p=0.001) and Komen (βKomen=0.80, p&lt;.0001).

Conclusion: Consistent with previous studies, we found that EAA in tumor samples varied across tumor subtypes. We also found that HK BC patients' epigenetic age accelerated at a different rate compared to predominantly white TCGA and Komen women, suggesting a potential racial biological difference. Large studies in other Asian populations are warranted to confirm our findings, which may provide biological insight into racial heterogeneity of BC, especially with regard to age at onset.

Citation Format: Hela Koka, Bin Zhu, Shelly Lap Ah Tse, Difei Wang, Maeve Kiely, Jennifer Lyn Guida, Priscilla Lee, Feng Wang, Cherry Wu, Koon Ho Tsang, Wing-cheong Chan, Sze Hong Law, Eric Karlins, Bin Zhu, Amy Hutchinson, Belynda Hicks, Xiaohong R. Yang. DNA methylation age of paired tumor-normal breast tissue in Chinese women with breast cancer [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 146.

Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Background

Heterogeneity of immune gene expression patterns of luminal breast cancer (BC), which is clinically heterogeneous and overall considered as low immunogenic, has not been well studied especially in non-European populations. Here, we aimed at characterizing the immune gene expression profile of luminal BC in an Asian population and associating it with patient characteristics and tumor genomic features.

Methods

We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 luminal BC patients from Hong Kong using RNA-sequencing data and used unsupervised consensus clustering to stratify tumors. We then used luminal patients from The Cancer Genome Atlas (TCGA, N = 564) and a Korean breast cancer study (KBC, N = 112) as replication datasets.

Results

Based on the expression of 130 immune-related genes, luminal tumors were stratified into three distinct immune subtypes. Tumors in one subtype showed higher level of tumor-infiltrating lymphocytes (TILs), characterized by T cell gene activation, higher expression of immune checkpoint genes, higher nonsynonymous mutation burden, and higher APOBEC-signature mutations, compared with other luminal tumors. The high-TIL subtype was also associated with lower ESR1/ESR2 expression ratio and increasing body mass index. The comparison of the immune profile in tumor and matched normal tissue suggested a tumor-derived activation of specific immune responses, which was only seen in high-TIL patients. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in TCGA and KBC, although the pattern was more similar in Asian populations. The germline APOBEC3B deletion polymorphism, which is prevalent in East Asian populations and was previously linked to immune activation, was not associated with immune subtypes in our study. This result does not support the hypothesis that the germline APOBEC3B deletion polymorphism is the driving force for immune activation in breast tumors in Asian populations.

Conclusion

Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification and a subset of luminal BC patients may benefit from checkpoint immunotherapy, at least in Asian populations.

The safety and tolerability of adenosine as a pharmacological stressor in stress perfusion cardiac magnetic resonance imaging in the Chinese population

OBJECTIVE

To investigate the safety profile and effectiveness of adenosine as a pharmacological stressor in patients with known or suspected coronary artery disease who underwent cardiac magnetic resonance imaging perfusion study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

All patients who underwent adenosine stress cardiac magnetic resonance imaging from May 2013 to August 2013 were prospectively interviewed during the scan.

MAIN OUTCOME MEASURES

Common side-effects of adenosine as well as any other discomfort experienced during the scan were recorded. Haemodynamic changes including systolic and diastolic blood pressure and pulse rate before and during adenosine administration were also recorded.

RESULTS

There were 98 consecutive patients with a mean (± standard deviation) age of 64.0 ± 11.4 years (range, 10-83 years) and mean body weight of 67.5 ± 12.0 kg. Male-to-female ratio was 2.5:1. Of the 98 patients interviewed, 62 (63.3%) experienced one or more adenosine-associated adverse effects. Chest discomfort was most frequently experienced (48.0%), followed by dyspnoea (29.6%) and headache (20.4%). No life-threatening event occurred. Following adenosine administration, a significant rise in pulse rate (75.1 ± 14.3 vs 93.2 ± 14.7 beats/min; P<0.01) and a significant drop in diastolic blood pressure (75.1 ± 13.3 vs 68.0 ± 13.9 mm Hg; P<0.01) were noted. There was a general decrease in systolic blood pressure, although no statistically significant difference was observed (144.9 ± 17.6 vs 143.1 ± 21.4 mm Hg; P=0.18).

CONCLUSION

Adenosine stress cardiac magnetic resonance perfusion study is safe and well tolerated in clinical practice.

Fetal and maternal levels of lipid peroxides in term pregnancies

OBJECTIVE

To examine the relationships between maternal and fetal concentrations of lipid peroxides in term pregnancies before the onset of labor.

METHODS

Umbilical cord arterial and venous blood samples were collected from 114 singleton term pregnancies delivered by elective cesarean section. Base excess, oxygen, carbon dioxide and pH were measured in both samples and compared to identify double venous samples. Maternal venous and umbilical cord arterial and venous concentrations of organic hydroperoxides and malondialdehyde were assayed.

RESULTS

Maternal plasma malondialdehyde was, on average, double that of cord blood, whereas maternal organic hydroperoxide was only 18% higher. Maternal organic hydroperoxide was correlated with cord arterial and venous levels of organic hydroperoxide but not with pH, carbon dioxide, oxygen or base excess. Maternal malondialdehyde concentration was significantly correlated with both umbilical arterial and venous values of malondialdehyde and with arterial oxygen. Multiple regression shows that 70% of the variation in maternal malondialdehyde can be accounted for by variation in arterial and venous malondialdehyde, and arterial oxygen and base excess. A similar regression analysis with maternal organic hydroperoxide as dependant variable incorporated only umbilical arterial organic hydroperoxide concentration.

CONCLUSION

These findings suggest that there is significant trans-placental transport of malondialdehyde from the fetal circulation.

Comparison of cephalometric analysis using a non-radiographic sonic digitizer (DigiGraph Workstation) with conventional radiography

Cephalometric analysis conventionally requires radiographic exposure which may not be compatible with the growing concern over radiation hazards. Recently, the Dolphin Workstation Imaging System introduced to the dental profession a non-radiographic system, called the DigiGraph Workstation which may be an alternative to cephalometric radiography. The aims of this study were to compare the validity and reproducibility of cephalometric measurements obtained from the DigiGraph Workstation with conventional cephalometric radiographs. The sample consisted of 30 human dry skulls. Two replicated sets of lateral cephalograms were obtained with steel ball markers placed at the majority of the cephalometric landmarks. Duplicate tracings prepared from each radiograph were digitized to obtain cephalometric measurements using the computer software, Dentofacial Planner. For the DigiGraph Workstation, double sonic digitizations were repeated twice for each skull, on two occasions. Fifteen angular and one linear measurements were obtained from both methods and these findings compared using ANOVA, paired t-tests and F-tests. All, except one, cephalometric measurement showed significant differences between the two methods (P < 0.0001). The DigiGraph Workstation consistently produced higher values in 11 measurements (mean differences +0.5 to +15.7 degrees or mm) and lower values in four measurements (mean differences -0.2 to -3.5 degrees). The standard deviations of the differences between readings of both methods were large (0.4-5.8 degrees or mm). The reproducibility of the DigiGraph Workstation measurements was lower than that of the radiographic measurements. The method error of the DigiGraph Workstation ranged from 7 to 70 per cent, while that of radiographic tracings was less than 2 per cent. It was concluded that measurements obtained with the DigiGraph Workstation should be interpreted with caution.

Lipid peroxidation in cord blood at birth: the effect of labour

OBJECTIVE

To determine the effect of labour on free oxygen radical activity in the fetus, as reflected by lipid peroxide levels in umbilical cord arterial blood.

DESIGN

Prospective, observational study.

SETTING

Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong.

METHODS

Umbilical cord arterial and venous blood samples were collected from singleton term infants delivered by elective caesarean section. Base excess, PO2, pCO2 and pH were measured in both samples and compared to identify double venous samples. Cord arterial acid-base balance and concentrations of organic hydroperoxides and malondialdehyde were compared with those obtained from normal vaginal deliveries.

RESULTS

Cord arterial blood samples, obtained from cases of uncomplicated labour followed by spontaneous vaginal delivery, had significantly higher lipid peroxide concentrations than those delivered following elective caesarean section. This was most marked for malondialdehyde with a median value increased by 105%, whilst organic hydroperoxide was increased by only 27%. Of the acid-base parameters, base excess was increased by 78%, with only minimal changes in pH, pCO2 and PO2. These differences remained highly significant after including other pregnancy characteristics in multivariate analysis.

CONCLUSION

The findings indicate that high levels of free oxygen radical activity in the fetus are a function of the labour process, as are changes in acid-base balance.

Cholesterol alterations in young dystrophic mice

Cholesterol and cholesteryl ester concentrations and cholesteryl ester fatty acid substituents have been measured during the first 10 weeks of life in tissues of normal and dystrophic mice. In normal Swiss and 129ReJ(+/?) mice the concentrations of both cholesterol and cholesteryl esters remain essentially constant in liver, increase in brain and fall sharply in both thigh (mixed fiber type muscles) and chest muscles (predominantly slow oxidative muscles) over this period. In all cases the concentration of free cholesterol exceeds that of esterified cholesterol. In dystrophic mice, similar patterns are found in brain and liver. In both thigh and chest muscles, however, the developmental pattern is significantly different. After an initial decrease the concentrations of cholesterol and cholesteryl esters increase rapidly with the largest increase occurring in the concentration of cholesteryl esters which by 10 weeks of age exceeds the concentration of cholesterol in chest muscle. During the same period the pattern of esterified fatty acids changes gradually in dystrophic tissues towards an increasing ratio of unsaturated/saturated fatty acids. By 10 weeks of age this ratio is significantly higher in dystrophic tissues than normal in all tissues tested.