When Left Does Not Seem Right: Epigenetic and Bioelectric Differences Between Left- and Right-Sided Breast Cancer

Abstract Background: During embryogenesis, lateral symmetry is broken giving rise to Left/Right (L/R) breast tissues with distinct identity. L/R-sided breast tumors exhibit consistently-biased incidence, gene expression, and DNA methylation. We postulate that a differential L/R tumor-microenvironment crosstalk generates different tumorigenesis mechanisms. Methods: We performed in-silico analyses on breast tumors of public datasets, developed xenografted tumors, and conditioned MDA-MB-231 cells with L/R mammary extracts. Results: We found L/R differential DNA methylation involved in embryogenic and neuron-like functions. Focusing on ion-channels, we discovered significant L/R epigenetic and bioelectric differences. Specifically, L-sided cells presented increased methylation of hyperpolarizing ion channel genes and increased Ca2+ concentration and depolarized membrane potential, compared to R-ones. Functional consequences were associated with increased proliferation in left tumors, assessed by KI67 expression and mitotic count. Conclusions: Our findings reveal considerable L/R asymmetry in cancer processes, and suggest specific L/R epigenetic and bioelectric differences as future targets for cancer therapeutic approaches in the breast and many other paired organs.

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Aquaporin 4 over-expression in metastases to the brain in breast cancer.

10.31219/osf.io/yra9e ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Brain Metastases ◽

Water Channel ◽

Breast Tumors ◽

Aquaporin 4 ◽

Primary Breast Tumor ◽

Over Expression ◽

Patients With Cancer ◽

Public Datasets ◽

The Brain

Brain metastases affect 10-15% of women with breast cancer (1). Metastasis is the most significant contributor to death in patients with cancer (2). We assessed what genes make brain metastases most different from the breast tumors from which they arose using public datasets (3, 4). The aquaporin 4 (AQP4) water channel (5) was one of the most differentially expressed genes in brain metastases when comparing the transcriptomes of matched tumor and metastasis samples from the brain and breast from 16 patients (2). Analysis of a separate dataset showed demonstrated the same result (4). In both cases, aquaporin 4 was expressed at significantly higher levels in metastases to the brain than in the primary breast tumor. This is the first report of aquaporin 4 differential over-expression in the brain metastases of patients with breast cancer.

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Direct Comparison of Metastasis-Related miRNAs Expression Levels in Circulating Tumor Cells, Corresponding Plasma, and Primary Tumors of Breast Cancer Patients

Clinical Chemistry ◽

10.1373/clinchem.2015.253716 ◽

2016 ◽

Vol 62 (7) ◽

pp. 1002-1011 ◽

Cited By ~ 30

Author(s):

Athina Markou ◽

Martha Zavridou ◽

Ioanna Sourvinou ◽

George Yousef ◽

Sofia Kounelis ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Patients ◽

Tumor Cells ◽

Peripheral Blood ◽

Breast Tumors ◽

Breast Cancer Patients ◽

Healthy Individuals ◽

Primary Tumors ◽

Expression Levels ◽

Breast Tissues

Abstract BACKGROUND Circulating tumor cells (CTCs) and microRNAs (miRNAs) are important in liquid biopsies in which peripheral blood is used to characterize the evolution of solid tumors. We evaluated the expression levels of miR-21, miR-146a, miR-200c, and miR-210 in CTCs of breast cancer patients with verified metastasis and compared their expression levels in corresponding plasma and primary tumors. METHODS Expression levels of the miRNAs were quantified by quantitative reverse transcription PCR (RT-qPCR) in (a) 89 primary breast tumors and 30 noncancerous breast tissues and (b) CTCs and corresponding plasma of 55 patients with metastatic breast cancer and 20 healthy donors. For 30 of these patients, CTCs, corresponding plasma, and primary tumor tissues were available. RESULTS In formalin-fixed, paraffin-embedded tissues, these miRNAs were differentially expressed between primary breast tumors and noncancerous breast tissues. miR-21 (P < 0.001) and miR-146a (P = 0.001) were overexpressed, whereas miR-200c (P = 0.004) and miR-210 (P = 0.002) were underexpressed. In multivariate analysis, miR-146a overexpression was significantly [hazard ratio 2.969 (1.231–7.157), P = 0.015] associated with progression-free survival. In peripheral blood, all miRNAs studied were overexpressed in both CTC and corresponding plasma. There was a significant association between miR-21 expression levels in CTCs and plasma for 36 of 55 samples (P = 0.008). In plasma, ROC curve analysis revealed that miR-21, miR-146a, and miR-210 could discriminate patients from healthy individuals. CONCLUSIONS Metastasis-related miRNAs are overexpressed in CTCs and corresponding plasma; miR-21 expression levels highly correlate in CTCs and plasma; and miR-21, miR-146a, and miR-210 are valuable plasma biomarkers for discriminating patients from healthy individuals.

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Exposures in early life: associations with DNA promoter methylation in breast tumors

Journal of Developmental Origins of Health and Disease ◽

10.1017/s2040174412000694 ◽

2012 ◽

Vol 4 (2) ◽

pp. 182-190 ◽

Cited By ~ 11

Author(s):

M.-H. Tao ◽

C. Marian ◽

P. G. Shields ◽

N. Potischman ◽

J. Nie ◽

...

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

Birth Order ◽

Promoter Methylation ◽

Early Life ◽

Breast Tumors ◽

Age At Menarche ◽

Breast Cancers ◽

Early Life Exposures ◽

E Cadherin

There is evidence that epigenetic changes occur early in breast carcinogenesis. We hypothesized that early-life exposures associated with breast cancer would be associated with epigenetic alterations in breast tumors. In particular, we examined DNA methylation patterns in breast tumors in association with several early-life exposures in a population-based case–control study. Promoter methylation of E-cadherin, p16 and RAR-β2 genes was assessed in archived tumor blocks from 803 cases with real-time methylation-specific PCR. Unconditional logistic regression was used for case–case comparisons of those with and without promoter methylation. We found no differences in the prevalence of DNA methylation of the individual genes by age at menarche, age at first live birth and weight at age 20. In case–case comparisons of premenopausal breast cancer, lower birth weight was associated with increased likelihood of E-cadherin promoter methylation (OR = 2.79, 95% CI, 1.15–6.82, for ⩽2.5 v. 2.6–2.9 kg); higher adult height with RAR-β2 methylation (OR = 3.34, 95% CI, 1.19–9.39, for ⩾1.65 v. <1.60 m); and not having been breastfed with p16 methylation (OR = 2.75, 95% CI, 1.14–6.62). Among postmenopausal breast cancers, birth order was associated with increased likelihood of p16 promoter methylation. Being other than first in the birth order was inversely associated with likelihood of ⩾1 of the three genes being methylated for premenopausal breast cancers, but positively associated with methylation in postmenopausal women. These results suggest that there may be alterations in methylation associated with early-life exposures that persist into adulthood and affect breast cancer risk.

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Obesity and menopause modify the epigenomic profile of breast cancer

Endocrine Related Cancer ◽

10.1530/erc-16-0565 ◽

2017 ◽

pp. 351-363 ◽

Cited By ~ 16

Author(s):

Ana B Crujeiras ◽

Angel Diaz-Lagares ◽

Olafur A Stefansson ◽

Manuel Macias-Gonzalez ◽

Juan Sandoval ◽

...

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

High Risk ◽

Risk Group ◽

Menopausal Status ◽

Breast Tumors ◽

Methylation Pattern ◽

High Risk Group ◽

Cpg Sites ◽

The Impact

Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumors were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern. Intriguingly, the DNA methylation pattern identified in association with the high-risk group (postmenopausal women with high BMI (>25) and premenopausal women with normal or low BMI < 25) exclusively characterized by hypermethylation of 1287 CpG sites as compared with the low-risk group. These CpG sites included the promoter region of fourteen protein-coding genes of which CpG methylation over the ZNF577 promoter region represents the top scoring associated event. In an independent cohort, the ZNF577 promoter methylation remained statistically significant in association with the high-risk group. Additionally, the impact of ZNF577 promoter methylation on mRNA expression levels was demonstrated in breast cancer cell lines after treatment with a demethylating agent (5-azacytidine). In conclusion, the epigenome of breast tumors is affected by a complex interaction between BMI and menopausal status. The ZNF577 methylation quantification is clearly relevant for the development of novel biomarkers of precision therapy in breast cancer.

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Long Noncoding RNAs-LET Behave as a Noncoding Signature for Early-Onset Menarche and Late-Onset Menopause in Breast Cancer Patients

Galen Medical Journal ◽

10.31661/gmj.v10i0.2108 ◽

2021 ◽

Vol 10 ◽

pp. e2108

Author(s):

Farzaneh Darbeheshti ◽

Hosein Mansoori ◽

Rasoul Abdollahzadeh ◽

Hassan Dastsooz ◽

Abdolreza Daraei ◽

...

Keyword(s):

Breast Cancer ◽

Early Onset ◽

Late Onset ◽

Noncoding Rnas ◽

Breast Tumors ◽

Normal Breast ◽

Long Noncoding Rnas ◽

Breast Cancer Patients ◽

Bioinformatics Analyses ◽

Breast Tissues

Background: Breast cancer (BC) as a major cause of cancer-related death in women shows a very complex molecular and clinical phenotype, which has reduced the effectiveness of medical interventions. Evidence suggests that long noncoding RNAs (lncRNAs) are responsible for an important part of this complexity. This study aims to assess the expression and clinical implication of lncRNA LET in the pathobiology of BC. Materials and Methods: Quantitative real-time polymerase chain reaction was used to measure the expression of lncRNA-LET in breast tumors and adjacent normal-appearing tissues from 4 BC patients, as well as normal mammary tissues. Moreover, a bioinformatics approach was applied to uncover the potential lncRNA-LET-mediated sponge regulatory network as LET/miRNA/mRNA crosstalk. Results: Our study revealed that lncRNA-LET was significantly down-expressed not only in breast tumors but also in normal appearing breast tissues samples from BC subjects compared with true normal breast tissues obtained from healthy women. The low level of lncRNA-LET was meaningfully associated with early-onset menarche (≤13 years) and late-onset menopause (≥50) in patients. Moreover, the bioinformatics analyses support that lncRNA-LET could function as a tumor suppressor miRNA sponge. Conclusion: The results indicate that normal appearing breast tissues can undergo tumor-related molecular changes. Furthermore, they reveal the potential role of the dysregulation in LET-mediated ceRNA network in the pathophysiology of BC.

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Interplay of ERα binding and DNA methylation in the intron-2 determines the expression and estrogen regulation of Cystatin A in breast cancer cells

10.1101/679043 ◽

2019 ◽

Author(s):

Dixcy Jaba Sheeba John Mary ◽

Girija Sikarwar ◽

Ajay Kumar ◽

Anil Mukund Limaye

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

Tumor Invasion ◽

Breast Cancer Cells ◽

Breast Tumors ◽

Invasion And Metastasis ◽

Estrogen Regulation ◽

Cpg Sites ◽

Cysteine Cathepsins ◽

Intron 2

AbstractDespite advances in early detection and treatment, invasion and metastasis of breast tumors remains a major hurdle. Cystatin A (CSTA, also called stefin A), an estrogen-regulated gene in breast cancer cells, is an inhibitor of cysteine cathepsins, and a purported tumor suppressor. Loss of CSTA expression in breast tumors evidently shifts the balance in favor of cysteine cathepsins, thereby promoting extracellular matrix remodeling, tumor invasion and metastasis. However, the underlying mechanism behind the loss of CSTA expression in breast tumors is not known. Here, we have analyzed CSTA expression, and methylation of upstream and intron-2 CpG sites within the CSTA locus in human breast cancer cell lines and breast tumors of the TCGA cohort. Results showed an inverse relationship between expression and methylation. Sequence analysis revealed a potential estrogen response element (ERE) in the intron-2. Analysis of ChIP-seq data (ERP000380) and our own ChIP experiments showed that 17β-estradiol (E2) enhanced ERα binding to this ERE in MCF-7 cells. This ERE was located amidst the differentially methylated intron-2 CpG sites, which provoked us to examine the possible conflict between estrogen-regulation of CSTA and DNA methylation in the intron-2. We analyzed the expression of CSTA and its regulation by estrogen in MDA-MB-231 and T47D cells subjected to global demethylation by 5-azacytidine (5-aza). 5-aza, not only enhanced CSTA expression in these cell lines but also restored estrogen-regulation of CSTA in these cells. Taken together, our results indicate that DNA methylation-dependent silencing could play a significant role in the loss of CSTA expression in breast tumors. The potential of DNA methylation as an indicator of CSTA expression or as a marker of tumor progression can be explored in future investigations. Furthermore, our results indicate the convergence of ERα-mediated estrogen regulation and DNA methylation in the intron-2, thereby offering a novel context to understand the role of estrogen-ERα signaling axis in breast tumor invasion and metastasis.

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Expression Pattern of a Homeotic Gene, HOXA5, in Normal Breast and in Breast Tumors

Analytical Cellular Pathology ◽

10.1155/2006/974810 ◽

2006 ◽

Vol 28 (5-6) ◽

pp. 305-313

Author(s):

Gregory S. Henderson ◽

Paul J. van Diest ◽

Horst Burger ◽

Jose Russo ◽

Venu Raman

Keyword(s):

Breast Cancer ◽

Expression Pattern ◽

Breast Tumors ◽

Normal Breast ◽

Receptor Expression ◽

Homeotic Genes ◽

Breast Carcinomas ◽

Expression Levels ◽

Egfr Expression ◽

Breast Tissues

Introduction: Homeotic (HOX) gene products are now known to be functionally associated with breast cancer biogenesis. Recent evidence has indicated that HOXA5 regulates both p53 and progesterone receptor expression levels in breast cancer cells. In addition, HOXA5 has been shown to interact and regulate the activity of another protein referred to as Twist. As homeotic genes play a pivotal role in development, we sought to decipher the expression pattern in both normal breast tissues and in breast carcinomas. Methods: RT-PCR and immunohistochemistry were performed, to assay the levels of HOXA5 expression, on a panel of normal breast tissue and its corresponding primary breast tumors. Results and Conclusions: We show that HOXA5 expression was maintained at stable levels at different reproductive stages of a woman's life, except during lactation. This evidence indicates that HOXA5 may play a role in maintaining the differentiated state within the breast epithelium. However, nearly 70% of all breast carcinomas had decreased HOXA5 protein levels as compared to normal breast tissues. In addition, we demonstrate that HOXA5 protein expression levels in breast carcinomas inversely co-relates with Epidermal Growth Factor Receptor (EGFR) expression. Furthermore, we found that the survival rate amongst the different low levels of HOXA5 expressing breast tumors was not significant, indicative of an early tumorigenesis process in the absence of innate levels of HOXA5 in normal breast cells.

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Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer

10.1101/2021.04.14.439799 ◽

2021 ◽

Author(s):

Jørgen Ankill ◽

Miriam Ragle Aure ◽

Sunniva Bjørklund ◽

Severin Langberg ◽

Vessela N. Kristensen ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Dna Methylation ◽

Transcription Factor ◽

Breast Tumors ◽

Epigenetic Alterations ◽

Factor Binding ◽

Chromatin Loops ◽

Cancer Pathogenesis ◽

Genome Wide

Breast cancer is a highly heterogeneous disease driven by multiple factors including genetic and epigenetic alterations. DNA methylation patterns have been shown to be altered on a genome-wide scale and previous studies have highlighted the critical role of aberrant DNA methylation on gene expression and breast cancer pathogenesis. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL), a method for integration of CpG methylation and gene expression to identify disease-driving genes under epigenetic control. By grouping these emQTLs by biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis such as proliferation and tumor infiltrating fibroblasts. We report hypomethylation at enhancers carrying transcription factor binding sites of key proliferation-driving transcription factors such as CEBP-β, FOSL1, and FOSL2, with concomitant high expression of cell cycle- and proliferation-related genes in aggressive breast tumors. The identified CpGs and genes were found to be connected through chromatin loops, together indicating that proliferation in aggressive breast tumors is under epigenetic regulation by DNA methylation. Interestingly, there was a significant correlation between proliferation-related DNA methylation and gene expression also within subtypes of breast cancer, thereby showing that varying proliferation may be explained by epigenetic profiles across breast cancer subtypes. Indeed, the identified proliferation gene signature was prognostic both in the Luminal A and Luminal B subtypes. Taken together, we show that proliferation in breast cancer is linked to hypomethylation at specific enhancers and transcription factor binding mediated through chromatin loops.

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Detectability of Breast Tumors in Excised Breast Tissues of Total Mastectomy by IR-UWB-Radar-Based Breast Cancer Detector

IEEE Transactions on Biomedical Engineering ◽

10.1109/tbme.2018.2887083 ◽

2019 ◽

Vol 66 (8) ◽

pp. 2296-2305 ◽

Cited By ~ 8

Author(s):

Hang Song ◽

Shinsuke Sasada ◽

Norio Masumoto ◽

Takayuki Kadoya ◽

Noriyuki Shiroma ◽

...

Keyword(s):

Breast Cancer ◽

Breast Tumors ◽

Total Mastectomy ◽

Uwb Radar ◽

Breast Tissues

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Aging leads to stochastic loss of silencing at transposons in mammary luminal epithelial cells

10.1101/2020.06.26.170043 ◽

2020 ◽

Author(s):

Parijat Senapati ◽

Masaru Miyano ◽

Mudaser Basam ◽

Rosalyn W. Sayaman ◽

Amy Leung ◽

...

Keyword(s):

Breast Cancer ◽

Dna Methylation ◽

Epithelial Cells ◽

Transposable Elements ◽

Regulatory Elements ◽

Breast Cancers ◽

Age Related ◽

Functional Consequences ◽

Methylation Patterns ◽

Luminal Epithelial Cells

AbstractThe aging process is characterized by an accumulation of cellular damage, including alterations to the epigenome. While it is clear that DNA methylation patterns change with age, the mechanisms behind these epigenomic alterations – and their functional consequences – have remained unclear. One of the primary roles of DNA methylation in mammalian genomes is in the repression of retrotransposons. Many of these repetitive elements contain regulatory sequences, and loss of repression can lead to aberrant transcriptional regulation. Aging-associated DNA methylation loss at transposable elements (TEs), therefore, has the potential to rewire gene expression networks to be favorable for pathologies, including age-related diseases such as cancer. However, the extent of loss of epigenetic silencing at transposable elements during aging and the functional consequences of this have remained unclear. Luminal epithelial cells in the breast tissue are a key cell lineage implicated in age-related luminal breast cancers. We report here that aging leads to distinct DNA methylation patterns at tissue-specific regulatory elements and TEs in luminal epithelial cells. DNA methylation changes at regulatory elements are driven by altered activity of lineage-specific transcription factors such as ELF5 and TP63. However, transposable elements, especially recently evolved TEs, exhibit stochastic loss of methylation and increased methylation entropy with age. TEs that lose methylation with age regulate known breast cancer genes and are associated with elevated breast cancer risk. Altogether, our results indicate that aging leads to DNA methylation loss at evolutionarily young TEs that can impact gene networks important for age-related breast cancers.

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