DNA Methylation In Breast Cancer Research Articles

Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation

BackgroundRecent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy.MethodsWe enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples.ResultsWe identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%.ConclusionsOur study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.

Abstract 6115: Genetic ancestry specific meQTLs control immune function regulation in a breast cancer cohort of African and European patients

Abstract Black women with significant African ancestry experience a disproportionately higher incidence of the most aggressive and invasive breast cancer subtypes, along with worse clinical outcomes across all demographic groups within the United States. These health disparities arise from complex interactions between genetic, sociocultural, and environmental factors. Epigenetic mechanisms, such as DNA methylation (DNAm), which regulate gene expression have been proposed as a means to capture the molecular impact of adverse environments on tumor biology. While DNAm levels can be influenced by environmental stimuli, they are also regulated by individual genotypes at methylation quantitative trait loci (meQTLs), posing a challenge to modeling the impact of the environment on cancer molecular characteristics. We hypothesized that ancestry differential DNAm in breast cancer is a result of differential genotype frequencies of SNPs due to ancestry at meQTL loci that can result in phenotypic differences between breast cancer patients of African and European ancestry through differential gene expression regulation. To investigate this hypothesis, we leveraged multi-omic data from The Cancer Genome Atlas (TCGA) breast cancer cohort to perform integrative analysis in patients of European and African ancestry (n=578). 804 CpGs were significantly differentially methylated between European and African ancestry breast cancer patients. meQTL analysis at these sites identified 37 cis-meQTLs and 748 trans-meQTLs, regulating methylation at CpG sites enriched in CpG Islands, enhancers, and other open chromatin regions. 54% of the cis- and 69% of the trans-meQTLs show evidence of differential genotype frequencies by ancestry. Association analysis between methylation and local gene expression revealed that 683 of the 804 ancestry differentially methylated sites regulate the expression of 5,774 genes. We found a statistically significant enrichment for genes involved in immune-related functions such as MHC class II protein complex assembly and the regulation of leukocyte cell-cell adhesion. Intriguingly, 10.5% of these genes encode transcription factors (TFs), and out of these ~23% are linked to African-ancestry specific open chromatin regions in breast cancer cell lines derived from African-ancestry donors. Our findings show that ancestry specific DNAm differences display strong genetic associations via ancestry associated meQTLs, affecting fundamental immunological processes in breast cancer. Our findings suggest that the effects of ancestry-specific genetic regulation may be more profound than previously appreciated, while pointing to the potential for confounding due to genetic ancestry when using DNA methylation as a molecular readout of environmental exposures. Citation Format: Kyriaki Founta, Nyasha Chambwe. Genetic ancestry specific meQTLs control immune function regulation in a breast cancer cohort of African and European patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6115.

Septin9 DNA methylation is associated with breast cancer recurrence or metastasis.

We aimed to explore the prognostic value of Septin9 DNA methylation in breast cancer. Breast cancer patients with and without recurrence or metastasis and matched non-breast cancer patients were screened retrospectively from 2014 to 2016. Bisulfite conversion and fluorescence quantitative methylation-specific polymerase chain reaction were used to detect the Septin9 methylation status and distribution levels in patient breast tissues. Septin9 DNA methylation was more frequent in breast cancer tissues than in non-breast cancer tissues, but was not significantly correlated with any relevant breast cancer patient clinicopathological characteristic. Septin9 methylation rates were higher in patients with recurrence or metastasis. Septin9 methylation, tumor size, lymph node status, and progesterone receptor (PR) expression could influence prognosis. Septin9 methylation was significantly associated with worse disease-free survival in breast cancer patients, with receiver operating characteristic curve analysis indicating that it had good prognostic ability, with an area under the curve (AUC) value of 0.719. The AUC values increased when Septin9 methylation was combined with tumor size, lymph node status, and PR to predict prognosis. Septin9 DNA methylation was an independent predictors of breast cancer prognostic risk. This could possibly help improve comprehensive prognosis prediction methods when combined with other risk factors.

Abstract C003: Analysis of genetic control of differential DNA methylation between breast cancer patients of African and European ancestry

Abstract Black women with significant African ancestry experience a disproportionately higher incidence of the most aggressive and invasive breast cancer subtypes, along with worse clinical outcomes across all population groups in the United States. These health disparities arise from complex interactions between genetic, sociocultural, and environmental factors. Although there is a critical need to understand how these non-genetic factors contribute to disease risk or etiology, they are difficult to measure reliably, and their long-term impacts are not well understood. Epigenetic mechanisms that regulate gene expression, such as DNA methylation (DNAm), have been proposed to capture the molecular impact of adverse environments on tumor biology. While DNAm levels can change in response to environmental cues, they are also regulated by individual genotypes at methylation quantitative trait loci (meQTLs), presenting a challenge for modeling environmental effects on cancer molecular phenotypes. We hypothesize that ancestry differential DNAm in breast cancer can be partially explained by ancestry differential genotype frequencies of SNPs at meQTL loci. We leveraged multi-omic data from The Cancer Genome Atlas (TCGA) breast cancer (BRCA) cohort to perform integrative analysis for patients of European and African ancestry (n=578), including ancestry-based differential methylation analysis, meQTL analysis and association testing of genotypes and ancestry. We identified 804 CpGs differentially methylated between European and African ancestry BRCA patients. meQTL analysis at these sites identified 130 cis-meQTLs and 1,019 trans-meQTLs. ~84% of the identified cis- and ~80% of the identified trans-meQTLs show evidence of differential genotype frequencies by ancestry. Gene set enrichment analysis of the meQTL target genes implicated genes involved in regulation of cell differentiation and developmental processes, phosphatase activity and phosphorylation processes. Our findings show that ancestry specific DNAm differences display strong genetic associations via ancestry associated meQTLs (a-meQTLs) affecting fundamental biological functions in breast cancer. This result points to the potential for confounding due to genetic ancestry in studies that use DNA methylation as a molecular readout of environmental exposures. Citation Format: Kyriaki Founta, Nyasha Chambwe. Analysis of genetic control of differential DNA methylation between breast cancer patients of African and European ancestry [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C003.

The Mechanism of DNA Methylation and miRNA in Breast Cancer.

Breast cancer is the most prevalent cancer in the world. Currently, the main treatments for breast cancer are radiotherapy, chemotherapy, targeted therapy and surgery. The treatment measures for breast cancer depend on the molecular subtype. Thus, the exploration of the underlying molecular mechanisms and therapeutic targets for breast cancer remains a hotspot in research. In breast cancer, a high level of expression of DNMTs is highly correlated with poor prognosis, that is, the abnormal methylation of tumor suppressor genes usually promotes tumorigenesis and progression. MiRNAs, as non-coding RNAs, have been identified to play key roles in breast cancer. The aberrant methylation of miRNAs could lead to drug resistance during the aforementioned treatment. Therefore, the regulation of miRNA methylation might serve as a therapeutic target in breast cancer. In this paper, we reviewed studies on the regulatory mechanisms of miRNA and DNA methylation in breast cancer from the last decade, focusing on the promoter region of tumor suppressor miRNAs methylated by DNMTs and the highly expressed oncogenic miRNAs inhibited by DNMTs or activating TETs.

Определение прогностически значимой сигнатуры ДНК-метилирования у пациенток с различными типами рака молочной железы

Breast cancer (BC) is the most frequently diagnosed cancer and one of the major causes of female mortality. The development of prognostic models based on multiomics data is the main goal of precision oncology. Aberrant DNA methylation in BC is a diagnostic marker of carcinogenesis. Despite the existing factors of BC prognosis, introduction of methylation markers would make it possible to obtain more accurate prognostic scores. The study was aimed to assess DNA methylation signatures in various BC subtypes for clinical endpoints and patients' clinicopathological characteristics. The data on methylation of CpG dinucleotides (probes) and clinical characteristics of BC samples were obtained from The Cancer Genome Atlas Breast Cancer database. CpG dinucleotides associated with the selected endpoints were chosen by univariate Cox regression method. The LASSO method was used to search for stable probes, while further signature construction and testing of the clinical characteristics independence were performed using multivariate Cox regression. The dignostic and prognostic potential of the signatures was assessed using ROC analysis and Kaplan–Meier curves. It has been shown that the signatures of selected probes have a significant diagnostic (AUC 0.76–1) and prognostic (p < 0.05) potential. This approach has made it possible to identify 47 genes associated with good and poor prognosis, among these five genes have been described earlier. If the genome-wide DNA analysis results are available, the research approach applied can be used to study molecular pathogenesis of BC and other disorders.

Global DNA Methylation Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast Cancer Stroma.

The first genome-wide map of DNA methylation in breast cancer-associated fibroblasts unravels a previously unknown facet of the dynamic plasticity of the stroma, with far-reaching therapeutic implications.

27-Hydroxycholesterol, The Estrogen Receptor Modulator, Alters DNA Methylation in Breast Cancer.

27-hydroxycholesterol (27-HC) is the first known endogenous selective estrogen receptor modulator (SERM), and its elevation from normal levels is closely associated with breast cancer. A plethora of evidence suggests that aberrant epigenetic signatures in breast cancer cells can result in differential responses to various chemotherapeutics and often leads to the development of resistant cancer cells. Such aberrant epigenetic changes are mostly dictated by the microenvironment. The local concentration of oxygen and metabolites in the microenvironment of breast cancer are known to influence the development of breast cancer. Hence, we hypothesized that 27-HC, an oxysterol, which has been shown to induce breast cancer progression via estrogen receptor alpha (ERα) and liver X receptor (LXR) and by modulating immune cells, may also induce epigenetic changes. For deciphering the same, we treated the estrogen receptor-positive cells with 27-HC and identified DNA hypermethylation on a subset of genes by performing DNA bisulfite sequencing. The genes that showed significant DNA hypermethylation were phosphatidylserine synthase 2 (PTDSS2), MIR613, indoleamine 2,3-dioxygenase 1 (IDO1), thyroid hormone receptor alpha (THRA), dystrotelin (DTYN), and mesoderm induction early response 1, family member 3 (MIER). Furthermore, we found that 27-HC weakens the DNMT3B association with the ERα in MCF-7 cells. This study reports that 27-HC induces aberrant DNA methylation changes on the promoters of a subset of genes through modulation of ERα and DNMT3B complexes to induce the local DNA methylation changes, which may dictate drug responses and breast cancer development.

A Novel Gene Prognostic Signature Based on Differential DNA Methylation in Breast Cancer.

Background: DNA methylation played essential roles in regulating gene expression. The impact of DNA methylation status on the occurrence and development of cancers has been well demonstrated. However, little is known about its prognostic role in breast cancer (BC). Materials: The Illumina Human Methylation450 array (450k array) data of BC was downloaded from the UCSC xena database. Transcriptomic data of BC was downloaded from the Cancer Genome Atlas (TCGA) database. Firstly, we used univariate and multivariate Cox regression analysis to screen out independent prognostic CpGs, and then we identified methylation-associated prognosis subgroups by consensus clustering. Next, a methylation prognostic model was developed using multivariate Cox analysis and was validated with the Illumina Human Methylation27 array (27k array) dataset of BC. We then screened out differentially expressed genes (DEGs) between methylation high-risk and low-risk groups and constructed a methylation-based gene prognostic signature. Further, we validated the gene signature with three subgroups of the TCGA-BRCA dataset and an external dataset GSE146558 from the Gene Expression Omnibus (GEO) database. Results: We established a methylation prognostic signature and a methylation-based gene prognostic signature, and there was a close positive correlation between them. The gene prognostic signature involved six genes: IRF2, KCNJ11, ZDHHC9, LRP11, PCMT1, and TMEM70. We verified their expression in mRNA and protein levels in BC. Both methylation and methylation-based gene prognostic signatures showed good prognostic stratification ability. The AUC values of 3-years, 5-years overall survival (OS) were 0.737, 0.744 in the methylation signature and 0.725, 0.715 in the gene signature, respectively. In the validation groups, high-risk patients were confirmed to have poorer OS. The AUC values of 3 years were 0.757, 0.735, 0.733 in the three subgroups of TCGA dataset and 0.635 in GSE146558 dataset. Conclusion: This study revealed the DNA methylation landscape and established promising methylation and methylation-based gene prognostic signatures that could serve as potential prognostic biomarkers and therapeutic targets.

Нарушения моноаллельного метилирования ДНК при раке молочной железы

Цель. Изучение изменений в образцах злокачественных опухолей молочной железы статуса метилирования остатков цитозина в составе CpG-островков, моноаллельно метилированных в норме. Методы. Для определения CpG-динуклеотидов, моноаллельно метилированных в опухолевых и нормальных тканях молочной железы, использовали полученные авторами ранее результаты широкогеномного бисульфитного секвенирования Xmal-RRBS. Изменения моноаллельного метилирования в опухолях визуализировали с помощью гистограмм для различных метилотипов молочной железы. Результаты. В геномах умеренно метилированных опухолей нормально моноаллельно метилированные CpG-динуклеотиды имеют тенденцию к почти равновероятному изменению как в неметилированное, так и в полностью метилированное состояния. В геномах гиперметилированных опухолей нормально моноаллельно метилированные CpG-динуклеотиды чаще меняют своё состояние на полностью метилированное. Заключение. Наблюдаемый характер изменений позволяет предположить, что динамика диктуется в умеренно метилированных опухолях процессами, не определяющими её вектор, а в гиперметилированных - дополнительно - направленным процессом, повышающим уровень метилирования CpG-динуклеотидов. По аналогии с ранее опубликованными результатами исследования динамики изменений метилирования импринтированных локусов в опухолях человека, мы предполагаем, что процесс случайного определения вектора изменения характера метилирования опосредован нарушениями копийности участков моноаллельного метилирования ДНК. Причиной равновероятных разнонаправленных изменений моноаллельного метилирования может быть геномный дисбаланс, который может случайным образом приводить к делециям (или приобретенной однородительской дисомии) либо метилированного, либо неметилированного аллеля. Aim: to evaluate changes in the methylation status of cytosine residues in CpG islands, monoallelically methylated in the norm, in samples of malignant breast tumors. Methods. To determine CpG dinucleotides monoallelically methylated in tumor and normal breast tissues, we used the results of Xmal-RRBS genome-wide bisulfite sequencing obtained earlier. Changes in monoallelic methylation in tumors were visualized using histograms for different breast methylotypes. Results. In the genomes of moderately methylated tumors, normally methylated CpG dinucleotides have a tendency to an almost equiprobable methylation change to both the unmethylated and fully methylated states. In the genomes of hypermethylated tumors, normally monoallelically methylated CpG dinucleotides more often change their state to fully methylated. Conclusions. The observed nature of the changes suggests that the dynamics is dictated in moderately methylated tumors by processes that do not determine their vector, and in hypermethylated tumors, additionally, by a directed process that increases the methylation level of CpG dinucleotides. By analogy with the previously published results of a study of the dynamics of changes in methylation of imprinted loci in human tumors, we assume that the process of random determination of the vector of methylation changes is mediated by copy number aberrations at the regions of monoallelic DNA methylation. The reason for the equally probable bidirectional changes in monoallelic methylation may be a genomic imbalance that can randomly lead to deletions (or acquired uniparental disomy) of either the methylated or unmethylated allele.

Curcumin from Turmeric Rhizome: A Potential Modulator of DNA Methylation Machinery in Breast Cancer Inhibition.

One of the most systematically studied bioactive nutraceuticals for its benefits in the management of various diseases is the turmeric-derived compounds: curcumin. Turmeric obtained from the rhizome of a perennial herb Curcuma longa L. is a condiment commonly used in our diet. Curcumin is well known for its potential role in inhibiting cancer by targeting epigenetic machinery, with DNA methylation at the forefront. The dynamic DNA methylation processes serve as an adaptive mechanism to a wide variety of environmental factors, including diet. Every healthy tissue has a precise DNA methylation pattern that changes during cancer development, forming a cancer-specific design. Hypermethylation of tumor suppressor genes, global DNA demethylation, and promoter hypomethylation of oncogenes and prometastatic genes are hallmarks of nearly all types of cancer, including breast cancer. Curcumin has been shown to modulate epigenetic events that are dysregulated in cancer cells and possess the potential to prevent cancer or enhance the effects of conventional anti-cancer therapy. Although mechanisms underlying curcumin-mediated changes in the epigenome remain to be fully elucidated, the mode of action targeting both hypermethylated and hypomethylated genes in cancer is promising for cancer chemoprevention. This review provides a comprehensive discussion of potential epigenetic mechanisms of curcumin in reversing altered patterns of DNA methylation in breast cancer that is the most commonly diagnosed cancer and the leading cause of cancer death among females worldwide. Insight into the other bioactive components of turmeric rhizome as potential epigenetic modifiers has been indicated as well.

Exploration of Euchromatin Cell-Free DNA Methylation in Breast Cancer

Circulating cell-Free DNA (cfDNA) is emerging as a non-invasive liquid biopsy biomarker for personalized and precision cancer management. While extensive tissue-based DNA methylation profiling at global and gene levels have been documented, studies regarding methylation status of cfDNA at the sub-genome scale as well as correlation with that of tissue-derived genomic DNA have yet to be explored. The ability to specifically interrogate DNA methylation status of the transcriptionally active regions within chromosomes, i.e., euchromatin, not only fulfills the knowledge gap but also provides a much needed longitudinal and real-time insight for early cancer detection and intervention. We have developed a proprietary technology for selective enrichment of euchromatin cfDNA and analyzed the 5-methylcytosine (5-mC) content in these circulating nucleocomplexes. Paired tissue and plasma DNA (n=28) were obtained from breast cancer patients at various stages with ages and genders matched to the control arm (n=21). Quantitative measurement of DNA methylation was determined by ELISA-based assays. Our results revealed significant lower methylation levels from breast cancer cohort as compared to the cancer-free group (P<0.01). Most importantly, the methylation quantification dataset from euchromatin cfDNA strongly correlated with that of tissue genomic DNA (R²=0.72). This is the first report on euchromatin cfDNA methylation and provides promising outcomes for its future clinical application

Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers.

Breast cancer is a common malignant tumor among women whose prognosis is largely determined by the period and accuracy of diagnosis. We here propose to identify a robust DNA methylation-based breast cancer-specific diagnostic signature. Genome-wide DNA methylation and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten common cancers from TCGA but also the healthy breast tissues from the Gene Expression Omnibus (GEO) were finally remained for logistic regression analysis. Another independent breast cancer DNA methylation dataset from GEO was used as the testing set. Lots of CpGs were hyper-methylated in breast cancer samples compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions. Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were finally retained. The diagnostic model was reliable in separating BRCA from normal samples. Besides, chromatin accessibility status of RIIAD1, ENPP2, ESPN and ETS1 showed great differences between MCF-7 and MDA-MB-231 cell lines. In conclusion, the present study should be helpful for breast cancer early and accurate diagnosis.

Progress of DNA methylation and hydroxymethylation in breast cancer

Breast cancer is one of the most common malignant tumors in women and the second leading cause of death in female cancer patients. In recent years, the incidence of breast cancer has been increasing in China year by year, and the age of breast cancer patients becomes younger and younger. The pathogenesis of breast cancer is complex and related to many factors, such as age, family history and genetic variation. With the development of epigenetics, DNA modification plays an important role in the occurrence and development of breast cancer. This article reviews the research of DNA methylation and hydroxymethylation in breast cancer. Key words: Breast neoplasms; DNA methylation; Hydroxymethylation; Molecular biology

DNA Methylation in Human Breast Cancer Cell Lines Adapted to High Nitric Oxide.

Nitric oxide (NO) exposure has been suggested to cause alterations in DNA methylation in breast cancer. We investigated the effect of NO on DNA methylation of promoters in cell lines of breast cancer. The methylation status of the promoters of breast cancer 1 (BRCA1), deleted in colon cancer (DCC), Ras-association domain family 1A (RASSF1A), O6-methylguanine-DNA methyltransferase (MGMT), and secreted frizzled related protein 1 (SFRP1) were analyzed in the parental and high nitric oxide-adapted cell lines of breast cancer using Illumina MiSequencing. Methylation of RASSF1A promoter in BT-20-HNO (74.7%) was significantly higher than that in BT-20 cells (72%) (p<0.05), whereas in MCF-7-HNO cells, methylation of MGMT promoter was found to have significantly decreased as compared to its parental cell line (45.1% versus 50.1%; p<0.0001). Promoter methylation of SFRP and DCC was elevated in T-47D-HNO relative to its parent cell line (p<0.05). Similarly to the double-edged effects of NO on tumorigenesis, its epigenetic effects through DNA methylation are diverse and contradictory in breast cancer.

20P - Matrix metalloproteinases and their tissue inhibitors genes abnormal DNA methylation in breast cancer

BackgroundMatrix metalloproteinases (MMPs) specifically hydrolyze the extracellular matrix proteins. MMPs are inhibited by tissue inhibitors of MMPs (TIMPs). Changes in the expression levels of MMPs and TIMPs have been described in various cancers, including breast cancer (BC). MethodsWe analyzed methylation status of 11 MMP genes (MMP2, MMP11, MMP14, MMP15, MMP16, MMP17, MMP21, MMP23B, MMP24, MMP25, MMP28) and 4 TIMP genes (TIMP1, TIMP2, TIMP3, TIMP4) in 183 BC samples and 183 matched samples of morphologically normal adjacent tissues, 6 BC cell lines (ZR711, HBL100, HS578T, BT474, T47D, MCF7), and 6 autopsy samples of normal breast tissues by methylation sensitive restriction enzyme digestion PCR (MSRE-PCR).Table20P MMP genes differentially methylated in BCTableGeneMethylated in BC, %Methylated in normal breast tissuesPresence (+) or absence (–) of methylation in BC cell linesZR751MCF7T47DBT474HBL100HS578TMMP27,7 (14/183)0+++---MMP23B17 (31/182)0+++-++MMP2411,9 (20/168)0---++-MMP2515,4 (28/182)0-++-+-MMP284,9 (9/183)0+++++- ResultsIn our collection of BC samples, cancer related abnormal methylation was observed for the MMP2, MMP23B, MMP24, MMP25, and MMP28 genes of the MMPs family (Table). Other MMP genes under study were nonmethylated both in tumors and in normal tissues, as well as the TIMP genes TIMP2 and TIMP3. The promoter regions of TIMP1, TIMP4, MMP14, and MMP21 were found to be constitutively methylated in breast tissues, no matter cancerous or normal. A multiple correspondence analysis demonstrated that nonmethylated status of the promoter regions of MMP2, MMP23B, MMP24, MMP25, MMP28 is associated with lack of HER2 expression. The methylated status of the MMP23B is associated with a higher level (3+) of HER2 expression. Table: MMP genes differentially methylated in BC. ConclusionsTaken that HER2-positive BC is a more aggressive disease, one can assume that unsuppressed expression of the MMP2, MMP23B, MMP24, MMP25, MMP28 genes allowed by the absence of abnormal methylation of their promoters is characteristic for less aggressive BCs. Legal entity responsible for the study: Research Centre for Medical Genetics. Funding: The research was carried out within the state assignment of Ministry of Science and Higher Education of the Russian Federation. Legal entity responsible for the studyResearch Centre for Medical Genetics. FundingMinistry of Science and Higher Education of the Russian Federation. DisclosureAll authors have declared no conflicts of interest.

Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

BackgroundBreast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer.MethodsWe analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis.ResultsWe identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types.ConclusionWe have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.

Clinical performance of an analytically validated assay in comparison to microarray technology to assess PITX2 DNA-methylation in breast cancer

Significant evidence has accumulated that DNA-methylation of the paired-like homeodomain transcription factor 2 (PITX2) gene can serve as a prognostic and predictive biomarker in breast cancer. PITX2 DNA-methylation data have been obtained so far from microarray and polymerase chain reaction (PCR)-based research tests. The availability of an analytically validated in vitro methylation-specific real-time PCR assay format (therascreen PITX2 RGQ PCR assay) intended for the determination of the percent methylation ratio (PMR) in the (PITX2) promoter 2 prompted us to investigate whether the clinical performance of these different assay systems generate comparable clinical outcome data. Mathematically converted microarray data of a previous breast cancer study (n = 204) into PMR values leads to a PITX2 cut-off value at PMR 14.73. Recalculation of the data to experimentally equivalent PMRs with the PCR PITX2 assay leads to a cut-off value at PMR 12 with the highest statistical significance. This cut-off predicts outcome of high-risk breast cancer patients to adjuvant anthracycline-based chemotherapy (n = 204; Hazard Ratio 2.48; p < 0.001) comparable to microarray generated results (n = 204; Hazard ratio 2.32; p < 0.0001). The therascreen PITX2 RGQ PCR assay is an analytically validated test with high reliability and robustness and predicts outcome of high-risk breast cancer patients to anthracycline-based chemotherapy.

DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence.

DNA methylation plays a role in the etiology of primary breast cancers. We analyzed paired primary and second breast tumors to elucidate the role of methylation in recurrence. Methylation profiles from paired primary and second breast tumors of 23 women were assessed using the HumanMethylation450 BeadChip. Twelve women had estrogen receptor positive (ERpos) primary and second tumors, five had estrogen receptor negative (ERneg) primary and second tumors, and six had an ERpos primary tumor but an ERneg second tumor. Stratifying tumors by occurrence revealed that the greater methylation previously associated with ERpos tumors, is more pronounced in primary tumors than in second tumors. Further, ERneg second tumors are more methylated than ERpos second tumors among women who had ERpos primary tumors. Pathway analyses using gene lists generated from comparisons of methylation in ERpos primary tumors from the paired sets with ERpos tumors from six women without recurrences, identified differences between groups based on the ER status of the second tumor. Hypermethylated genes of significantly enriched pathways were differentially associated with survival. DNA methylation profiles of ERpos primary breast tumors support the development and use of tumor methylation profiles for stratifying women with breast cancer both for prognosis and therapy.

Microarray-based analysis of whole-genome DNA methylation profiling in early detection of breast cancer.

Emerging evidence indicated that changes in DNA methylation early in breast cancer (BC) development might be clinically relevant for therapeutic decisions. Through analysis of whole-genome gene expression microarray and DNA methylation microarray, we explored genes with abnormal DNA methylation in BC for early detection. Firstly, human BC tissues and adjacent non-cancerous tissues were collected from nine BC patients. Gene expression microarray sequencing was conducted for identifying differentially expressed genes and DNA methylation microarray sequencing for differentially methylated genes in BC. Differentially expressed genes and methylated genes in BC were further explored using the Cancer Genome Atlas database. The correlation between DNA methylation and gene expression was illustrated by multiple comparisons. In other 60 clinical samples, methylation specific polymerase chain reaction (PCR) and reverse transcription quantitative PCR were applied for the methylation of HOXA4 and IGF1 genes in BC and adjacent non-cancerous tissues. In total, 1680 upregulated genes and 1249 downregulated genes were determined in BC. Chromosome 16 and 17 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in each gene region. Chromosome 19 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in the exoniensis 1, untranslated region-5 and transcriptional start site 200 gene regions. In other 60 clinical samples, HOXA4 and IGF1 in BC tissues presented increased DNA methylation and decreased gene expression in BC. MCF7 cells treated with RG108 showed decreased HOXA4 and IGF1 expressions. It was estimated that HOXA4 and IGF1 were identified with increased DNA methylation and decreased gene expression in BC, which may serve as biomarkers in early BC detection.