Mutant p53 binds to estrogen receptor negative promoter via DNMT1 and HDAC1 in MDA-MB-468 breast cancer cells

Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis

Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.

Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors

Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.

DNMT1: A key drug target in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Altered epigenetics regulation including DNA hypermethylation by DNA methyltransferase 1 (DNMT1) has been implicated as one of the causes of TNBC tumorigenesis. In this review, the oncogenic functions rendered by DNMT1 in TNBCs, and DNMT1 inhibitors targeting TNBC cells are presented and discussed. In summary, DNMT1 expression is associated with poor breast cancer survival, and it is overexpressed in TNBC subtype. The oncogenic roles of DNMT1 in TNBCs include: (1) Repression of estrogen receptor (ER) expression; (2) Promotion of epithelial-mesenchymal transition (EMT) required for metastasis; (3) Induces cellular autophagy and; (4) Promotes the growth of cancer stem cells in TNBCs. DNMT1 confers these phenotypes by hypermethylating the promoter regions of ER, multiple tumor suppressor genes, microRNAs and epithelial markers involved in suppressing EMT. DNMT1 inhibitors exert anti-tumorigenic effects against TNBC cells. This includes the hypomethylating agents azacitidine, decitabine and guadecitabine that might sensitize TNBC patients to immune checkpoint blockade therapy. DNMT1 represents an epigenetic target for TNBC cells destruction as well as to derail their metastatic and aggressive phenotypes.

Identification of Novel Breast Cancer Genes based on Gene Expression Profiles and PPI Data

Background:

Breast cancer is one of the most common malignancies, and a threat to female health all over the world. However, the molecular mechanism of breast cancer has not been fully discovered yet.

Objective:

It is crucial to identify breast cancer-related genes, which could provide new biomarker for breast cancer diagnosis as well as potential treatment targets.

Methods:

Here we used the minimum redundancy-maximum relevance (mRMR) method to select significant genes, then mapped the transcripts of the genes on the Protein-Protein Interaction (PPI) network and traced the shortest path between each pair of two proteins.

Results:

As a result, we identified 24 breast cancer-related genes whose betweenness were over 700. The GO enrichment analysis indicated that the transcription and oxygen level are very important in breast cancer. And the pathway analysis indicated that most of these 24 genes are enriched in prostate cancer, endocrine resistance, and pathways in cancer.

Conclusion:

We hope these 24 genes might be useful for diagnosis, prognosis and treatment for breast cancer.

Associating expression and genomic data using co-occurrence measures

Abstract

Recent technological evolutions have led to an exponential increase in data in all the omics fields. It is expected that integration of these different data sources, will drastically enhance our knowledge of the biological mechanisms behind genomic diseases such as cancer. However, the integration of different omics data still remains a challenge. In this work we propose an intuitive workflow for the integrative analysis of expression, mutation and copy number data taken from the METABRIC study on breast cancer. First, we present evidence that the expression profile of many important breast cancer genes consists of two modes or ‘regimes’, which contain important clinical information. Then, we show how the co-occurrence of these expression regimes can be used as an association measure between genes and validate our findings on the TCGA-BRCA study. Finally, we demonstrate how these co-occurrence measures can also be applied to link expression regimes to genomic aberrations, providing a more complete, integrative view on breast cancer. As a case study, an integrative analysis of the identified MLPH-FOXA1 association is performed, illustrating that the obtained expression associations are intimately linked to the underlying genomic changes.

Reviewers

This article was reviewed by Dirk Walther, Francisco Garcia and Isabel Nepomuceno.

Electronic supplementary material

The online version of this article (10.1186/s13062-019-0240-2) contains supplementary material, which is available to authorized users.

Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma

Our current view of DNA methylation processes is strongly moving: First, even if it was generally admitted that DNMT3A and DNMT3B are associated with de novo methylation and DNMT1 is associated with inheritance DNA methylation, these distinctions are now not so clear. Secondly, since one decade, many partners of DNMTs have been involved in both the regulation of DNA methylation activity and DNMT recruitment on DNA. The high diversity of interactions and the combination of these interactions let us to subclass the different DNMT-including complexes. For example, the DNMT3L/DNMT3A complex is mainly related to de novo DNA methylation in embryonic states, whereas the DNMT1/PCNA/UHRF1 complex is required for maintaining global DNA methylation following DNA replication. On the opposite to these unspecific DNA methylation machineries (no preferential DNA sequence), some recently identified DNMT-including complexes are recruited on specific DNA sequences. The coexistence of both types of DNA methylation (un/specific) suggests a close cooperation and an orchestration between these systems to maintain genome and epigenome integrities. Deregulation of these systems can lead to pathologic disorders.

Functional assessment of MeCP2 in Rett syndrome and cancers of breast, colon, and prostate

Ever since the first report that mutations in methyl-CpG-binding protein 2 (MeCP2) causes Rett syndrome (RTT), a severe neurological disorder in females world-wide, there has been a keen interest to gain a comprehensive understanding of this protein. While the classical model associated with MeCP2 function suggests its role in gene suppression via recruitment of co-repressor complexes and histone deacetylases to methylated CpG-sites, recent discoveries have brought to light its role in transcription activation, modulation of RNA splicing, and chromatin compaction. Various post-translational modifications (PTMs) of MeCP2 further increase its functional versatility. Involvement of MeCP2 in pathologies other than RTT, such as tumorigenesis however, remains poorly explored and understood. This review provides a survey of the literature implicating MeCP2 in breast, colon and prostate cancer.

Methylation patterns of estrogen receptor α promoter correlate with estrogen receptor α expression and clinicopathological factors in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the seventh most common type of cancer; notably, the incidence of HCC is four to eight times higher in men than women. Previous studies reported that the estrogen receptor (ER) signaling pathway is involved in the pathogenesis of HCC, although the extent of its involvement is unclear due to several conflicting reports. In the present study, tumor and paired adjacent non-cancerous tissues from 157 HCC patients were collected. Transcriptome sequencing and real-time quantitative polymerase chain reaction were used to quantify the ER α (ESR1) expression levels, and the Sequenom EpiTYPER assay was used to delineate the methylation patterns in the ESR1 promoter. We found that ESR1 expression was significantly reduced in tumor tissues (P < 0.001) compared to adjacent non-cancerous tissues. The CpG sites around the transcription start site were significantly hypermethylated in the tumor (P < 0.0001). This methylation pattern also correlated with the gene expression (P < 0.0001). Additionally, we found that the hypermethylation of ESR1 was associated with the presence of fibrous capsules (P = 1.2 × 10^-4), the absence of microvascular invasions (P = 8.0 × 10^-4), thin trabecular pattern (P = 0.025), and lower histologic gradings (P = 5.2 × 10^-3). Thus, ESR1 expression is a candidate tumor suppressor gene in HCC. Further, promoter hypermethylation may be a mechanism by which expression of ESR1 is repressed, and the extent of hypermethylation of ESR1 may be a marker for HCC status and progression.

Induction of the mesenchymal to epithelial transition by demethylation- activated microRNA-200c is involved in the anti-migration/invasion effects of arsenic trioxide on human breast cancer cells

Breast cancer is a major health problem worldwide. Current standard practices for treatment of breast cancer are less than satisfactory because of high rates of metastasis. Arsenic trioxide (As(2)O(3)), which induces demethylation of DNA and causes apoptosis, has been used as an anti-tumor agent. Little is known, however, regarding its anti-metastatic effects. The microRNA-200c (miR-200c), which is frequently lowly expressed in triple negative breast cancers (TNBCs), inhibits metastasis by inducing the mesenchymal to epithelial transition (MET). Here, we report that As(2)O(3) attenuates the migratory and invasive capacities of breast cancer cells, MDA-MB-231 and BT-549. Notably, As(2)O(3) induces an MET in vitro and in vivo, as determined by the increased expression of the epithelial marker, E-cadherin and decreased expressions of mesenchymal markers, N-cadherin and vimentin. Moreover, As(2)O(3) up-regulates the expression of miR-200c through demethylation. Over-expression of miR-200c enhances the expression of E-cadherin and decreases the expressions of N-cadherin and vimentin. Further, in MDA-MB-231 cells exposed to As(2)O(3), knockdown of miR-200c blocks the As(2)O(3) -induced MET. Finally, in MDA-MB-231 and BT-549 cells exposed to As(2)O(3), knockdown of miR-200c decreases the As(2)O(3) -induced inhibition of the migratory and invasive capacities. By identifying a mechanism whereby As(2)O(3) regulates miR-200c and MET, the results establish the anti-migration/invasion potential of arsenic trioxide.