Regulation of class IIa HDAC activities: It is not only matter of subcellular localization

In response to environmental cues, enzymes that influence the functions of proteins, through reversible post-translational modifications supervise the coordination of cell behavior like orchestral conductors. Class IIa histone deacetylases (HDACs) belong to this category. Even though in vertebrates these deacetylases have discarded the core enzymatic activity, class IIa HDACs can assemble into multiprotein complexes devoted to transcriptional reprogramming, including but not limited to epigenetic changes. Class IIa HDACs are subjected to variegated and interconnected layers of regulation, which reflect the wide range of biological responses under the scrutiny of this gene family. Here, we discuss about the key mechanisms that fine tune class IIa HDACs activities

MicroRNA Regulation of Epigenetic Modifiers in Breast Cancer

Epigenetics refers to the heritable changes in gene expression without a change in the DNA sequence itself. Two of these major changes include aberrant DNA methylation as well as changes to histone modification patterns. Alterations to the epigenome can drive expression of oncogenes and suppression of tumor suppressors, resulting in tumorigenesis and cancer progression. In addition to modifications of the epigenome, microRNA (miRNA) dysregulation is also a hallmark for cancer initiation and metastasis. Advances in our understanding of cancer biology demonstrate that alterations in the epigenome are not only a major cause of miRNA dysregulation in cancer, but that miRNAs themselves also indirectly drive these DNA and histone modifications. More explicitly, recent work has shown that miRNAs can regulate chromatin structure and gene expression by directly targeting key enzymes involved in these processes. This review aims to summarize these research findings specifically in the context of breast cancer. This review also discusses miRNAs as epigenetic biomarkers and as therapeutics, and presents a comprehensive summary of currently validated epigenetic targets in breast cancer

Identification of a cancer stem cell-specific function for the histone deacetylases, HDAC1 and HDAC7, in breast and ovarian cancer

Tumours are comprised of a highly heterogeneous population of cells, of which only a small subset of stem-like cells possess the ability to regenerate tumours in vivo. These cancer stem cells (CSCs) represent a significant clinical challenge as they are resistant to conventional cancer therapies and play essential roles in metastasis and tumour relapse. Despite this realization and great interest in CSCs, it has been difficult to develop CSC-targeted treatments due to our limited understanding of CSC biology. Here, we present evidence that specific histone deacetylases (HDACs) play essential roles in the CSC phenotype. Utilizing a novel CSC model, we discovered that the HDACs, HDAC1 and HDAC7, are specifically over-expressed in CSCs when compared to non-stem-tumour-cells (nsTCs). Furthermore, we determine that HDAC1 and HDAC7 are necessary to maintain CSCs, and that over-expression of HDAC7 is sufficient to augment the CSC phenotype. We also demonstrate that clinically available HDAC inhibitors (HDACi) targeting HDAC1 and HDAC7 can be used to preferentially target CSCs. These results provide actionable insights that can be rapidly translated into CSC-specific therapies

GeromiRs Are Downregulated in the Tumor Microenvironment during Colon Cancer Colonization of the Liver in a Murine Metastasis Model

Cancer is a phenomenon broadly related to ageing in various ways such as cell cycle deregulation, metabolic defects or telomerases dysfunction as principal processes. Although the tumor cell is the main actor in cancer progression, it is not the only element of the disease. Cells and the matrix surrounding the tumor, called the tumor microenvironment (TME), play key roles in cancer progression. Phenotypic changes of the TME are indispensable for disease progression and a few of these transformations are produced by epigenetic changes including miRNA dysregulation. In this study, we found that a specific group of miRNAs in the liver TME produced by colon cancer called geromiRs, which are miRNAs related to the ageing process, are significantly downregulated. The three principal cell types involved in the liver TME, namely, liver sinusoidal endothelial cells, hepatic stellate (Ito) cells and Kupffer cells, were isolated from a murine hepatic metastasis model, and the miRNA and gene expression profiles were studied. From the 115 geromiRs and their associated hallmarks of aging, which we compiled from the literature, 75 were represented in the used microarrays, 26 out of them were downregulated in the TME cells during colon cancer colonization of the liver, and none of them were upregulated. The histone modification hallmark of the downregulated geromiRs is significantly enriched with the geromiRs miR-15a, miR-16, miR-26a, miR-29a, miR-29b and miR-29c. We built a network of all of the geromiRs downregulated in the TME cells and their gene targets from the MirTarBase database, and we analyzed the expression of these geromiR gene targets in the TME. We found that Cercam and Spsb4, identified as prognostic markers in a few cancer types, are associated with downregulated geromiRs and are upregulated in the TME cells.This work was supported by grants from Instituto de Salud Carlos III (AC17/00012), cofounded by the European Union projects (European Regional Development Fund/European Science Foundation, Investing in your future), (ERA-Net program EracoSysMed, JTC-2 2017) and (H2020-FETOPEN, Circular Vision, Project 899417); Diputación Foral de Gipuzkoa and the Department of Economic Development and Infrastructures of the Basque Government (DFG109/20) and the Department of Economic Development and Infrastructures of the Basque Government (DFG109/Grants Health Department of the Basque Government (Spain), RIS3 call, Exp. No. 2020333039 and 2020333001. 20)

The effect of histone deacetylase inhibitors on gene expression in breast cancer cell lines

Histone deacetylase inhibitors (HDIs) are a novel class of chemotherapeutics that have potent anti-proliferative and cytotoxic properties in many cancer-derived cell lines. Research has demonstrated that these compounds can activate genes such as the cell cycle inhibitor p21WAF1, while repressing the SRC and MYC proto-oncogenes. To investigate the effects of several HDI compounds in a panel of breast cancer-derived cell lines, a reverse transcriptase qPCR (RT-qPCR) and immuno-blotting approach was used. These compounds corresponded to various classes of these therapeutic drugs, and include Trichostatin A (TSA), Apicidin, Entinostat and Mocetinostat, while the cell lines were representative of the heterogeneity of breast cancer. It was hypothesised that while these drugs demonstrate similar cellular responses such as enhanced histone acetylation, cytotoxicity and p21WAF1 induction, they have different effects on their ability to repress genes. Using qPCR techniques, the expression of the p21WAF1, SRC and MYC was analysed following HDI treatment in four cell lines. SRC repression were observed in all cell lines following TSA and Apicidin treatment, whereas the effects of Entinostat and Mocetinostat were more diverse; these compounds had no effect or induced expression of SRC in T47D, Hs578T and HCC-1419 cell lines while repressing expression in the BT-474 cell line. The expression of MYC was down-regulated with TSA only in T47D and BT474 cell lines, while Apicidin, Entinostat and Mocetinostat induced expression in all cell lines. However, these four inhibitors induced p21WAF1 while exhibiting cytotoxicity and histone acetylation. In addition, it has been illustrated in the literature that RNA polymerase II-transcribed miRNA can be epigenetically modulated by chromatin-remodelling drugs. Therefore, the expression of tumour suppressor miRNA was analysed following drug treatment, and it was observed that HDIs up-regulated the expression of certain miRNAs in a cell-specific manner. miR-129-5p was induced with TSA and Entinostat in the T47D cell line, while miR-424 increased following TSA, Entinostat and Mocetinostat treatment in T47D and Hs578T cell lines. In addition, TSA induced expression of miR-9-3p in T47D, Hs578T and HCC-1419 cell lines. It was further determined that induction of these miRNA genes down-regulated the protein and/or mRNA expression of their target genes. The data presented in this thesis highlight the complex nature and the myriad effects of these inhibitors, and suggest that certain chemotherapeutics might have a clinical advantage over others in treating certain types of breast cancer

Epigenomic Regulation of Androgen Receptor Signaling: Potential Role in Prostate Cancer Therapy.

Androgen receptor (AR) signaling remains the major oncogenic pathway in prostate cancer (PCa). Androgen-deprivation therapy (ADT) is the principle treatment for locally advanced and metastatic disease. However, a significant number of patients acquire treatment resistance leading to castration resistant prostate cancer (CRPC). Epigenetics, the study of heritable and reversible changes in gene expression without alterations in DNA sequences, is a crucial regulatory step in AR signaling. We and others, recently described the technological advance Chem-seq, a method to identify the interaction between a drug and the genome. This has permitted better understanding of the underlying regulatory mechanisms of AR during carcinogenesis and revealed the importance of epigenetic modifiers. In screening for new epigenomic modifiying drugs, we identified SD-70, and found that this demethylase inhibitor is effective in CRPC cells in combination with current therapies. The aim of this review is to explore the role of epigenetic modifications as biomarkers for detection, prognosis, and risk evaluation of PCa. Furthermore, we also provide an update of the recent findings on the epigenetic key processes (DNA methylation, chromatin modifications and alterations in noncoding RNA profiles) involved in AR expression and their possible role as therapeutic targets

Epigenetics: Dissecting Gene Expression Alteration in PDAC

Pancreatic cancer is the fourth leading cause of cancer deaths, with a low 5-year survival rate of about 7% due to its highly invasive nature. Pancreatic ductal adenocarcinoma (PDAC) comprises more than 90% of all pancreatic cancer cases. At the time of detection, around 80% of cases harbor metastases due to the lack of early diagnosis. For decades, scientists have primarily focused on dissecting the origin of pancreatic cancer through genetic alterations and their contribution to diagnosis. Recently, PDAC research has turned into epigenetics to revolutionize our understanding about the silencing of critical regulatory genes. Epigenetic events can be divided mechanistically into various components, including DNA methylation, histone posttranslational modification, nucleosome remodeling, and regulation of transcription or translation by microRNA. The identified epigenetic processes in PDAC contribute to its specific epigenotype and are correlated phenotypic features. Strikingly, some of them have been suggested to have potential as cancer biomarkers, for disease monitoring, prognosis, and risk validation. As epigenetic aberrations are reversible, their correction will become as a promising therapeutic target

Novel epigenetic therapeutic strategies and targets in cancer

The critical role of dysregulated epigenetic pathways in cancer genesis, development, and therapy has typically been established as a result of scientific and technical innovations in next generation sequencing. RNA interference, histone modification, DNA methylation and chromatin remodelling are epigenetic processes that control gene expression without causing mutations in the DNA. Although epigenetic abnormalities are thought to be a symptom of cell tumorigenesis and malignant events that impact tumor growth and drug resistance, physicians believe that related processes might be a key therapeutic target for cancer treatment and prevention due to the reversible nature of these processes. A plethora of novel strategies for addressing epigenetics in cancer therapy for immuno-oncological complications are currently available - ranging from basic treatment to epigenetic editing. - and they will be the subject of this comprehensive review. In this review, we cover most of the advancements made in the field of targeting epigenetics with special emphasis on microbiology, plasma science, biophysics, pharmacology, molecular biology, phytochemistry, and nanoscience

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA

Breast: up and downstream SNVs model. (CSV 22.1 kb