Readers, writers and erasers

The epigenetic landscape is deregulated in cancer due to aberrant activation/ inactivation of enzymes maintaining and modifying the epigenome. Aberrations at the global histone level and/or specific histone modifications may produce distorted patterns of gene expression and malfunction of proteins that regulate chromatin structure. Recent whole genome studies demonstrated that histones and chaperone proteins harbour mutations that may result in gross alterations of the epigenome leading to genome instability. IDH1/2 (isocitrate dehydrogenase 1/2) mutations have been detected in hematologic malignancies and certain solid tumours. Point mutations in IDH1/2 confer a gain-of-function in cancer cells, resulting in accumulation of the D-2-hydroxyglutarate (D-2HG). High levels of D-2HG interfere with cellular metabolism and epigenetic regulation by inhibiting histone and DNA demethylases, which results in blocking cellular differentiation. Histone deacetylases (HDACs) are critical regulators of gene expression that promote chromatin changes by deacetylating histones. Aberrant regulation of HDACs contributes to malignant transformation and progression in many human cancers. Dysfunction of the histone lysine methyltransferase EZH2 occurs in numerous cancers. EZH2 a part of the polycomb repressive complex 2 which catalyses trimethylation of histone H3 lysine 27. It supports undifferentiated phenotype and blocks differentiation during embryonic development and carcinogenesis. Epigenetic-based mechanisms are reversible and 'resetting' the abnormal cancer epigenome by pharmacological compounds targeting epigenetic enzymes is a promising strategy. Several novel drugs targeting tumours with mutated IDH1/2/ and numerous HDAC inhibitors have been identified. These compounds cause cell cycle arrest or death, inhibit DNA repair and some entered clinical trials for cancer treatment.

An increasing body of evidence is implicating several epigenetic mechanisms as driving forces of neoplastic transformation. Among these, aberrant DNA methylation is, by far, the most widely studied, followed by deregulated expression of chromatin machinery proteins and non-coding RNAs, including microRNAs. Importantly, cancer-related epigenetic alterations may provide novel cancer biomarkers, intended for early detection and diagnosis, assessment of prognosis, and prediction of response to therapy. The importance of early diagnosis in Oncology has been emphasised and although current methodologies (such as cytology, histopathology, immunohistochemistry, etc) play a critical role, molecular markers may complement or, eventually, replace them if more effective. Because epigenetic alterations often precede the emergence of the malignant phenotype, they are advantageous for early cancer detection. They might also be detected in clinical samples, including those obtained by biopsy, as well from those obtained by non-invasive methods, such as urine. Moreover, early detection of cancer relapse before it manifests clinically (or on imaging during routine patient follow-up) might be accomplished through epigenetic-based biomarkers. Some epigenetic alterations have also been associated with tumour behaviour and may, thus, serve as prognostic biomarkers. 

In this talk, Professor Jerónimo will focus on the major recent findings obtained by her research team regarding epigenetic mechanisms implicated in urological tumorigenesis as well as the potential usefulness of epigenetic-based biomarkers for detection and prognostication in these cancers. 

Aberrant activity of epigenetic enzymes plays a role in tumorigenesis. Reversal of these aberrant modifications has emerged as a strategy for cancer treatment. By applying epigenome-based patient stratification, the group identified a set of chromatin areas predictive for standard treatment resistance in leukaemias. Professor Altucci reports that a novel dual-epidrug, as effective in standard treatment resistant cancers. The group identified both the mechanistic insights of this action and biomarkers that might turn into a differential diagnostic tool for leukaemia patients. Together, the group provides proof of concept for the use of epigenome profiling coupled to epi-drugs to ‘personalise’ precision medicine.

Cardiovascular disease is a major cause of mortality and morbidity world-wide. Current algorithms for cardiovascular risk prediction, which combine behavioural, clinical, and biochemical markers, are, however, of limited accuracy. Understanding novel factors and mechanisms for cardiovascular disease development can contribute to the identification of at-risk individuals, who could benefit the most from preventive interventions. Non-essential environmental metals are emerging as major contributing factors to cardiovascular health in study populations exposed to low or moderate metal dose through air, food or water. Moreover, metals accumulate in the body where they can induce long-term damages. Dr Tellez-Plaza will be discussing available evidence in support of metals as environmental determinants of both epigenetic markers and cardiovascular disease in general populations. The identification of epigenomic regions that are environmentally regulated and may be involved in pathways related to cardiometabolic risk can enable the implementation of both population-based and personalised strategies for the control of cardiovascular disease in the population. Moreover, several lines of evidence suggest that environmental exposures can influence health outcomes in subsequent generations, due to epigenetic changes.  It is of interest, thus, to explore novel epigenetic approaches for prevention and treatment of disease, which may be relevant for future generations.

Fungal endophytes are known to produce a wide variety of secondary metabolites (SMs) involved in their adaptation and survival within higher plants. Plant-microbe interaction may influence the expression of some biosynthetic pathways, otherwise cryptic in these fungi when grown in laboratory conditions. Epigenetic small-molecule modifiers of Histone Deacetylase (HDAC) and DNA methyltransferase (DNMT) activities have been successfully used to perturb the fungal secondary biosynthetic mechanisms, which has led to the induction of the expression of silent metabolite pathways. Adding epigenetic elicitors in fungal endophyte fermentations may induce the expression of biosynthetic pathways which may occur naturally in plant-microbe interaction.

The effects of 7 epigenetic modifiers will be described for a case study group of 13 fungal endophytes fermented during 7 and 14 days to evaluate the possible activation of silent biosynthetic pathways compared to their growth in standard conditions. The increase in production titers of global SMs profiles in some of the strains was slightly higher when the elicitors were present from that inoculum stage. Strains that produced differential SMs in presence of the small elicitors were studied in detail and their principal induced components identified and quantified by metabolomics.

The described use of epigenetic modifiers in a systematic approach ensured a successful generation of new SMs on regular basis. Current scale-up, purification and chemical characterisation of other selected strains/conditions will be described for the most promising new metabolites induced.

Dietary agents from various sources target mechanisms involved in epigenetic gene regulation, including DNA methylation, histone modifications and noncoding RNAs. Recent research has indicated that gut microbial metabolites might be important mediators of these diet-epigenome interaction (Hullar MA, Fu BC. Cancer J 2014). Folate and B vitamins required to generate SAM for methylation reactions are provided by the gut microbiota. Phenolic acids generated by microbial degradation of dietary polyphenols inhibit DNMTs and HDAC activities. Berries and nuts are rich in ellagitannins, which are hydrolysed to ellagic acid and further microbially metabolised to urolithins. Whereas ellagitannin regulated the expression of small non-coding microRNAs, urolithins inhibit the activities or expression of HDACs and HATs in cultured cells. Glucosinolates from cooked cruciferous vegetables require gut bacterial thioglycosidases for cleavage to reactive isothiocyanates (ITCs). The diversity of the gut microbiome therefore affects the bioavailability of ITCs, which can be further metabolized to HDAC inhibitors. Fermentation of dietary fibre leads to formation of short chain fatty acids including butyrate. Butyrate has a dose-dependent dual effect on HATs and HDACs and both promotes proliferation and induces cell cycle arrest and differentiation Donohoe et al. Mol Cell 2012). Long-chain omega-3-fatty acids (LC ω-3-FA) regulate histone methylation and miRNA expression in vitro and in vivo. The availability and efficacy of LC ω-3 FA might be affected by gut microbial metabolism to conjugated linolenic acids (CLA), which were shown to modify methylation patterns of genes and expression of miRNAs involved in energy balance and lipid metabolism. In summary, these examples indicate that the gut microbiota interacts with the epigenome in various ways. Future studies need to integrate information on dietary intake, microbiome and metabolome, with genome-wide epigenetic profiling results to draw conclusions on how to influence this complex system in the direction of improved human health.