Intragenic CpG islands and imprinting

In mammals, DNA methylation is essential for development and differentiation and targets mainly the cytosines located in the CpG context. Whereas the genome is globally depleted in this dinucleotide, there are clusters of CpGs known as CpG islands (CGI). When associated with promoter regions, CGIs are globally devoid of DNA methylation but where these regions are methylated, this is correlated with repression. By contrast, CGIs localised in the gene body (or intragenic CGIs, iCGIs), are prone to acquiring DNA methylation during differentiation and development. Interestingly, most of this iCGIs also show tissue-specific promoter activity and expression from the host gene and the CGI is important in the regulation of this tissue- and developmental stage-specific methylation patterns. This suggests important crosstalk between iCGIs and their host genes and an important role for iCGIs in cell fate specification. This is supported by our studies, in mouse, at the imprintedMcts2/H13 locus where the expression of the imprinted retrogene Mcts2 from an iCGI leads to alternative polyadenylation at the host gene transcript (H13). In this context, our project is to elucidate how intragenic promoter activity is regulated and how this activity could influence the transcript diversity from the host gene with a special focus on alternative polyadenylation. To answer these questions, our group combine genome-wide studies on in vitro differentiation systems and detailed molecular analysis at the Mcts2/H13locus model.

Cancer epigenetics and tumour metabolism

Epigenetic deregulation is a cardinal manifestation of tumourigenesis and a well-recognised hallmark of cancer. Deregulation of metabolic networks in cancer cells allows them to divert building blocks to biomass production and can cause changes in the epigenetic landscape. Using pheochromocytomas and paragangliomas (PPGLs) as a paradigm, our group studies the interactions between the metabolome, hypoxia and epigenetic regulation in cancer. PPGLs are the most heritable type of cancer and can appear in multiple body sites. Recently, inactivating mutations in a number of key metabolic genes (e.g. succinate dehydrogenase SDHx, fumarate hydratase FH, malate dehydrogenase MDH2) have been shown to induce abnormal levels of intermediate products that inhibit α-ketoglutarate-dependent dioxygenases. This very diverse family of enzymes includes TET and Jumonji-domain demethylases and results in DNA and histone hypermethylation. Using a combination of experimental and bioinformatic approaches we study the effects these mutations have on the epigenome. We also want to find novel ways to exploit the epigenetic aberrations in these tumours and use DNA hypermethylation as a method to classify genetic variants of unknown significance in patients. As part of King’s Health Partners, we have very strong collaborations with local clinicians who care for patients with PPGLs and as a tertiary centre for this disease, we have collected a very large number of samples. Additionally, we have multiple national and international collaborations with academic centres and research institutes and we are active members of the European Network for the Study of Adrenal Tumours.

European Network for the Study of Adrenal Tumours

Epigenetic and genetic mechanisms in heart valve formation

Endocardial cells (ECs) form the inner lining of the heart and are critical for heart valve formation. They have a unique ability to undergo endothelial-to-mesenchymal transition, a process essential for valve development, and are characterised by the early expression of the Nfatc1 transcription factor during heart development. These characteristics make ECs unique from endothelial cells (ETs), despite both sharing a common precursor origin and morphological features. We hypothesize that ECs become distinct from ETs via the expression of a subset of genes that are regulated differently and are critical for valve formation. Currently, we are investigating RNA-seq data from ECs and ETs generated using an NFATc1-mcherry transgenic mouse line to identify key genes specific for EC-fate determination. Candidate genes and regulatory elements are being validated via qPCR and in situ hybridisation assays with functional assays ablating candidates in vitro assays. Further ‘omics analyses aim to encompass single-cell RNA-seq and capture HiC to delineate individual transcriptomes and detect long-range tissue-specific contacts respectively.

Epigenetics in Haematological cancer

Hydroxyurea (HU) is the first-line treatment for high risk myeloid proliferative neoplasms (MPN) which acts by inhibiting the cell cycle. However, HU is also a treatment for sickle cell disease, where its therapeutic effect is manifested through the induction of foetal haemoglobin. This drug has been used for more than 40 years, and its mechanism of action still doesn’t explain it multiples effects seen in patients. In this study, we aim to understand the effects of HU treatment from an epigenetic perspective by analysing gene expression and DNA methylation in MPN patients and in a mouse model of the disease. We have identified significant changes in the expression of genes involved in the immune system and protein translation at the stem cell level. Moreover, using these data coupled to DNA methylation data, we have identified relevant disease genes that are affected by HU. These genes are still under investigation, and these novel findings may potentially lead to new therapeutic targets for treatment.

HIV-1 mediated reprogramming of T cell gene expression networks

A collaborative project connecting epigenetics and infection centres around the characterisation of the transcriptomic and epigenomic response to HIV-1 infection in CD4+ T cells. Though merging techniques used in traditional molecular virology with that of genome-wide transcriptomics and epigenomics, this project aims to uncover novel molecular pathways important in virus production, persistence and dissemination as well as those involved in the antiviral immune response.