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Epigenome-targeted therapy for cholangiocarcinoma.

Periodic Reporting for period 1 - EpiTarget (Epigenome-targeted therapy for cholangiocarcinoma.)

Berichtszeitraum: 2017-02-01 bis 2019-01-31

Cholangiocarcinoma (CCA) comprise a family of rare orphan malignancies arising throughout the biliary tract. These cancers are typified by asymptomatic presentation, late diagnosis and extremely poor prognosis. The majority (70-90%) of CCA patients who are diagnosed with advanced disease, in addition to resected patients whose tumours recur, undergo chemotherapy with gemcitabine and cisplatin. This regimen is purely palliative, non-FDA-approved for CCA and median patient survival under this treatment regimen is less than 12 months. Overall, 0-5% CCA patients remain alive at 5 years post-diagnosis.

Unlike other cancers, CCA incidence and mortality rates have increased among males and females in Europe and the wider world. Together, these atypical clinical trends indicate CCA patients comprise a growing demographic of society for whom modern healthcare can do little. Furthermore, even if robust biomarkers for early disease detection are discovered in the future, general population screening for this rare disease would be practically and economically infeasible. Therefore, it is evident that new therapeutic regimens are urgently needed for the majority of patients who present with advanced and metastatic disease.

Initially, the interpretation of sequencing studies in CCA was somewhat bleak as they painted a picture of biliary tumours as highly heterogeneous malignancies with low-to-moderate mutation frequencies in ‘classic’ cancer-associated genes and identified significant proportions of patients with no mutations at all in such genes. However, these studies universally highlighted recurrent mutations in epigenetic regulators which, given their normal function in epigenome homeostasis, implicates extensive epigenome dysregulation in CCA. Epigenome-targeted therapy affords several advantages over mutation-based approaches, including the innate reversibility of epigenetic marks and the fundamental importance of epigenetic plasticity and remodelling to chemoresistance and metastasis. Accordingly, the objectives of this EpiTarget fellowship were to decipher the genomic and epigenomic landscapes of patient tumours and synergistically evaluate the therapeutic potential of clinically-tolerable epigenetic drugs in CCA.
To investigate the therapeutic potential of epigenome-targeted therapy for CCA, I treated 10 different CCA cell line models with 11 different ‘epigenetic drugs (‘epi-drugs’) which target different epigenetic enzymes. By modelling the response of CCA cells to broad epi-drug concentrations , I identified GSK J4 HCl (a histone demethylase inhibitor) as the most promising drug candidate. Subsequent experiments at physiologically-attainable concentrations revealed that this while this epi-drug significantly impeded tumor cell proliferation, it did not actively induce cell death. These data indicate that the effects of epi-drug treatment are largely cytostatic and that it should be pursued as part of a combination therapy instead.

The modest survival advantage of current chemotherapy agents (<1 year) is indicative that new compounds should be evaluated as combination therapy partners for our epi-drugs. To streamline prospectively novel targeted-therapies into clinical use for CCA patients, we applied state-of-the-art high-throughput drug repositioning experiments in our previously screened cell lines. Importantly, all 465 compounds tested are already in routine clinical use or have reached the late stages of clinical trials for other diseases. Among these, I have identified a significant number of compounds with potent tumour-selective therapeutic potential, in particular heat shock protein inhibitors and chemotherapies used for other cancers.

In parallel to cell line experiments, I profiled and analysed transcriptomic, epigenomic and mutational data from over 400 CCA patients with localized disease. As expected, extensive epigenomic remodelling was identified as a hallmark of CCA which converged to dysregulate key cancer pathways. Importantly, I further obtained access to unique CCA patient autopsy samples which comprised primary tumours with matched distant metastases. Through integrative genomics, I tracked the molecular evolution of primary tumours as they spread to ultimately kill the patients and revealed that the epigenetic alterations in the primary tumour are consistently inherited by the metastases. These data suggest that metastases inherit the same epigenetic vulnerabilities as the primary tumours and therefore our candidate epigenome-directed therapies may be of benefit irrespective of the tumor stage of patients at diagnosis.

These results have been disseminated by presentations at ‘New Targets to Fight Cancer’ MSCA IF monitoring meeting (Brussels, 2017), EASL ILC (Paris, 2018), ILCA (London, 2018) and Danish Cancer Society’s ‘Metastasis as a Systemic Disease’ meeting (Copenhagen, 2017). To date, this EpiTarget fellowship has produced one first co-author research paper (PMID: 29278425) and one first co-author review paper (PMID: 28645654). Throughout my MSCA fellowship, I have generated novel datasets (epi-drug, high-throughput drug repositioning, transcriptomics, epigenomics) on CCA patients and models which will be further exploited throughout my new position as Assistant Professor in the host lab at University of Copenhagen (Feb 2019 – Jan 2023). In turn, I anticipate that this work will generate two further first author publications, one focusing on epigenomic analysis of patient tumours and the other corresponding to epigenetic agents in novel combination therapies for CCA.
Through this EpiTarget fellowship, several significant advances have been achieved in the field of CCA genomic medicine – these include exploitation of expansive patient material available in the host laboratory to generate statistically powerful patient datasets, including the first ever reported (epi)genomic profiling of metastatic CCA; application of cutting-edge technologies (microarrays, sequencing) to patient and cell line biomaterial; and state-of-the-art high-throughput screening with a customized library of repositioned, ‘ready-for-action’ drugs.

Due to the extensive amount of data generated during this project, several prominent outstanding questions have emerged which hold potential to significantly contribute to advancing knowledge of the pathobiological architecture of biliary tumours and improving clinical management of CCA patients. Specifically, I will further investigate the mechanism(s) underpinning therapeutic response to GSK J4 HCl epi-drug through genetic manipulation of its target lysine demethylases that are found to be dysregulated in CCA patients. I will apply ‘chemoinformatics’ strategies to predict and later experimentally confirm synergistic drug partners for GSK J4 HCl from our high-throughput drug repositioning screen. Finally, I will evaluate the therapeutic efficacy of GSK J4 HCl monotherapy and GSK J4 HCl combination therapy in mouse models subjected to liver transplantation of CCA cells.

Economically, our use of a drug repositioning strategy which aims to identify new purposes for old drugs in CCA eliminates the protracted development time and high cost of developing new compounds. Socially, our data in support of the therapeutic efficacy of these ‘old drugs’ in CCA facilitates streamlining of these safe and tolerable agents into clinical trials for patients who currently lack viable treatment options.
Overview figure of EpiTarget project (the problem, the project, the future)