Epigenomic basis of drug resistance in Multiple Myeloma

Multiple myeloma (MM) is a cancer of white blood cells that predominantly affects patients aged over 65. With around 5700 new diagnoses every year, MM accounts for 2% of the annual cancer mortality in the UK. It is currently treated with a combination of medications (chemotherapy) with the addition of an autologous stem cell transplant (bone marrow transplant) in patients who are eligible. Several new drugs have been added to the repertoire of treatments available for MM, including third-generation immunomodulatory drugs (IMiDs, e.g. pomalidomide), second-generation proteasome inhibitors (PIs, e.g. carfilzomib and ixazomib), and monoclonal antibodies (mAbs) (e.g. elotuzumab and daratumumab).

Unfortunately, the vast majority of MM patients develop resistance to these treatments within months, leaving MM an incurable disease. Recent developments in whole-genome sequencing have revealed that myeloma is a genetically complex tumour. In particular, the Myeloma Genome project (MGP) has provided unprecedented insights into the disease. Additionally, even within individual patients, the tumour cells varied from one another (intra-tumour heterogeneity). However, these findings still fail to explain the observed treatment resistance patterns. Furthermore, structural changes in the genome remain practically irreversible.

In parallel there are multiple lines of evidence suggesting an important role for epigenetic deregulation in MM. The epigenome is composed of mechanisms that control how genes are turned "on" or "off". Enzymes involved in these mechanisms include Histone deacetylases (HDACs), DNA methyltransferases (DNMTs) and several other classes. The MGP identified recurrent mutations in epigenetic enzymes occur in over the half the patients analysed (e.g. NSD1, SETD2, KDM6A, DNMT3A,
EZH2). Of these, EZH2 an enzyme involved in methylation of histone, H3K27 was shown to be upregulated in association with resistance to bortezomib (a first-generation proteasome inhibitor). Using an experimental EZH2 inhibitor in these mice increased the MM cells' sensitivity to bortezomib treatment.

Our hypothesis is that drug resistance patterns are being driven by specific epigenetic mechanisms. Specifically, this project aims to define and map epigenome-wide critical parameters that drive drug resistance to two major classes of drugs used in multiple myeloma. Human myeloma cell lines will be used to model the disease in vitro. From each parent cell line, we will generate drug sensitive, single drug resistant and multi-drug derivatives, representing the patterns of resistance seen clinically. The epigenome will be interrogated systematically using Chromatin-Immunoprecipitation and Assay for Transposase Accessible Chromatin combined with high-throughput sequencing experiments (ChIP-seq and ATAC-seq, respectively). The generated data will be scrutinised using integrated computational analysis in co-ordination with transcriptomic data for the cell lines. The cell lines will be interrogated using both bulk and single-cell methods, allowing us to investigate both inter-tumour and intra-tumour variations in resistance development. The identified pathways will be validated using patient-derived samples. Subsequently, candidate pathways will be functionally interrogated using specific epigenetic inhibitors and chemical tools developed by the Oppermann group. Importantly, for several classes of epigenetic inhibitors, drugs are approved (e.g. HDAC inhibitors such as Panabinostat, DNMT inhibitors such as 5-Azacytadine) or are in clinical trials (e.g. several histone-methyltransferase inhibitors targeting e.g. EZH2 or DOT1L, or multiple BET bromodomain inhibitors). Successful validation could thus lead to clinical translation to improve patient survival in multiple myeloma.