MICA - Developing novel single-cell multiplexing methods to identify drug targets for the treatment of multiple myeloma

Multiple Myeloma is a bone marrow cancer that affects over 5,700 new patients a year in the UK. Current response rates to treatment are varied and there is a mean survival age of only 4-5 years, with a 10-year survival rate of only ~3%. A significant proportion of treatment failure is due to the emergence of multi-drug resistance, which arise because of changes (mutations) in the nucleotides that form the building blocks of our DNA. RNA is a type of DNA and mostly acts as a messenger to carry out the instructions of DNA. Epigenetics is the addition of information on top of the DNA sequence that can modify the behaviour of a cell. This is achieved by adding a variety of chemical modifications or "marks" to the nucleotides.

Historically, scientists have investigated complex disease biology by mashing up pieces of tissue and taking biological measurements to work out the causes of disease. This is akin to blending fruit into a smoothie and then giving it to someone else to work out the ingredients by looking through the glass. Some fruit may be easy to identify, while others may be impossible to recognise. More recently, scientists have developed technologies that have allowed us to reconstruct the smoothie more easily by looking at its individual parts in finer detail. These "single-cell" technologies allow us to look at the components of the tissue one cell at a time and permit us to work out what may be causing disease. With this information we can design better drugs that target disease. In this fellowship, I will develop novel single-cell technology that are capable of capturing many more biological readouts than previously possible with currently technologies. This technology will then be applied to understand DNA, RNA and epigenetic mechanisms that contribute to the development of a bone cancer called Multiple Myeloma (MM).

In partnership with a biotechnology company, I have developed such a technology within in my lab that is capable of measuring RNA and DNA simultaneously from the same single cell. The first aim of this fellowship will be to extend the utility of this technology so that I can increase the different types of measurements that are possible. For example, I will develop a method that makes it possible to measure both RNA and the epigenetic marks on the DNA. Next, I will use this technology to investigate MM disease.

Specifically, I will ask the following questions:
1) why do patients develop MM? and
2) why do patients develop resistance to current clinical therapies?

Ultimately, the main goal of my research is to better understand MM disease biology so we can develop new medicines to treat this incurable disease.

In order to work out why drug resistance occurs we need to make sense of the patterns of data that are generated using our single-cell technologies. Given the large amount of data generated during this project, I will use my skills as a software developer to generate computer code that will automate this process. Ultimately, outputs from this code will allow me to generate a map of disease that I can then use to identify drug targets for treating MM patients.

Why does this project have a greater chance of success?

Very few methods have been developed that can look at more than one biological measurement simultaneously. The assays that I will develop during this fellowship, which are based on our unique single-cell technology, will provide and unparalleled understanding of the complex mechanisms that contribute to the development of MM and drug resistance. This timely technology will allow me to identify novel drug targets for MM, which will then be followed up in pre-clinical models within the Oxford Centre for Multiple Myeloma Research and ultimately translated towards the clinic.

My goal is to develop novel multiplexed single-cell technologies to identify the mechanisms that contribute to Multiple Myeloma (MM) disease pathology. MM is a cancer of plasma cells in the bone marrow, that due to its rapid proliferative function, can quickly develop resistance to first line proteasome therapy. Currently, the mechanisms that contribute to MM development or drug resistance are poorly understood. A better understanding of the complexity and diversity of the MM bone marrow tumour microenvironment (TME) is required to identify novel treatment targets. Given the cellular heterogeneity within the TME, the TME needs to be studied at the single-cell level. However, current single-cell methods are costly, specialised and most are restricted to measuring only one analyte at a time, typically RNA.

In collaboration with colleagues at a UK biotechnology firm, we have established cost-effective multiplexed single-cell technology that is capable of capturing both RNA and DNA on the same oligonucleotide. This technology therefore enables the measurement of both the transcriptome as well as the accessibility of the chromatin, within the same cell - an important advance in the area of single-cell technology. To realise the full potential of our technology, I will expand its utility to include the multiplexing of transcriptomics with epigenomics and genomics (mutational profiling). These improvements will be used to profile bone marrow samples isolated from pre-malignant patients, patients with MM, and MM patients with drug resistance. To facilitate biological interpretation of the data, I will develop single-cell computational tools and systems biology methodologies. These will allow me to map the interactions between the different biological components of the TME and inform how MM develops and drug resistance occurs. Ultimately, I will generate a list of priority drug targets that will be followed up by the Oxford Centre for MM Research, University of Oxford.