SC-Plasticity · Applying novel single-cell multiomics to elucidate leukaemia cell plasticity in resistance to targeted therapy

Novel targeted therapies are increasingly applied against a wide range of cancers. Although such agents can induce cures, most patients suffer from relapsed disease. Acute myeloid leukaemia (AML) is a prime example of a deadly disease, but we have a chance to dramatically improve outcomes if we can better understand resistance mechanisms against targeted agents that are transforming AML treatment, such as the BCL2 inhibitor venetoclax. AML is characterised by profound alterations in the epigenome that are correlated with poor survival. I therefore hypothesise that targeted drug pressure induces epigenetic plasticity that allows cancer cells to sample alternate chromatin or transcriptional states, a subset of which confer drug resistance. A major challenge is to define how mutations of epigenetic regulators in AML affect therapy responses due to clonal heterogeneity. To address this challenge, I will use and further develop my recently published single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method to link the genotype of expressed genes to transcription and methylation profiles of thousands of single cells. In this research proposal, I aim to (1) develop a new method linking epigenetic landscape, genotype and transcriptome at a single-cell level and define the impact of treatment on these interactions. (2) Analyse the genome-wide impact of epigenetic therapies. (3) Define the association between drug sensitivity and epigenetic modifications regulating pro-survival genes. To achieve my goals, I will apply my novel single-cell multiomics to samples from AML patients treated with venetoclax alone or in combination with epigenetic therapies and apply state-of-the-art technologies to established laboratory models. Our new approaches to fully understand the relationship between the genome, epigenome and transcriptome will advance fundamental biology. This has the potential to yield new therapeutic strategies to prevent and overcome resistance.