Defining the impact of chromatin and transcriptional regulator-driven phase separation in cancer cell behaviour.

About the Project

Oesophageal adenocarcinoma (OAC) is a deadly disease with poor survival statistics, is one of the highest incidence cancer types and is growing in prevalence, particularly in the developing world. A major reason for this, is the lack of treatment options, due mainly to our lack of knowledge of molecular targets that arise from a detailed molecular understanding of the disease. Over the past decade, our own work has helped to bridge this gap by investigating the gene regulatory mechanisms that lead to and maintain the cancer state in OAC (eg see Rogerson et al., 2019; Ogden et al., 2022; Ahmed et al., 2023; Yang et al., 2024). However, numerous questions remain. For example, although we have discovered that the precursor metaplastic state, Barrett’s oesophagus, shares gene regulatory networks with early developmental populations (Baker et al., 2025), how this is reconfigured in OAC progression and then reutilised following therapeutic drug treatment is poorly understood. Furthermore, there are numerous uncharacterised gene regulatory proteins beyond these networks that have been implicated in OAC, and we have identified dozens of potential new players from a recent CRISPR viability screen.

Liquid-liquid phase separation (LLPS) is being increasingly recognised as an important contributor to gene regulatory outcomes. Many chromatin and transcriptional regulators have been shown to function through harnessing this property, which is thought to compartmentalise and enhance the efficiency of regulatory activities. A growing number of examples have been revealed in cancer scenarios, particularly in the context of oncogenic fusion proteins. This provides a potential novel therapeutic opportunity by directly targeting phase separated regulatory complexes through approaches such as “kill switches” or targeted drug delivery.

In this project we will study a set of essential chromatin and transcriptional regulators that are essential for OAC viability (and hence potential therapeutic targets). We will identify which of these undergo LLPS, then identify important residues driving this process. Mutant alleles will be created through CRISPR-mediated genome editing and functional consequences on molecular activities a cellular behaviour revealed. Regulatory proteins will then be selected based on the importance of LLPS for their activity and reagents developed that target this property with a view to generating novel therapeutics.

Outcome: A comprehensive understanding of chromatin and transcriptional regulators use of LLPS to drive cancer specific functions in OAC, leading to novel therapeutic possibilities.

Training and techniques provided: This project will involve training in a variety of laboratory techniques, supplemented with bioinformatics approaches. The core modalities will include protein biochemistry and advanced molecular biology techniques, encompassing genome-wide sequencing based assays and CRISPR-mediated genome editing. Further experience will be gained in light microscopy. Bioinformatics training will also be provided for analysing genome-wide regulatory events.