Deciphering the role of RNA localisation in cancer progression

Each cell in our body contains the same genetic information, yet this information is decoded in vastly different manners, allowing different cells to acquire distinct roles, which are together needed for the proper functioning of our tissues and organs. Importantly, accurate decoding of the genetic information is often disrupted in diseases such as cancer, allowing the malignant cells to acquire undesired properties such as uncontrollable cell division, evasion of the immune system, or invasion and colonisation of the other parts of the body. The genetic information is stored in DNA molecules, which reside in a part of cell called nucleus. To allow the stored information to be read and acted upon, an intermediate molecule, called RNA, acts as the messenger carrying the information outside of the nucleus. The RNA then moves around the cell until it is delivered to protein making factories called ribosomes, which use it as a blueprint to produce the many different types of proteins that are needed for distinct cellular functions. A major unanswered question in cell biology is how RNA molecules move around the cell, and how their distribution inside the cell affects the decoding of the genetic information. Another important question is whether the distribution of RNA molecules is disrupted in cancer cells, and if so, how such disruption can promote different aspects of malignancy.

To address these questions in a comprehensive manner, we have developed a new method to simultaneously monitor the distribution of all RNA and protein molecules inside of the cell. Using this method, we have analysed cells at different stages of becoming cancerous, showing that certain RNA molecules greatly change their distributions as cells become more malignant. Now, we want to understand how these changes occur at the molecular level, and more importantly, how they assist the cells to become more malignant and aggressive during the course of cancer development. To do this, we will use a variety of state-of-art molecular and cellular approaches to investigate which cancer-related changes in RNA distributions are commonly seen in patients. We will then reveal the molecular mechanisms that are responsible for mediating these changes. Finally, we will assess how these changes promote malignancy in animal models of cancer. Addressing these questions will not only greatly advance our understanding of RNA distribution inside the cell and its impact on cancer development, but will also have a major impact on development of novel molecular therapeutic strategies that can target cancer cells by modulating the distributions of specific RNA molecules.

Recent studies have shown that the majority of eukaryotic RNAs are localised to specific subcellular compartments. However, how spatial organisation of RNAs impacts on post-transcriptional regulation, and how this is dysregulated in diseases such as cancer, remains unclear. Our previous studies have demonstrated that RNA localisation to actin-rich protrusions plays an important role in regulation of growth and invasion in highly aggressive cancers (Mardakheh et al., 2015, Dev Cell; Dermit et al., 2020, Dev Cell). This raises the possibility that RNA localisation to other subcellular compartments may also play an important role in cancer progression. To study the role of RNA localisation in a systematic manner, we have developed a novel multi-omics method named Crosslinking & Fractionation (CLIF), which enables genome-wide profiling of RNA and protein localisations to different subcellular compartments. Using this method, we have revealed several changes in RNA localisation patterns that occur in a model of breast cancer progression. In this proposal, we aim to reveal which of these patterns of RNA localisation change are conserved during the progression of human breast cancers, assess their functional impact on post-transcriptional regulation of the affected transcripts, before dissecting the molecular mechanisms that mediate the localisation changes during malignant progression. We will then assess the functional impact of the identified RNA localisation-mediated dysregulations on breast cancer progression, in vivo. This work will systematically uncover novel post-transcriptional mechanisms that regulate cancer progression through RNA localisation. Since a significant degree of gene expression dysregulation that occurs in cancer is post-transcriptional, our findings will have profound implications with regards to how such dysregulations can be detected via monitoring RNA localisation, or therapeutically targeted via interfering with the localisation mechanisms.