Project ID CM-HD2023_09


Co Supervisor 1A Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical BiosciencesWebsite

Co Supervisor 1B Dept Infectious Diseases, School of Immunology and Microbial SciencesWebsite

LARP RNA binding proteins promote tumorigenesis via distinct subcellular RNA targets and mechanisms

RNA-binding proteins (RBPs) coordinate posttranscriptional gene expression via multiple mechanisms, including modulating coding and ncRNA processing and maturation, subcellular localisation or RNA translation.

Many RBPs are now known to be deregulated or mutated in numerous cancers. Despite being more numerous than transcription factors, RBP-mediated control is relatively unexplored. This project will elucidate molecular mechanisms and functions by which RBPs dysregulate translation promoting tumorigenesis.

We will focus on La-related protein superfamily (LARPs). We have shown that LARPs’ altered expression or aberrant activation facilitates tumour-specific gene and metabolic reprogramming. However, data is limited. We aim to investigate LARP molecular mechanisms in cancer-related phenotypes, which can lead to improved therapeutics.

1. To reveal the mechanisms by which LARPs promote invasion and metastasis, we will perform and integrate three types of high-throughput data: (1) individual-nucleotide resolution crosslinking immunoprecipitation sequencing (iCLIP-seq) to identify direct RNA targets, (2) Frac-seq (Figure 1) to determine how LARPs regulate RNA expression, (3) metabolomics to determine metabolic reprogramming. We will use specific cancer cell models depleted in LARPs using siRNA and/or CRISPR/Cas9. Years 1-2
2. To elucidate how LARPs select and modulate their targets, we will explore candidates from goal 1 and perform in vitro biochemical, biophysical and structural analyses. Years 2-3
3. To validate mechanisms of action we will evaluate the effect of dysregulated genes on transcriptomics and metabolism of cancer cells following small molecule inhibition and/or selected mutagenesis (from goal 2). Years 3-4

One representative publication from each co-supervisor:

• Cruz-Gallardo, I., Martino, L., Kelly, G., Atkinson, A., Trotta, R., De Tito, S., Coleman, P., Ahdash, Z., Gu, Y., Bui, T.TT Conte, M.R.* (2019) LARP4A recognises polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res., 47:4272-4291, doi: 10.1093/nar/gkz144.

• Martinez-Nunez et al., Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq. (2018) J Immunol., 201:251-263. doi: 10.4049/jimmunol.1701798.