Cancer cells have altered metabolism to cope with high energy demands associated with cell proliferation, migration and survival. The Conte and Grigoriadis labs explore the use of metabolic profiling, transcriptomics and proteomics to elucidate the role of two RNA binding proteins, LARP4A and LARP4B, that are key regulators of cancer cell behaviour and tumour progression.
We recently demonstrated that silencing of LARP4A and 4B inhibits cancer cell properties in vitro, and reduces tumour formation in xenograft models in vivo. LARP4A and 4B regulate the translation of a subset of mRNAs but the full list of target RNAs regulated by each LARP4 protein and the mechanisms linking mRNA translation regulation, cancer cell behaviour and tumourigenesis is not known. We have used NMR-based metabolomics, cell bioenergetics and RNAseq analyses of LARP4A/B-depleted cancer cells to identify the metabolic and signalling pathways affected by these proteins, and multiomics analysis identified targets involving hypoxia and glycolysis that are perturbed in knockdown cells. Moreover, LARP4A and LARP4B deletion appears to show differential cellular response at mitochondrial level. In this project the student will be trained in complementary skills of both Conte and Grigoriadis labs, including RNA structural biology, cancer cell biology and in vivo technology to achieve the following goals:
Year 1: Perform metabolomics, respirometry and proteomics profiles of cancer cell lines under different stress conditions (hypoxia, starvation) that are depleted in LARP4A and/or LARP4B using siRNA and CRISPR/Cas9 technologies. Experiments will be analysed by targeted and untargeted profiling for analysis of global changes.
Year 2: Validation of selected dysregulated genes, analyse metabolic profiles and function following small molecule inhibition and selected mutagenesis.
Years 2-3: Functional investigation of targets in vivo using multiple xenograft transplantation approaches; molecular analysis of LaRP4A/B RNA target interactions and write-up.
These studies will shed light for the first time on the mechanisms underlying the cancer-related functions of LARP4A and LARP4B.
During the rotation the student will focus on metabolism analysis of MG63 osteosarcoma cells, and how this is affected by sliencing LaRP4A/B proteins. Techiques will include cell biology, western blotting, respirometry and omics analysis. Details will be worked out with the student and will depend on latest data generated in the labs.