Investigating the impact of CDKN2A loss on lipid and sterol metabolism in ccRCC

Primary supervisor: Barry Peck, Queen Mary University of London

Secondary supervisor: Samra Turajlic, Francis Crick Institute

Project

Clear cell Renal Cell Carcinomas (ccRCC) are an aggressive subtype of kidney cancer and tumour type of significant clinical unmet need due to the lack of efficient targeted therapies. These tumours are histologically distinct due to the presence of large subcellular organelles, called lipid droplets, that store fatty acids and cholesteryl esters, meaning ccRCCs are metabolically distinct and may be more sensitive to perturbations in the metabolic network, particularly lipid and sterol metabolism. Interestingly, driver alterations in CDKN2A in gliomas are known to impact lipid metabolism resulting in cells becoming sensitive to perturbations in the lipid peroxidase GPX4, resulting in ferroptosis. CDKN2A is recurrently altered in ccRCCs and we posit that its loss is influencing lipid and sterol metabolism, and this will impart sensitivity to metabolic enzyme inhibition that could be a novel vulnerability of CDKN2A-deplete primary and metastatic ccRCCs.

We have previously identified several novel anti-cancer targets involved with lipid metabolism, including SCD, FABP3 and ACSS2 (Peck & Schug et al 2016, Schug & Peck et al 2015, Lewis et al 2015). As a consequence of this work and others, small molecule inhibitors that target SCD and ACSS2 have been generated and are now being tested in patients (NCT04990739).
We have performed functional genomics and small molecule inhibitor screens in ccRCC cells and identified several enzymes involved with cholesterol metabolism to be required for cancer cell growth. Interestingly, silencing of several of these genes at the terminal end of the mevalonate pathway were shown to be more efficacious than targeting the initial steps of cholesterol metabolism i.e. the target of statins. One of these reductases, DHCR24, is upregulated in ccRCCs and associated with a poorer overall survival. Our novel and unpublished data show that it is also a potent anti-cancer target. Excitingly, in collaboration with Prof. Matthew Fuchter (Imperial College), we have designed, synthesized and tested novel selective small molecule inhibitors of DHCR24 and have shown that these, like GPX4 inhibitors, induce ferroptosis in ccRCC cells. Moreover, these inhibitors only work in cells with high lipid droplet number and are more efficacious that standard chemotherapies or inhibitors that target other metabolic enzymes.

Aims & Hypothesis: The aim of this project is to use cancer cell line spheroids and novel human plasma-like culture media, to more readily recapitulate the unfavourable tumour microenvironment encountered in vivo, and validate that loss of CDKN2A alters ccRCC lipid and sterol metabolism, rendering these cells more sensitive to inhibitors of sterol metabolism i.e. inhibitors of DHCR24. This project will uncover the exact mechanisms of this dependency at subcellular resolution, investigate SREBP signalling, lipid generation, accumulation and storage. We will validate this dependency in 3D models of ccRCC, including established cell lines derived from primary cancers and metastasis, and organoids.

Expected outcomes: We predict that DHCR24 dependency in CDKN2A-deplete ccRCCs is currently an unknown Achilles heel of these cancers and this project will generate significant clinical evidence that DHCR24 is upregulated in human ccRCCs and defines disease trajectory and treatment response.

References

1. The glutathione redox system is essential to prevent ferroptosis caused by impaired lipid metabolism in clear cell renal cell carcinoma. Miess H, Dankworth B, Gouw AM, Rosenfeldt M, Schmitz W, Jiang M, Saunders B, Howell M, Downward J, Felsher DW, Peck B & Schulze A. Oncogene (2018) 37, 5435-5450
2. Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal. Turajlic S, Xu H, Litchfield K, Rowan A et al. Cell (2018) 173 (3), 581-594.
3. Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Gatto F, Miess H, Schulze A & Nielsen J. Sci Reports (2015)
4. Lipid metabolism at the nexus of diet and tumor microenvironment. B Peck, A Schulze. Trends in Cancer (2019) 5 (11), 693-703
5. Improving the metabolic fidelity of cancer models with a physiological cell culture medium. Voorde JV, Ackermann T, Pfetzer N, Sumpton D, Mackay G, Kalna G, Nixon C, Blyth K, Gottlieb E & Tardito S. Sci Advances (2019) 5, 1 DOI: 10.1126/sciadv.aau7314