Understanding how CDKs control nuclear organisation and cell proliferation
Cell proliferation is important for health, but when uncontrolled it often leads to cancer. Cyclin-dependent kinases (CDKs) are key regulators of cell proliferation, and they trigger both DNA replication and mitosis. These distinct cell cycle phases are complex processes that require nuclear or even cellular reorganisation; their disruption is thought to underlie the genomic instability that is a hallmark of cancer cells. Although there exist multiple different CDK complexes, it appears that a single one suffices to promote these sequential transitions, at least in some cellular models. How the same enzyme can control two such radically different biological processes in a timely manner is not fully understood. Our current model (reference 1) is that the net balance of CDK activity and opposing phosphatase activity results in switch-like changes in phosphorylation of its substrates – of which there are many. If CDKs are the conductors of this orchestra, how do they keep it from becoming a cacophony? What are the underlying principles? And can we use this knowledge to generate more effective and less toxic cancer therapies?
To answer these questions, we use several biological systems, including mammalian cell lines and genetically modified mice, in combination with state-of-the-art techniques (genome engineering, high-resolution live microscopy, multi-omics approaches). We also collaborate extensively with specialists in different fields, for example in biochemistry, structural biology, molecular and mathematical modelling, and mouse embryonic development. Our main projects are the following:
How phosphorylation of CDK substrates alters their biochemical and biophysical properties.
Our recent work has identified a likely general mechanism whereby CDK-mediated phosphorylation of structurally disordered proteins controls biological phase separation and thereby assembly and disassembly of membraneless organelles. We are currently investigating the generality of this model using a combination of proteomics, biochemistry, molecular modelling and optogenetic approaches in combination with live cell imaging (see references 2, 3). We also want to know whether a single CDK-cyclin complex can promote different transitions in the vertebrate cell cycle by a similar mechanism; to test this we are using inducible genetic models to simplify the vertebrate cell cycle regulatory network.
The physiological roles and mechanisms of action of the cell proliferation antigen and CDK substrate, Ki-67.
Our recent work has shown that although Ki-67 expression is linked to cell proliferation because it is controlled by cell cycle regulators, it is not required for mammalian cell proliferation nor for mouse development and homeostasis. Instead, it controls global transcriptional programmes and is required for the characteristic organisation of heterochromatin. It is also required for multiple steps of carcinogenesis: transformation, tumour growth, metastasis. Ki-67 additionally influences drug sensitivity and anti-tumour immune responses (references 4-8). We are currently trying to link these observations to derive a mechanistic model of Ki-67 function. We are also investigating the effects of Ki-67 phosphorylation by CDKs.
Targeting the cell cycle for cancer therapy.
Many pharmacological inhibitors of CDKs have been developed, several of which have been approved in combination therapy for treatment of ER-positive metastatic breast cancer and are also being investigated for other cancers. As with many if not all cancer therapies, the main problems with CDK inhibitors are the incomplete understanding of their mechanisms of action in vivo, and the compromise between therapeutic effectiveness and toxicity, which allows resistance to emerge. A promising innovative approach to prolong the effectiveness and reduce toxicity of treatments is Adaptive Therapy, which is designed to harness the intra-tumoral heterogeneity in order to alter the evolutionary trajectory of tumours. We validated the underlying principle of Adaptive Therapy using CDK inhibitors (reference 9), and we are now extending this to more clinically relevant in vivo models.
1.Fisher, D. and Krasinska, L. (2022) Explaining redundancy in CDK-mediated control of the cell cycle: unifying the continuum and quantitative models. Cells. 11, 2019. doi: 10.3390/cells11132019.
2. Valverde, J.-M.†, Dubra, G.†, van den Toorn, H., van Mierlo, G., Vermeulen, M., Heck, A.J.R., Elena-Real, C., Fournet, A., Al Ghoul, E., Chahar, D., Haider, A., Paloni, M., Constantinou, A., Barducci, A., Ghosh, K., Sibille, N., Bernado, P., Knipscheer, P., Krasinska, L.‡, Fisher, D.‡*, Altelaar, M.‡* (2022) A CDK-mediated phosphorylation switch of disordered protein condensation. Preprint available at Research Square; https://doi.org/10.21203/rs.3.rs-1370895/v1.
3.Krasinska, L. and Fisher, D. (2022) A mechanistic model for cell cycle control in which CDKs act as switches of disordered protein phase separation. Cells 11, 2189. doi: 10.3390/cells11142189.
4. Sobecki, M., Mrouj, K., Camasses, A., Parisis, N., Nicolas, E., Llères, D., Gerbe, F., Prieto, S., Krasinska, L., David, A., Eguren, M., Birling, M.-C., Urbach, S., Hem, S., Déjardin, J., Malumbres, M., Jay, P., Dulic, V., Lafontaine, D.L.J., Feil, R. and Fisher, D. (2016). The cell proliferation antigen Ki-67 organises heterochromatin. eLife, 5, e13722. doi:10.7554/eLife.13722.
5. Sobecki, M. † and Mrouj, K. †, Colinge, J., Gerbe, F., Jay, P., Krasinska, L., Dulic, V. and Fisher, D. (2017) Cell cycle regulation accounts for variability in Ki-67 expression levels. Cancer Res 77, 2722–2734. doi: 10.1158/0008-5472.CAN-16-0707.
6. Mrouj, K., Andrés-Sánchez, N., Dubra, G., Singh, P., Sobecki, M., Chahar, D., Al Ghoul, E., Aznar, A., Prieto, S., Pirot, N., Bernex, F., Bordignon, B., Hassen-Khodja, C., Villalba, M., Krasinska, L. and Fisher, D. (2021) Ki-67 regulates global gene expression and promotes sequential stages of carcinogenesis. Proc. Natl. Acad. Sci. USA, 118(10):e2026507118.
7. Andrés-Sánchez, N., Fisher, D.* and Krasinska, L.* (2022) Physiological functions and roles in cancer of the proliferation marker Ki-67. J Cell Sci. 135, jcs258932. doi: 10.1242/jcs.258932.
8. Dupont, C., Chahar, D., Trullo, A., Gostan, T., Surcis, C., Grimaud, C., Fisher, D., Feil, R. and Llères, D. (2023) Evidence for low nanocompaction of heterochromatin in living embryonic stem cells. EMBO J., e110286. doi: 10.15252/embj.2021110286.
9. Bačević, K.*, Noble, R.*, Soffar, A., Ammar, O.W., Boszonyik, B., Prieto, S., Vincent, C., Hochberg, M.E. †, Krasinska, L. † and Fisher, D. †. (2017) Spatial competition constrains resistance to targeted cancer therapy Nat Commun 8(1):1995. doi: 10.1038/s41467-017-01516-1.
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