Research Focus

Our lab investigates the fascinating mechanisms that coordinate the cell cycle with developmental and physiological processes in multicellular organisms. Disruptions to this coordination can lead to serious health consequences, including cancer, tissue degeneration, and ageing. To better understand this critical coordination, we focus on a group of evolutionarily conserved proteins called “Cell Cycle Regulators (CCRs).” Recent research, including our own, has revealed that CCRs not only control the cell cycle but also regulate cell fate and differentiation through previously unknown molecular functions, making them “intracellular proliferation-differentiation coordinators” (Kimata et al., 2020).

To explore these novel functions, we use advanced genetics and cutting-edge technologies such as in vivo imaging, multi-omics analysis, and artisan biochemical techniques in the fruit fly Drosophila melanogaster, a powerful model organism for multicellular research. We also examine these mechanisms in human cells and mammalian organoids to translate our findings from Drosophila to humans. Our research aims to decipher the evolutionarily conserved molecular mechanisms that integrate cell proliferation with the development and physiology of multicellular organisms. Ultimately, our findings will contribute to the development of new approaches to treat incurable diseases such as cancer, while bridging the gap between cell biology and developmental biology.

We welcome potential collaborators and students who are interested in contributing to our ongoing projects, which include:

1. Unveiling novel cell cycle-independent functions of CCRs in cell fate choice and differentiation control

In vivo, various cell behaviors such as cell differentiation and morphogenesis are orchestrated by intra/intercellular signal transduction and transcription factors mainly through gene regulation. Recent research indicates that some CCRs directly regulate the activities of these developmental factors in concert with cell cycle regulation. One of the prime examples is the Anaphase-Promoting Complex (APC/C), a master CCR, which inhibits the transcriptional activity of a major extracellular signaling pathway, Wnt pathway, by degrading its positive modulator Nek2 in the Drosophila eye imaginal disc. Through this mechanism, APC/C coordinates the cell cycle exit of progenitor cells with the induction of differentiation into specialized cell types (Martins et al., 2017).

We have extended this initial finding by conducting genome-wide screens of CCRs to identify novel non-cell cycle functions of CCRs in Drosophila. Through this screen, we have identified several CCRs that severely impair retinal differentiation upon knockdown. We are currently characterising the underlying molecular mechanisms of some of these CCRs, including CDKs. We are also studying the conserved functions of human orthologs of Nek2 in the control of Wnt signalling in human cells and intestinal organoids. This study will enable us to unravel the conserved mechanism of CCRs in the regulation of cell fate choice and differentiation.

The genome-wide screen for cell cycle-independent functions of CCRs

2. Unlocking the Secrets of Dormant Cells: Investigating Regulatory Mechanisms of G0 Phase and Cell Cycle Exit

A significant proportion of cells in adult animals are in a dormant state and not actively dividing. Tissue-specific stem cells, for example, are often in a reversible quiescent state known as the “G0 phase,” dividing only when necessary to repair tissue damage. Meanwhile, differentiated cells such as neurons and muscle cells have irreversibly exited from the cell cycle and no longer proliferate. The mechanisms that control and maintain these dormant cell cycle states and coordinate them with cell type- and tissue-specific functions remain largely unknown.

We are investigating these enigmatic cell cycle states both in vivo and in vitro. In Drosophila, we study terminally differentiated tissues such as the brain and gut of adult flies to investigate how the quiescent states of tissue-specific stem cells and differentiated cells are controlled in vivo, and how deregulation of these states affects tissue homeostasis and function. We are also examining the precise regulatory mechanisms that coordinate entry into the G0 phase with genetic and epigenetic states of the genome in cultured human cells, using recently developed rapid protein targeting systems. Our goal is to gain insights into the fundamental mechanisms that control the G0 phase and cell cycle exit, and how their regulation can contribute to tissue health and disease.

3. Molecular Interactions between CCRs and the Centrosome: Characterisation of Functions in Development and Disease

The centrosome is an organelle found in animal cells that provides spatial and directional control and mechanical strength by regulating the cytoskeleton. In non-dividing cells, centrosomes can transform into primary cilia, which play a critical role in signal transduction and mechanical sensing. Centrosome abnormalities are associated with various disorders, including cancer, macrocephalies and ciliopathies.

There is mounting evidence that various CCRs interact with centrosomes and primary cilia and reciprocally control each other’s functions in multicellular organisms. In collaboration with David Glover’s lab and Pietro Lio’s lab at the University of Cambridge, we previously found that the APC/C activator CDH1 (Fzr in Drosophila) directly binds to a conserved centrosome component, Spd2/CEP192 in Drosophila tissues, through in vivo proteomic analysis. We showed that Spd2 recruits CDH1 onto the centrosome to promote the degradation of Aurora A, a centrosomal substrate of APC/C, which is important for maintaining the number of neural stem cells in the developing adult brain (Meghini et al., 2016). We also found that the protein levels of Spd2 are in turn regulated through APC/C-dependent degradation, and abnormal accumulation of Spd2 affects the function of interphase centrosomes that are crucial for the division axis maintenance of neural stem cells (Meghini et al., 2023). Moreover, in collaboration with Renata Basto at the Institute Curie in France, we demonstrated that this interaction is critical for the centrosome regulation specific to asymmetric division of neural stem cells (Gambarotto et al, 2019).

Furthermore, using the CRISPR genome editing technique to create new dominant mutations in an APC/C cofactor Vihar/Ube2C, we recently showed that APC/C controls the migration of centrosomes to the future oocyte during oocyte specification. This control is mediated by the degradation of Polo/Plk1 kinase, another key centrosomal kinase whose levels are often upregulated in cancer cells (Braun et al., 2021).

We are continuing to explore the interactions between CCRs and centrosome/cilia components and their functions in various Drosophila tissues and human cells and organoids.

Recent publications

1. Meghini F, Martins T, Zhang Q, et al., APC/C-dependent degradation of Spd2 regulates centrosome asymmetry in Drosophila neural stem cells. EMBO Rep. 2023 April.
2. Braun AL, Meghini F, Villa-Fombuena G, et al., The careful control of Polo kinase by APC/C-Ube2C ensures the intercellular transport of germline centrosomes during Drosophila oogenesis. Open Biol. 2021 June.
3. Kimata Y, Leturcq M, Aradhya R. Emerging roles of metazoan cell cycle regulators as coordinators of the cell cycle and differentaition. FEBS Letters. 2020 July.
4. Ochi T, Quarantotti V, Lin H, et al. CCDC61/VFL3 is a paralog of SAS6 and promotes ciliary functions. Structure. 2020 June.
5. Gambarotto D, Pennetrier C, Rynaiawec JM, et al. Plk4 regulates centriole asymmetry and spindle orientation in neural stem cells. Developmental Cell. 2019 Jul.
6. Kimata Y. APC/C Ubiquitin Ligase: Coupling Cellular Differentiation to G1/G0 Phase in Multicellular Systems. Trends in Cell Biology. Apr. 2019
7. Martins T, Meghini F, Florio F, Kimata Y. The APC/C coordinates retinal differentiation with G1 arrest through the Nek2-dependent modulation of Wingless signalling. Developmental Cell. 2017 Jan.
8. Meghini F, Martins T, Tait X (equally contributed), Fujimitsu K, Yamano H, Glover DM, Kimata Y. Targeting of Fzr/Cdh1 for timely activation of the APC/C at the centrosome during mitotic exit. Nature Comms. 2016 Aug 25;7:12607.