Publications related to Cell cycle

An in vitro study of the effects of temperature on apoptosis and cell cycle in the GS-NS0 cell line

2013

Adeno-associated virus (AAV) is a small DNA virus belonging to the family of the parvoviridae. AAV infects the human population, however no disease has been associated with this virus. On the contrary, AAV was reported to have oncosuppressive activities. The AAV genome contains two genes: the Rep gene encoding four non-structural proteins (Rep78, 68, 52 and 40) and the Cap gene encoding the three capsid proteins. Rep78 is implicated in transcription, replication and site-specific integration of the viral DNA. It has been shown to block the cell cycle in G1, G2 and S phase with a complete inhibition of DNA synthesis. To be able to induce such a strong cell cycle arrest, Rep78 affects several proteins implicated in the regulation of the cell cycle, such as the family of the cell division cycle 25 (Cdc25) phosphatases. Rep78 has been shown to inactivate Cdc25A by binding to it and preventing it from accessing its substrates. Cdc25B shares conserved domains with Cdc25A and moreover has an important role in cell cycle regulation, especially in giving the signal for entry into mitosis. Thus, in this work, the interaction between Cdc25B and Rep78 was examined in more detail. Rep78 was found to bind to Cdc25B and to alter its intracellular localisation. Cdc25B is nuclear, but has to migrate into the cytoplasm at the end of the G2 phase to activate proteins needed for the entry into mitosis. The expression of Rep78, which is nuclear, leads to the sequestration of Cdc25B in the nucleus. Moreover, Rep78 by interacting with Cdc25B not only changes its localisation, but also inhibits its phosphatase activity. Our model is that Rep78 interacts with Cdc25B and thus retains it in the nucleus. This sequestration of Cdc25B in the nucleus prevents it from activating the proteins in the cytoplasm needed to give the entry signal into mitosis, thus contributing to the G2/M arrest induced by Rep78. Moreover, the inhibition of Cdc25B phosphatase activity by Rep78 may also contribute to the cell cycle block. Rep78 also interacts with a number of cellular proteins implicated in DNA replication, DNA repair or recombination. Interactions between Rep78 and mini-chromosome maintenance 3 (MCM3), DNA polymerases α and δ, proliferating cell nuclear antigen (PCNA), Rad50 and Rad51 were identified in this work as well as possible interactions between Rep78 and Ataxia telangiectasia mutated (ATM) or Ataxia telangiectasia and Rad3 related (ATR) proteins. These interactions may contribute to AAV genome replication as well as its integration into the host DNA.

EPFL2009

The chromatin remodeller Chd7 and the calcium ATPase Serca2 - adding new facets to the role of Notch in Hematopoiesis and T-ALL

Monique Coersmeyer

Project I: Chd7 Deficiency does not affect N1-driven T-ALL Induction and Maintenance nor impair Hematopoiesis Notch1 has been shown to be a key driver in pediatric T-cell acute lymphobastic leukemia (T-ALL). Previous work in the lab identified the chromatin-remodeling enzyme Chd7 to be highly over-expressed in aggressive versus pre-malignant disease. The aim of this project was to study if Chd7 is required during T-ALL initiation and disease maintenance as well as to characterize its role in the hematopoietic system under physiological and stress conditions. Therefore, Chd7 cKO animals were crossed with the MxCre deleter to ablate Chd7 specifically in BM progenitors. Chd7 deficiency did not induce any overt phenotype in the hematopoietic system, when studied under âsteadyâ state or stress conditions. In addition, Chd7 proved to be dispensable in the initiation and maintenance of murine and human Notch1-driven T-ALL. Therefore, we can rule out a role of Chd7 during late-stage leukemogenesis in Notch1-induced murine and human T-ALL. Project II: Serca2, a putative drug target to fight Notch1-driven T cell acute lymphoblastic leukemia, and its role in Hematopoiesis The Notch signalling pathway represents a bona fide drug target. We and Roti et al. performed a chemical compound screen and identified Cyclopiazonic acid (CPA) as potent Notch inhibitor. Biological target of this compound is the Sarco/Endoplasmic Reticulum ATPase2 (Serca2) that is involved in calcium homeostasis within the cell. Recently, it was shown that Serca2 regulates Notch1 (N1) receptor maturation and inhibition of Serca ATPases, using thapsigargin, blocks T-ALL progression in xenografts (Roti et al., 2013). The putative global effects of Serca2 inhibition on hematopoiesis have, however, not been addressed in this study. Aim of this study was to characterize the function of Serca2 in the hematopoietic system. Therefore, we crossed Serca2 cKO with MxCre to ablate Serca2 function in BM progenitors. Serca2 haploinsufficiency did not lead to any overt phenotype under physiological or competitive conditions. In contrast, Serca2ÎMxCre chimeras showed (i) impaired long-term reconstitution capacity upon transplantation, (ii) a severe reduction of total BM, splenic and thymic cellularity and (iii) an enrichment of KLS cells, the cell pool that contains HSCs. Mature lineages were highly apoptotic, while KLS were not majorly affected by apoptosis, resided predominantly in G0 phase of the cell cycle, exhibited slower cycling kinetics and were functionally impaired as they formed less and smaller colony forming units in vitro. Deregulated calcium levels can lead to an accumulation of unfolded proteins in the ER. In order to resolve ER stress, the cell activates the unfolded protein response (UPR). In case of unresolved ER stress, however, the cell undergoes apoptosis. We demonstrate that mature hematopoietic lineages up-regulate UPR-associated and pro-apoptotic genes, while KLS cells, in contrast, show unperturbed expression of these genes. In addition, we performed in vitro experiments, inhibiting Serca function in Lin- BM cells via thapsigargin (TH) treatment. TH induced severe apoptosis in the overall cell population, while KLS accumulated and were blocked in the G0 phase, closely mimicking Serca2 LOF in vivo. We therefore question the therapeutic approach of targeting Serca2 in N1-driven T-ALL due to severe side effects induced by Serca2 inactivation in the BM.

EPFL2015

Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat array

Jean-Bernard Nobs

How cells grow and divide is a question that was raised more than 100 years ago. Despite years of research and in-depth knowledge of several molecular mechanisms, the complete system that regulates and coordinates both of those activities within Schizosaccharomyces pombe is still unknown. A systemic approach might provide some help to decipher them. Fission yeast is one of the most actively used model organisms to study cell-cycle and cell growth. The first single-cell measurements of its growth profile were performed already in the nineteen-sforties. Despite the huge amount of studies performed, only very few methods were provided to scientists to investigate growth profiles. All the proposed approaches are highly time consuming and have technological drawbacks. Furthermore, they do not allow long-term imaging and are time-limited by their design. Recent advances in the microfluidic field allowed to design culture chambers that can achieve long-term and stable culturing of cells in a constant and tightly controlled environment. The surrounding cell growth conditions can be rapidly and easily changed over time. In this thesis, we aimed at coupling microfluidic devices with an automated microscope and an image analysis pipeline to record accurate and numerous growth profiles. Our platform allowed to handle tens of thousands of images and we could record more than 100’000 division events within a single fifty hour experiment. We automatically extracted data regarding basic physiological parameters such as cell size, time to divisions and elongation rate. Our complete analysis pipeline does not require any specific "marker" and relies exclusively on bright-field images. Using our platform, we characterized the evolution of several parameters regarding cell length and time to divisions during a temperature shift experiment in which cells were first grown at 30° followed by a transition to 25°. A similar experiment was performed in an upward transition from 30° to 33°. Cell length was nearly identical at the three temperatures, whereas time related parameters as well as elongation rate underwent changes. We quantified the distributions of each parameter at steady state and were able to detect transient size changes in respect to the single-cell growth phase when facing the transition. Indeed, an upshift of temperature induced an immediate division in cells that are less than halfway through their cell cycle resulting in a shortened cell length at divisions. In the opposite direction, a downshift of temperature delayed the beginning of the division process for cells that accomplished less than half of their cycle, leading to an increased cell length at division. Furthermore, those transient effects impacted the daughter cells (second generation) before the situation was back to normal in the third generation of cells. The involved temperature sensitive processes are highly correlated to the cell-cycle status of single-cells and despite the fact that our culture was unsynchronized it was possible to detect them precisely. Our platform is thus applicable to measure fine details of S.pombe cell-cycle dynamics and could be an interesting tool to help unravel the complex mechanisms maintaining cell homoeostasis. Basically, the study of any cell-cycle related processes that require accurate and numerous numbers of division events can be pushed forward with such a tool.

EPFL2014

Physiological regulation of the CDK16/PCTAIRE-1 protein kinase and its proposed role in the brain

Saifeldin Nasser Mohamed Ibrahim Shehata

Cell signalling, mediated to a large extent by protein kinase phosphorylation, plays a vital role in regulation of cellular function. PCTAIRE-1 (also known as cyclin-dependent protein kinase (CDK)16), is a Ser/Thr kinase that has been implicated in many cellular processes, including cell cycle, apoptosis, insulin secretion, spermatogenesis, neurite outgrowth, and vesicle trafficking. Most recently, it has been proposed as a novel X-linked intellectual disability (XLID) gene, where loss-of-function mutations have been found in patients. The precise molecular mechanisms that regulate PCTAIRE-1 remained largely obscure, and only few substrates have been proposed with no clear functional significance and physiological role. To understand the function of PCTAIRE-1, we previously utilised a peptide library screen to determine the consensus phosphorylation motif. We showed that PCTAIRE-1 preferentially phosphorylated peptide motifs that differed from the classical CDK family substrate preference, suggesting a more distinct role for the kinase. Furthermore, we showed that cyclin Y, a novel cyclin, robustly binds and activates PCTAIRE-1 > 100-fold. In this thesis, we have identified two phosphorylation sites on cyclin Y that are essential for binding the well-known adaptor protein 14-3-3, which we propose stabilizes cyclin Y in a favourable PCTAIRE-1-binding conformation. Mutation of these sites to non-phosphorylatable Ser residues abolished PCTAIRE-1 binding and activation. Furthermore, we have cloned human PCTAIRE-1 mutants identified in XLID patients, and confirmed their failure to bind the cyclin Y-14-3-3 activating complex. In order to understand the physiological relevance of PCTAIRE-1 activity, we have utilised a chemical genetics approach that exploits the ability of an engineered PCTAIRE-1 mutant to selectively modify its substrates, allowing them to be uniquely purified. We have identified three PCTAIRE-1 substrates (AAK1, dynamin 1 and synaptojanin 1) in mouse brain that regulate crucial steps of receptor endocytosis, namely receptor binding, vesicle scission and vesicle uncoating, which are all involved in the regulation of neuronal synaptic transmission. Collectively, this thesis work has provided key molecular regulatory mechanisms and potential downstream targets of PCTAIRE-1, which has laid the foundations for future studies of the role that PCTAIRE-1 plays in specific cellular functions and physiological and pathological settings.

EPFL2017

Cdk2 strengthens the intra-S checkpoint and counteracts cell cycle exit induced by DNA damage

Katarina Bacevic, Gérald Joseph Paul Lossaint

Although cyclin-dependent kinase 2 (Cdk2) controls the G1/S transition and promotes DNA replication, it is dispensable for cell cycle progression due to redundancy with Cdk1. Yet Cdk2 also has non-redundant functions that can be revealed in certain genetic backgrounds and it was reported to promote the G2/M DNA damage response checkpoint in TP53 (p53)-deficient cancer cells. However, in p53-proficient cells subjected to DNA damage, Cdk2 is inactivated by the CDK inhibitor p21. We therefore investigated whether Cdk2 differentially affects checkpoint responses in p53-proficient and deficient cell lines. We show that, independently of p53 status, Cdk2 stimulates the ATR/Chk1 pathway and is required for an efficient DNA replication checkpoint response. In contrast, Cdk2 is not required for a sustained DNA damage response and G2 arrest. Rather, eliminating Cdk2 delays S/G2 progression after DNA damage and accelerates appearance of early markers of cell cycle exit. Notably, Cdk2 knockdown leads to down-regulation of Cdk6, which we show is a non-redundant pRb kinase whose elimination compromises cell cycle progression. Our data reinforce the notion that Cdk2 is a key p21 target in the DNA damage response whose inactivation promotes exit from the cell cycle in G2.

Springer Nature2017

Coordination between cell growth, division and chromosome replication cycles in mycobacteria

Gaëlle Madeleine Vuaridel

Propagation of microorganisms is based on three fundamental processes: cell growth, DNA replication, and cell division. Although important for antibacterial drug development, these processes are poorly understood in Actinobacteria, a medically important phylum that includes Mycobacterium tuberculosis. Using microfluidic cultures and time-lapse microscopy, we studied single-cell growth, DNA replication, and cell division in the model organism Mycobacterium smegmatis.M. smegmatis is rod-shaped and grows by tip elongation in a biphasic manner due to a "new end take-off" (NETO) event. We find that pole elongation speed is increased and NETO occurs earlier in fast-growing cells than in slow-growing cells. As a consequence of variable timing of NETO, single-cell growth can be monophasic, biphasic, or triphasic. We propose that cells optimize pole growth speed and the timing of NETO to maximize their overall growth.We show that fast-growing cells initiate DNA replication earlier than slow-growing cells. We also find that single-cell growth speed is linked to cell-cycle progression, which is similar when comparing cells growing at the same speed under different conditions. We also report that multifork replication occurs when the time between DNA replication initiation events is shorter than the C period, which may occur even in slow-growing cells with interdivision times longer than the C period.Division site selection in many bacteria is governed by the nucleoid occlusion (Noc) and minicell (Min) systems. Mycobacteria do not encode homologs of these proteins and have no known mechanism for division site selection. We found that the DNA replisome and cell division ring colocalize and move together in a biphasic trajectory determined by the chromosome partitioning (Par) system. We propose a model in which Par-dependent movement of the replisome and division ring ultimately determines the site of cell division.Coordination of cell growth and division is required for cell size homeostasis. Three models of division control have been proposed: sizer (cells divide after reaching a critical size), timer (cells divide at a certain time after birth), and adder (cells add a specific amount of mass before dividing). We show that the single-cell growth model (exponential, linear, or bilinear) constrains the possible division control models. Thus, it is crucial to know the true model of single-cell growth in order to distinguish the true mechanism of cell size homeostasis.

EPFL2021

Spatial control of nucleoporin condensation by fragile X-related proteins

Alessandro Berto

Nucleoporins (Nups) build highly organized nuclear pore complexes (NPCs) at the nuclear envelope (NE). Several Nups assemble into a sieve-like hydrogel within the central channel of the NPCs. In the cytoplasm, the soluble Nups exist, but how their assembly is restricted to the NE is currently unknown. Here, we show that fragile X-related protein 1 (FXR1) can interact with several Nups and facilitate their localization to the NE during interphase through a microtubule-dependent mechanism. Downregulation of FXR1 or closely related orthologs FXR2 and fragile X mental retardation protein (FMRP) leads to the accumulation of cytoplasmic Nup condensates. Likewise, models of fragile X syndrome (FXS), characterized by a loss of FMRP, accumulate Nup granules. The Nup granule-containing cells show defects in protein export, nuclear morphology and cell cycle progression. Our results reveal an unexpected role for the FXR protein family in the spatial regulation of nucleoporin condensation.

WILEY2020

Correlation between cell cycle and calcium phosphate transient transfection of CHO cells

Frédéric Grosjean

Calcium phosphate transfection is a widely used method to produce recombinant proteins in mammalian cells. However, the mechanisms involved in plasmid DNA transfer to the nucleus of the transfected cells remain poorly understood and result in great variation of transfection efficiency. The role of the cell cycle in transfection by the calcium phosphate method was studied using Chinese Hamster Ovary (CHO) cells as a model system. Adherent cell cultures were synchronized at the G1/S boundary using mimosine. At various time points after the removal of the drug the cells were transfected with reporter plasmids that expressed either the enhanced green fluorescent protein (EGFP) or a red fluorescent protein (DsRedExpress). Fluorescent protein expression was monitored by fluorometry and live imaging. Cell cycle was monitored by flow cytometry. It was shown that the cell cycle had major implications on at least two levels. The correlation between the percentage of cells in S phase at the time of transfection complex addition and the resulting reporter gene expression demonstrated that efficient transfer of exogenous DNA in mammalian cells was dependent on the cell cycle. A faster transfection protocol, developed within this work, showed that the optimal timing for the transfection complex addition was different depending on the transfection set-ups used. Further investigations demonstrated that mitosis played a key role, probably due to the nuclear membrane disruption, to provide access to the nuclear environment for the plasmid DNA molecules. The glycerol shock performed at the end of the transfection was also shown to play an important role for efficient transfer of reporter gene in nuclei. This strong osmotic shock resulted in a cellular volume decrease of approximately 55%. As no intracellular plasmids were lost during the process, this resulted in a significant increase in intracellular plasmid concentration. Glycerol shock has to be performed while cells proceed through mitosis. The nuclear membrane disruption and the increasing intracellular plasmid concentration probably facilitate the access to the nuclear environment. The synergy of glycerol shock and cells proceeding through mitosis was a requirement for efficient reporter gene transfer in the nuclei. If one of those two was omitted, or if they did not happened at the same time, very low reporter gene expression levels were achieved. As it was found that plasmid DNA was driving reporter gene expression even after a delay of 45 minutes post cellular uptake, it was possible to efficiently target additional sub-populations of cells as they proceeded through mitosis with additional glycerol shocks. Those repetitive glycerol shocks resulted in an increase of positive cells among the transfected populations. In conclusion, the results obtained in this work permitted to define a model explaining the importance of the cell cycle in the calcium phosphate transfection, highlighting mitosis and glycerol shock as key events in plasmid DNA molecules transfer to the nucleus.

EPFL2003

Circadian rhythm and cell cycle

Rosamaria Cannavo

Circadian rhythms are biological processes found in most living organisms, displaying a roughly 24-hour period, responding primarily to light darkness cycles in an organism's environment. At the cellular level, the circa-24h rhythmicity is generated by a molecular clock based on a transcription-translation feedback network and consists of a cell-autonomous and self-sustained oscillator. In conditions where cells proliferate, the cell division cycle can be also considered as an oscillator. Since both processes run with similar periods in several mammalian cells, it is reasonable to expect that interactions between these two cycles may cause synchronization. Many studies reported evidences of interactions between the circadian and the cell cycles in different organisms. In particular, it appeared that in several systems, specific cell cycle phases occur in distinct temporal windows rather than being randomly distributed in time. These findings led to the concept of circadian gating of the cell cycle, through which the circadian clock can favor or forbid cell cycle transitions at specific circadian phases. However, it was also reported the converse, namely an effect of cell division on the circadian oscillator. Even though interactions between the circadian clock and the cell cycle have been identified in both directions, the dynamical consequences and the directionality of the coupling at the single-cell level were not extensively investigated. In order to better characterize the potential synchronization in mammalian cells, we estimated the mutual interactions between circadian clock and cell cycle in NIH3T3 mouse fibroblasts by the use of time-lapse fluorescent microscopy in combination with statistical analysis and mathematical modeling. NIH3T3 cells, harboring a fluorescent reporter under the control of the circadian RevErb-a gene promoter, were imaged for several days allowing the simultaneous detection of circadian oscillations and time of divisions. The analysis of thousands of circadian cycles in dividing cells indicated that both oscillators are synchronized, with cell divisions occurring about 5 h before the peak of the circadian RevErb-a reporter. We tested several perturbations such as different serum concentrations, different temperatures, treatment with pharmacological compounds and shRNA-mediated knockdown of circadian regulators. Surprisingly, this showed that circadian rhythm and cell cycle remain synchronized over the wide range of conditions probed. Our data showed that this synchronization state reflects an unexpected predominant influence of the cell cycle on the circadian oscillator, and did not support the leading hypothesis about a circadian gating of the cell cycle. The stochastic modeling of two interacting phase oscillators allowed us to identify the parameters of the coupling functions, revealing an acceleration of circadian phase after the division. The work presented in this thesis sheds light on the interaction between two fundamentally recurrent cellular processes in mammalian cells and provides a deeper understanding of the role of the circadian clock in proliferating cells and tissues. These findings might have significant implications for chronobiology and chronotherapeutics.

EPFL2016