Biology subjects

Cicek, E.

Publications and source records attributed to Cicek, E..

5 recordsLinked to original sources

bioRxiv2026

Proximity labeling reveals cell cycle-specific NEK2 interactions and a regulatory axis controlling NUSAP1 stability

NEK2 is a cell cycle-regulated kinase best known for its role in centrosome separation, yet the phase-specific organization of its interaction network has remained unclear. Here, we combine a doxycycline-inducible TurboID system with mass spectrometry to generate a cell cycle-resolved NEK2 interactome in synchronized U2OS cells. Using generalized additive models (GAMs), we identified different enrichment trajectories of the NEK2 interacting proteins across G1/S, late S, and G2/M, linking NEK2 to chromosome and spindle regulation, RNA-ribonucleoprotein processes, vesicle/lysosome compartments, and ubiquitin-associated pathways. Targeted validations (streptavidin pull-down, co-immunoprecipitation, and immunofluorescence) confirmed the interaction and binding for selected partners. Focusing on NUSAP1, NEK2 induction led to rapid loss of NUSAP1 protein without changes in mRNA levels, and this decrease was blocked by the proteasome inhibitor MG-132. Consistently, NUSAP1 exhibited slower decay in cycloheximide chase assays and reduced ubiquitination in NEK2 knockout cells, indicating NEK2-dependent proteasomal turnover. Global proteomic analysis of NEK2-deficient cells revealed widespread remodeling of protein abundance, including increased NUSAP1 and decreased KIF2C, accompanied by coordinated changes in pathways governing mitotic progression, microtubule organization, and ubiquitin-mediated protein turnover. Together, these findings provide a dynamic map of the NEK2 interactome across the cell cycle and uncover a NEK2-NUSAP1 degradation pathway, offering a framework to study how kinase interactomes are remodeled by cell cycle progression.

cancer biology↗

bioRxiv2026

Stress adaptation pathways and HA-CD44 signaling maintain the survival of pancreatic cancer cells with centrosome amplification

Centrosome amplification (CA) is a hallmark of aggressive cancers, including pancreatic ductal adenocarcinoma (PDAC), and is linked to genomic instability and poor prognosis. While CA promotes tumor evolution, it also imposes substantial intracellular stress that cells must overcome to survive. However, the specific metabolic adaptations that enable cancer cells to tolerate stress induced by supernumerary centrosomes remain poorly understood. Here, we show that PDAC cells with CA acquire distinct metabolic dependencies that sustain survival. A metabolism-focused CRISPR-Cas9 screen, coupled with functional validations, identified critical vulnerabilities in three inter-connected axes: redox homeostasis, nucleotide sugar metabolism, and the unfolded protein response (UPR). Specifically, CA elevates intracellular reactive oxygen species (ROS), creating a reliance on glutamine metabolism and NRF2-driven antioxidant signaling. CRISPR screen hits in the hexosamine and uronic acid pathways revealed dependencies that converge on hyaluronic acid (HA) metabolism, and functional assays demonstrated that the HA-CD44 axis is required for centrosome clustering and mitotic fidelity, with its disruption increasing lethal multipolar divisions. In parallel, CA activated all branches of the UPR, and both hyper-activation and suppression of ER stress proved detrimental, indicating a finely tuned proteostatic equilibrium is essential for adaptation. Together, these findings show that, in a PLK4-driven model, centrosome-amplified cells rely on coordinated redox control, proteostatic buffering, and extracellular matrix signaling to tolerate CA-induced stress, revealing selective vulnerabilities that could be therapeutically exploited to target aggressive, therapy-resistant tumor subpopulations.

cancer biology↗

bioRxiv2023

Less is More: Nek2A Unclusters Extra Centrosomes and Induces Cell Death in Cancer Cells via KIF2C Interaction

Unlike normal cells, cancer cells frequently exhibit extra centrosomes, leading to formation of multipolar spindles that can trigger cell death. Nevertheless, they manage to divide successfully and escape the deadly consequences of unequal segregation of genomic material by coalescing their extra centrosomes into two poles. This unique trait of cancer cells presents a promising target for cancer therapy, focusing on selectively attacking cells with supernumerary centrosomes. Nek2A is a kinase involved in mitotic regulation, including the centrosome cycle, where it phosphorylates linker proteins to separate centrosomes. In this study, we investigated if Nek2A also unclusters extra centrosomes, akin to its separation function. Reduction of Nek2A activity, achieved through knockout, silencing, or inhibition, promotes centrosome clustering, whereas its overexpression results in unclustering. Significantly, this unclustering activity induces cell death, but only in cancer cells with extra centrosomes, both in vitro and in vivo. Notably, none of the known centrosomal (e.g., CNAP1, Rootletin, Gas2L1) or non-centrosomal (e.g., TRF1, HEC1) Nek2A targets were implicated in this unclustering activity. Additionally, Nek2A operated via a mechanism distinct from other unclustering factors like HSET and NuMA. Through TurboID proximity labeling analysis, we identified novel proteins associated with the centrosome or microtubules, expanding the known interaction partners of Nek2A. KIF2C, in particular, emerged as a novel interactor, confirmed through coimmunoprecipitation and localization analysis. The silencing of KIF2C diminished the impact of Nek2A on centrosome unclustering and rescued cell viability. Additionally, elevated Nek2A levels were indicative of better patient outcomes, specifically in those predicted to have excess centrosomes. Therefore, while Nek2A is a proposed target, its use must be specifically adapted to the broader cellular context, especially considering centrosome amplification. Discovering partners such as KIF2C offers fresh insights into cancer biology and new possibilities for targeted treatment.

cancer biology↗

bioRxiv2023

Prolonged over-expression of PLK4 amplifies centrosomes through formation of inter-connected centrosome rosette clusters

The centrosome cycle is a tightly regulated process to ensure proper segregation of chromosomes. Not surprisingly, centriole number is tightly controlled via multiple mechanisms, one of which involves PLK4, an upstream kinase facilitating centriole biogenesis and duplication. Aberrations in this process can result in supernumerary centrosomes, which are frequently observed in a variety of cancers due to high levels of PLK4. Interestingly, extra centrosomes induced by PLK4 over-expression go through unique intermediate structures called the centrosome rosettes (CRs), where the mother centriole is surrounded by numerous daughter centrioles. The maturation and molecular nature of these CRs have not been investigated in detail. Upon prolonged PLK4 over-expression, cells exhibited large centrosomes that were clustered and contained more than two CRs, which we defined as centrosome rosette clusters (CRCs). As expected, these structures required high PLK4 levels at two consecutive cell cycles and were still interconnected with canonical centrosomal linker proteins such as C-Nap1, Rootletin, and Cep68. Knockout of these linker proteins resulted in distancing of CRs and CRCs as observed by increased diameter of the CRCs in interphase. In contrast, Nek2 knockout inhibited the separation of CRCs in prometaphase, providing functional evidence for the binding of CRC structures with centrosomal linker proteins. These results suggest a cell cycle dependent model for PLK4 induced centrosome amplification, which occurs in two consecutive cell cycles: (i) CR state in the first cell cycle, and (ii) CRC state in the second cell cycle. Author summaryThe overexpression of PLK4 can lead to the formation of centrosome rosette structures, which harbor two centrioles around the mother centriole. Although the generation of centrosome rosettes by PLK4 overexpression has been previously investigated, little is known about the cell cycle-dependent maturation and linking of these structures. Here, we report that prolonged PLK4 overexpression results in amplification of centrosomes through the generation of centrosome rosette clusters (CRCs). These CRCs are interconnected via canonical centrosomal linker proteins such as C-Nap1, Rootletin, and CEP68 and are regulated by mechanisms controlling centrosome linking and separation. We also describe two different spatial binding types of amplified centrosomes following PLK4 induction: planar-oriented and circular-oriented. Since PLK4-associated centrosome amplification occurs naturally in both cancer and multiciliated cells, we believe that this research will contribute to a better understanding of the canonical mechanism of PLK4-induced centrosome amplification.

cell biology↗

bioRxiv2018

Model-based analysis of positive selection significantly expands the list of cancer driver genes, including RNA methyltransferases

Identifying driver genes is a central problem in cancer biology, and many methods have been developed to identify driver genes from somatic mutation data. However, existing methods either lack explicit statistical models, or rely on very simple models that do not capture complex features in somatic mutations of driver genes. Here, we present driverMAPS (Model-based Analysis of Positive Selection), a more comprehensive model-based approach to driver gene identification. This new method explicitly models, at the single-base level, the effects of positive selection in cancer driver genes as well as highly heterogeneous background mutational process. Its selection model captures elevated mutation rates in functionally important sites using multiple external annotations, as well as spatial clustering of mutations. Its background mutation model accounts for both known covariates and unexplained local variation. Simulations under realistic evolutionary models demonstrate that driverMAPS greatly improves the power of driver gene detection over state-of-the-art approaches. Applying driverMAPS to TCGA data across 20 tumor types identified 159 new potential driver genes. Cross-referencing this list with data from external sources strongly supports these findings. The novel genes include the mRNA methytransferases METTL3-METTL14, and we experimentally validated METTL3 as a potential tumor suppressor gene in bladder cancer. Our results thus provide strong support to the emerging hypothesis that mRNA modification is an important biological process underlying tumorigenesis.

genomics↗