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Kalkan, B. M.

Publications and source records attributed to Kalkan, B. M..

5 recordsLinked to original sources

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↗

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↗

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↗

Development of Small Molecule MEIS Inhibitors that modulate HSC activity

Meis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34low cells) and human (CD34+, CD133+, and ALDHhi cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1, Hif-2 and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.

molecular biology↗

Development of Gene Editing Strategies for Human β-Globin (HBB) Gene Mutations

Recent developments in gene editing technology have enabled scientists to modify DNA sequence by using engineered endonucleases. These gene editing tools are promising candidates for clinical applications, especially for treatment of inherited disorders like sickle cell disease (SCD). SCD is caused by a point mutation in human {beta}-globin gene (HBB). Clinical strategies have demonstrated substantial success, however there is not any permanent cure for SCD available. CRISPR/Cas9 platform uses a single endonuclease and a single guide RNA (gRNA) to induce sequence-specific DNA double strand break (DSB). When this accompanies a repair template, it allows repairing the mutated gene. In this study, it was aimed to target HBB gene via CRISPR/Cas9 genome editing tool to introduce nucleotide alterations for efficient genome editing and correction of point mutations causing SCD in human cell line, by Homology Directed Repair (HDR). We have achieved to induce target specific nucleotide changes on HBB gene in the locus of mutation causing SCD. The effect of on-target activity of bone fide standard gRNA and newly developed longer gRNA were examined. It is observed that longer gRNA has higher affinity to target DNA while having the same performance for targeting and Cas9 induced DSBs. HDR mechanism was triggered by co-delivery of donor DNA repair templates in circular plasmid form. In conclusion, we have suggested methodological pipeline for efficient targeting with higher affinity to target DNA and generating desired modifications on HBB gene. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/908319v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18f810org.highwire.dtl.DTLVardef@1461dfcorg.highwire.dtl.DTLVardef@5a9546org.highwire.dtl.DTLVardef@fe5815_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG HighlightsO_LIHBB gene were targeted by spCas9 in close proximity to the SCD mutation C_LIO_LILong gRNA, which is designed to target SCD mutation, is sickle cell disease specific and exhibits indistinguishable level of cleavage activity on target locus. C_LIO_LIFunctional HBB HDR repair templates with 1 Kb and 2 Kb size were generated to cover all known mutations in the HBB gene. C_LIO_LIReplacement of PAM sequence in HDR template with HindIII recognition sequence allowed a quick assessment of the HDR efficiency. C_LIO_LIHDR template: Cas9-GFP vector 2:1 ratio yielded the highest HDR events/GFP+ cells. C_LI

molecular biology↗