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Publication Metadata only A tour de force of primary cilium biogenesis(Nature Portfolio, 2021) N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 206349N/APublication Open Access An examination of the putative role of melatonin in exosome biogenesis(Frontiers, 2021) Amini, Hassan; Rezabakhsh, Aysa; Hassanpour, Mehdi; Hashemzadeh, Shahriar; Ghaderi, Shahrouz; Rahbarghazi, Reza; Reiter, Russel J.; Heidarzadeh, Morteza; Sokullu, Emel; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Graduate School of Health Sciences; N/A; 163024During the last two decades, melatonin has been found to have pleiotropic effects via different mechanisms on its target cells. Data are abundant for some aspects of the signaling pathways within cells while other casual mechanisms have not been adequately addressed. From an evolutionary perspective, eukaryotic cells are equipped with a set of interrelated endomembrane systems consisting of intracellular organelles and secretory vesicles. Of these, exosomes are touted as cargo-laden secretory vesicles that originate from the endosomal multivesicular machinery which participate in a mutual cross-talk at different cellular interfaces. It has been documented that cells transfer various biomolecules and genetic elements through exosomes to sites remote from the original cell in a paracrine manner. Findings related to the molecular mechanisms between melatonin and exosomal biogenesis and cargo sorting are the subject of the current review. The clarification of the interplay between melatonin and exosome biogenesis and cargo sorting at the molecular level will help to define a cell's secretion capacity. This review precisely addresses the role and potential significance of melatonin in determining the efflux capacity of cells via the exosomal pathway. Certain cells, for example, stem cells actively increase exosome efflux in response to melatonin treatment which accelerates tissue regeneration after transplantation into the injured sites.Publication Open Access Aurora kinase A proximity map reveals centriolar satellites as regulators of its ciliary function(Wiley, 2021) Rauniyar, N.; Yates, J. R. III; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Arslanhan, Melis Dilara; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; Graduate School of Sciences and Engineering; 206349; N/AAurora kinase A (AURKA) is a conserved kinase that plays crucial roles in numerous cellular processes. Although AURKA overexpression is frequent in human cancers, its pleiotropic functions and multifaceted regulation present challenges in its therapeutic targeting. Key to overcoming these challenges is to identify and characterize the full range of AURKA interactors, which are often weak and transient. Previous proteomic studies were limited in monitoring dynamic and non-mitotic AURKA interactions. Here, we generate the proximity interactome of AURKA in asynchronous cells, which consists of 440 proteins involving multiple biological processes and cellular compartments. Importantly, AURKA has extensive proximate and physical interactions to centriolar satellites, key regulators of the primary cilium. Loss-of-function experiments identify satellites as negative regulators of AURKA activity, abundance, and localization in quiescent cells. Notably, loss of satellites activates AURKA at the basal body, decreases centrosomal IFT88 levels, and causes ciliogenesis defects. Collectively, our results provide a resource for dissecting spatiotemporal regulation of AURKA and uncover its proteostatic regulation by satellites as a new mechanism for its ciliary functions.Publication Metadata only Author correction: combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma(Nature Research, 2024) Mazur PK, Herner A, Mello SS, Wirth M, Hausmann S, Sánchez-Rivera FJ, Lofgren SM, Kuschma T, Hahn SA, Vangala D, Trajkovic-Arsic M, Gupta A, Heid I, Noël PB, Braren R, Kleeff J, Sipos B, Sayles LC, Heikenwalder M, Heßmann E, Ellenrieder V, Esposito I, Jacks T, Bradner JE, Khatri P, Sweet-Cordero EA, Attardi LD, Schmid RM, Schneider G, Sage J, Siveke JT.; Koç University HospitalIn the originally published version of this article, there were errors in the histological sections depicted in Supplementary Figs. 4 and 10. Specifically: In Supplementary Fig. 4, the image of the Ki67 immunohistochemistry (IHC) for the Gemcitabine+JQ1 group was incorrect In Supplementary Fig. 10, the pSTAT3 image for the IHC for the JQ1 group was incorrect In Supplementary Fig. 10, Ki67 and MYC IHC images for JQ1 and JQ1+SAHA were swapped In Supplementary Fig. 4, the image of the Ki67 immunohistochemistry (IHC) for the Gemcitabine+JQ1 group was incorrect In Supplementary Fig. 10, the pSTAT3 image for the IHC for the JQ1 group was incorrect In Supplementary Fig. 10, Ki67 and MYC IHC images for JQ1 and JQ1+SAHA were swapped The original data were available and these errors have been corrected in the Supplementary Information accompanying this notice. Additionally, the authors wish to clarify that the Sirius Red staining for the control and JQ1 groups were identical in both Supplementary Figs. 4 and 10 because the control mice (JQ1 only or control treatment) were shared between experiments. To avoid confusion, the sections depicting Sirius Red staining for the control and JQ1 groups in Supplementary Fig. 4 were replaced with alternative sections from the same respective samplesPublication Open Access C-Abl is not activated in DNA damage-induced and Tap63-mediated oocyte apoptosis in human ovary(Springer, 2018) Department of Molecular Biology and Genetics; N/A; N/A; Bildik, Gamze; Ayhan, Ceyda Açılan; Şahin, Gizem Nur; Karahüseyinoğlu, Serçin; Öktem, Özgür; Teaching Faculty; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; School of Medicine; Graduate School of Health Sciences; N/A; N/A; N/A; 110772; 102627There is a controversy in literature as to whether c-Abl is crucial for the induction of TAp63-mediated apoptosis and whether that inhibition of c-Abl with imatinib, which was designed to inhibit the oncogenic kinase BCR-ABL and c-kit, protects oocytes from chemotherapy-induced apoptosis in mice. No human data are available on this issue. We therefore aimed to explore whether genomic damage induced by chemotherapy drug cisplatin activates c-Abl along with TAp63 and the inhibition of c-Abl with imatinib prevents cisplatin-induced oocyte death and follicle loss in human ovary. Exposure to cisplatin induced DNA damage, activated TAp63 and SAPK/JNK pathway, and triggered apoptosis in the oocytes and granulosa cells. However, TAp63 activation after cisplatin was not associated with any increase in the expression of c-Abl. Imatinib did not prevent cisplatin-induced apoptosis of the granulosa cells or oocytes. Moreover, treatment with this drug resulted in the formation of bizarre shaped follicles lacking oocytes and increased follicular atresia by inducing apoptosis of granulosa cells and oocytes. Similar toxic effects were observed when ovarian tissue samples were incubated with a c-kit antagonist drug anti-CD117, but not with another c-Abl tyrosine kinase inhibitor GNF-2, which lacks an inhibitory action on c-kit. Intraperitoneal administration of imatinib to the xenografted animals produced similar histomorphological abnormalities in the follicles in human ovarian grafts and did not prevent cisplatin-induced follicle loss when co-administered with cisplatin. Our findings provide, for the first time, a molecular evidence for ovarian toxicity of this drug in human. Furthermore, this study together with two previous case reports of a severely compromised ovarian response to gonadotropin stimulation and premature ovarian failure in patients, while receiving imatinib, further heighten the concerns about its potential gonadotoxicity on human ovary and urge caution in its use in young female patients.Publication Open Access CCDC57 cooperates with microtubules and microcephaly protein CEP63 and regulates centriole duplication and mitotic progression(Elsevier, 2020) Lince Faria, Mariana; Department of Molecular Biology and Genetics; Gürkaşlar, Hazal Kübra; Culfa, Efraim; Arslanhan, Melis Dilara; Karalar, Elif Nur Fırat; Master Student; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 206349Centrosomes function in key cellular processes ranging from cell division to cellular signaling. Their dysfunction is linked to cancer and developmental disorders. Here, we identify CCDC57 as a pleiotropic regulator of centriole duplication, mitosis, and ciliogenesis. Combining proximity mapping with superresolution imaging, we show that CCDC57 localizes to the proximal end of centrioles and interacts with the microcephaly protein CEP63, centriolar satellite proteins, and microtubules. Loss of CCDC57 causes defects in centriole duplication and results in a failure to localize CEP63 and CEP152 to the centrosome. Additionally, CCDC57 depletion perturbs mitotic progression both in wild-type and centriole-less cells. Importantly, its centrosome-targeting region is required for its interaction with CEP63 and functions during centriole duplication and cilium assembly, whereas the microtubule-targeting region is required for its mitotic functions. Together, our results identify CCDC57 as a critical interface between centrosome and microtubule-mediated cellular processes that are deregulated in microcephaly.Publication Open Access Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation(Wiley, 2019) Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Odabaşı, Ezgi; Karalar, Elif Nur Fırat; Gül, Şeref; Kavaklı, İbrahim Halil; Other; Researcher; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; N/A; 206349; N/A; 40319Centriolar satellites are ubiquitous in vertebrate cells. They have recently emerged as key regulators of centrosome/cilium biogenesis, and their mutations are linked to ciliopathies. However, their precise functions and mechanisms of action remain poorly understood. Here, we generated a kidney epithelial cell line (IMCD3) lacking satellites by CRISPR/Cas9-mediated PCM1 deletion and investigated the cellular and molecular consequences of satellite loss. Cells lacking satellites still formed full-length cilia but at significantly lower numbers, with changes in the centrosomal and cellular levels of key ciliogenesis factors. Using these cells, we identified new ciliary functions of satellites such as regulation of ciliary content, Hedgehog signaling, and epithelial cell organization in three-dimensional cultures. However, other functions of satellites, namely proliferation, cell cycle progression, and centriole duplication, were unaffected in these cells. Quantitative transcriptomic and proteomic profiling revealed that loss of satellites affects transcription scarcely, but significantly alters the proteome. Importantly, the centrosome proteome mostly remains unaltered in the cells lacking satellites. Together, our findings identify centriolar satellites as regulators of efficient cilium assembly and function and provide insight into disease mechanisms of ciliopathies.Publication Open Access Clock regulation of metabolites reveals coupling between transcription and metabolism(Elsevier, 2017) Sancar, Aziz; Krishnaiah, Saikumari Y.; Wu, Gang; Altman, Brian J.; Growe, Jacqueline; Rhoades, Seth D.; Coldren, Faith; Venkataraman, Anand; Olarerin-George, Anthony O.; Francey, Lauren J.; Mukherjee, Sarmistha; Girish, Saiveda; Selby, Christopher P.; Ubeydullah, E.R.; Sianati, Bahareh; Sengupta, Arjun; Anafi, Ron C.; Baur, Joseph A.; Dang, Chi V.; Hogenesch, John B.; Weljie, Aalim M.; Department of Chemical and Biological Engineering; Kavaklı, İbrahim Halil; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40319; N/AThe intricate connection between the circadian clock and metabolism remains poorly understood. We used high temporal resolution metabolite profiling to explore clock regulation of mouse liver and cell-autonomous metabolism. In liver, similar to 50% of metabolites were circadian, with enrichment of nucleotide, amino acid, and methylation pathways. In U2 OS cells, 28% were circadian, including amino acids and NAD biosynthesis metabolites. Eighteen metabolites oscillated in both systems and a subset of these in primary hepatocytes. These 18 metabolites were enriched in methylation and amino acid pathways. To assess clock dependence of these rhythms, we used genetic perturbation. BMAL1 knockdown diminished metabolite rhythms, while CRY1 or CRY2 perturbation generally shortened or lengthened rhythms, respectively. Surprisingly, CRY1 knockdown induced 8 hr rhythms in amino acid, methylation, and vitamin metabolites, decoupling metabolite from transcriptional rhythms, with potential impact on nutrient sensing in vivo. These results provide the first comprehensive views of circadian liver and cell-autonomous metabolism.Publication Metadata only Co-regulation proteomics reveals substrates and mechanisms of apc/c-dependent degradation(Wiley, 2014) Singh, Sasha A.; Winter, Dominic; Kirchner, Marc; Chauhan, Ruchi; Ahmed, Saima; Tzur, Amit; Steen, Judith A.; Steen, Hanno; Department of Molecular Biology and Genetics; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 105301Using multiplexed quantitative proteomics, we analyzed cell cycle-dependent changes of the human proteome. We identified >4,400 proteins, each with a six-point abundance profile across the cell cycle. Hypothesizing that proteins with similar abundance profiles are co-regulated, we clustered the proteins with abundance profiles most similar to known Anaphase-Promoting Complex/Cyclosome (APC/C) substrates to identify additional putative APC/C substrates. This protein profile similarity screening (PPSS) analysis resulted in a shortlist enriched in kinases and kinesins. Biochemical studies on the kinesins confirmed KIFC1, KIF18A, KIF2C, and KIF4A as APC/C substrates. Furthermore, we showed that the APC/C-CDH(1)-dependent degradation of KIFC1 regulates the bipolar spindle formation and proper cell division. A targeted quantitative proteomics experiment showed that KIFC1 degradation is modulated by a stabilizing CDK1-dependent phosphorylation site within the degradation motif of KIFC1. The regulation of KIFC1 (de-)phosphorylation and degradation provides insights into the fidelity and proper ordering of substrate degradation by the APC/C during mitosis.Publication Metadata only Constructing structural networks of signaling pathways on the proteome scale(Current Biology Ltd, 2012) Nussinov, Ruth; Department of Chemical and Biological Engineering; N/A; Department of Computer Engineering; Keskin, Özlem; Kuzu, Güray; Gürsoy, Attila; Faculty Member; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 26605; N/A; 8745Proteins function through their interactions, and the availability of protein interaction networks could help in understanding cellular processes. However, the known structural data are limited and the classical network node-and-edge representation, where proteins are nodes and interactions are edges, shows only which proteins interact; not how they interact. Structural networks provide this information. Protein-protein interface structures can also indicate which binding partners can interact simultaneously and which are competitive, and can help forecasting potentially harmful drug side effects. Here, we use a powerful protein-protein interactions prediction tool which is able to carry out accurate predictions on the proteome scale to construct the structural network of the extracellular signal-regulated kinases (ERK) in the mitogen-activated protein kinase (MAPK) signaling pathway. This knowledge-based method, PRISM, is motif-based, and is combined with flexible refinement and energy scoring. PRISM predicts protein interactions based on structural and evolutionary similarity to known protein interfaces.