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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Multifunctional alginate-based hydrogel with reversible crosslinking for controlled therapeutics delivery(Elsevier, 2020) Ekinci, Duygu; N/A; Department of Chemical and Biological Engineering; Batool, Syeda Rubab; Nazeer, Muhammad Anwaar; Kızılel, Seda; Şahin, Afsun; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 28376; 171267Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision.Publication Open Access The MHC class I MICA gene is a histocompatibility antigen in kidney transplantation(Springer Nature, 2022) Carapito, Raphael; Aouadi, Ismail; Verniquet, Martin; Untrau, Meiggie; Pichot, Angelique; Beaudrey, Thomas; Bassand, Xavier; Meyer, Sebastien; Faucher, Loic; Posson, Juliane; Morlon, Aurore; Kotova, Irina; Delbos, Florent; Walencik, Alexandre; Aarnink, Alice; Kennel, Anne; Suberbielle, Caroline; Taupin, Jean-Luc; Matern, Benedict M.; Spierings, Eric; Congy-Jolivet, Nicolas; Essaydi, Arnaud; Perrin, Peggy; Blancher, Antoine; Charron, Dominique; Cereb, Nezih; Maumy-Bertrand, Myriam; Bertrand, Frederic; Garrigue, Valerie; Pernin, Vincent; Weekers, Laurent; Naesens, Maarten; Kamar, Nassim; Legendre, Christophe; Glotz, Denis; Caillard, Sophie; Ladriere, Marc; Giral, Magali; Anglicheau, Dany; Bahram, Seiamak; Süsal, Caner; Other; School of MedicineThe identity of histocompatibility loci, besides human leukocyte antigen (HLA), remains elusive. The major histocompatibility complex (MHC) class I MICA gene is a candidate histocompatibility locus. Here, we investigate its role in a French multicenter cohort of 1,356 kidney transplants. MICA mismatches were associated with decreased graft survival (hazard ratio (HR), 2.12; 95% confidence interval (CI): 1.45-3.11; P < 0.001). Both before and after transplantation anti-MICA donor-specific antibodies (DSA) were strongly associated with increased antibody-mediated rejection (ABMR) (HR, 3.79; 95% CI: 1.94-7.39; P < 0.001; HR, 9.92; 95% CI: 7.43-13.20; P < 0.001, respectively). This effect was synergetic with that of anti-HLA DSA before and after transplantation (HR, 25.68; 95% CI: 3.31-199.41; P = 0.002; HR, 82.67; 95% CI: 33.67-202.97; P < 0.001, respectively). De novo-developed anti-MICA DSA were the most harmful because they were also associated with reduced graft survival (HR, 1.29; 95% CI: 1.05-1.58; P = 0.014). Finally, the damaging effect of anti-MICA DSA on graft survival was confirmed in an independent cohort of 168 patients with ABMR (HR, 1.71; 95% CI: 1.02-2.86; P = 0.041). In conclusion, assessment of MICA matching and immunization for the identification of patients at high risk for transplant rejection and loss is warranted.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 Open Access An information theoretical analysis of human insulin-glucose system toward the internet of bio-nano things(Institute of Electrical and Electronics Engineers (IEEE), 2017) Department of Electrical and Electronics Engineering; Abbasi, Naveed Ahmed; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and EngineeringMolecular communication is an important tool to understand biological communications with many promising applications in Internet of Bio-Nano Things (IoBNT). The insulin-glucose system is of key significance among the major intra-body nanonetworks, since it fulfills metabolic requirements of the body. The study of biological networks from information and communication theoretical (ICT) perspective is necessary for their introduction in the IoBNT framework. Therefore, the objective of this paper is to provide and analyze for the first time in the literature, a simple molecular communication model of the human insulin-glucose system from ICT perspective. The data rate, channel capacity, and the group propagation delay are analyzed for a two-cell network between a pancreatic beta cell and a muscle cell that are connected through a capillary. The results point out a correlation between an increase in insulin resistance and a decrease in the data rate and channel capacity, an increase in the insulin transmission rate, and an increase in the propagation delay. We also propose applications for the introduction of the system in the IoBNT framework. Multi-cell insulin glucose system models may be based on this simple model to help in the investigation, diagnosis, and treatment of insulin resistance by means of novel IoBNT applications.Publication Open Access Solution chemical properties and anticancer potential of 8-hydroxyquino-line hydrazones and their oxidovanadium(IV) complexes(Elsevier, 2022) Ribeiro, Nadia; Posa, Vivien; Sciortino, Giuseppe; Pessoa, Joao Costa; Maia, Luisa B.; Ugone, Valeria; Garribba, Eugenio; Enyedy, Eva A.; Correia, Isabel; Bulut, İpek; Sergi, Barış; Ayhan, Ceyda Açılan; Master Student; PhD Student; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; N/A; N/A; 219658We report the synthesis and characterization of a family of benzohydrazones (L-n, n = 1-6) derived from 2-car-baldehyde-8-hydroxyquinoline and benzylhydrazides containing different substituents in the para position. Their oxidovanadium(IV) complexes were prepared and compounds with 1:1 and 1:2 metal-to-ligand stoichiometry were obtained. All compounds were characterized by elemental analyses and mass spectrometry as well as FTIR, UV-visible absorption, NMR (ligand precursors) and EPR (complexes) spectroscopies, and by DFT computational methods. Proton dissociation constants, lipophilicity and solubility in aqueous media were determined for all ligand precursors. Complex formation with V(IV)O was evaluated by spectrophotometry for L-4 (Me-substituted) and L-6 (OH-substituted) and formation constants for mono [VO(HL)](+), [VO(L)] and bis [VO(HL)(2)], [VO(HL) (L)], [VO(L)(2)](2- )complexes were determined. EPR spectroscopy indicates the formation of [VO(HL)](+) and [VO (HL)(2)], with this latter being the major species at the physiological pH. Noteworthy, the EPR data suggest a different behaviour for L-4 and L-6, which confirm the results obtained in the solid state. The antiproliferative activity of all compounds was evaluated in malignant melanoma (A-375) and lung (A-549) cancer cells. All complexes show much higher activity on A-375 (IC50 < 6.3 mu M) than in A-549 cells (IC50 > 20 mu M). Complex 3 (F-substituted) shows the lowest IC50 on both cell lines and lower than cisplatin (in A-375). Studies identified this compound as the one showing the highest increase in Annexin-V staining, caspase activity and induction of double stranded breaks, corroborating the cytotoxicity results. The mechanism of action of the complexes involves reactive oxygen species (ROS) induced DNA damage, and cell death by apoptosis.Publication Open Access Pancreas-specific activation of mTOR and loss of p53 induce tumors reminiscent of acinar cell carcinoma(BioMed Central, 2016) Kong, Bo; Cheng Tao; Qian, Chengjia; Wu, Weiwei; Steiger, Katja; Cao, Jing; Schlitter, Anna Melissa; Regel, Ivonne; Raulefs, Susanne; Friess, Helmut; Esposito, Irene; Kleeff, Joerg; Michalski, Christoph W.; N/A; Erkan, Murat Mert; Faculty Member; School of Medicine; 214689Background: Pancreatic acinar cell carcinoma (ACC) is a rare tumor entity with an unfavorable prognosis. Recent whole-exome sequencing identified p53 mutations in a subset of human ACC. Activation of the mammalian target of rapamycin (mTOR) pathway is associated with various pancreatic neoplasms. We thus aimed at analyzing whether activation of mTOR with a concomitant loss of p53 may initiate ACC. Methods: We generated transgenic mouse models in which mTOR was hyperactivated through pancreas-specific, homozygous tuberous sclerosis 1 (Tsc1) deficiency, with or without deletion of p53 (Tsc1(-/-) and Tsc1(-/-); p53(-/-)). Activity of mTOR signaling was investigated using mouse tissues and isolated murine cell lines. Human ACC specimens were used to corroborate the findings from the transgenic mouse models. Results: Hyperactive mTOR signaling in Tsc1(-/-) mice was not oncogenic but rather induced a near-complete loss of the pancreatic acinar compartment. Acinar cells were lost as a result of apoptosis which was associated with p53 activation. Concomitantly, ductal cells were enriched. Ablation of p53 in Tsc1-deficient mice prevented acinar cell death but promoted formation of acinar cells with severe nuclear abnormalities. One out of seven Tsc1(-/-); p53(-/-) animals developed pancreatic tumors showing a distinctive tumor morphology, reminiscent of human ACC. Hyperactive mTOR signaling was also detected in a subset of human ACC. Conclusion: Hyperactive mTOR signaling combined with loss of p53 in mice induces tumors similar to human ACC.Publication Open Access Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients(EMBO Press, 2021) Altay, O.; Arif, M.; Li, X.; Yang, H.; Fredolini, C.; Kim, W.; Schwenk, J.M.; Zhang, C.; Shoaie, S.; Nielsen, J.; Uhlen, M.; Boren, J.; Mardinoğlu, A.; Zeybel, Müjdat; Ural, Dilek; Gönenli, Mehmet Gökhan; Akyıldız, Murat; Kurtoğlu, Burçin Sağlam; Faculty Member; Faculty Member; Teaching Faculty; Faculty Member; School of Medicine; Koç University Hospital; 214694; 1057; 350445; 123080; N/ANonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.Publication Open Access Bidirectional optical neuromodulation using capacitive charge-transfer(The Optical Society (OSA) Publishing, 2020) Department of Electrical and Electronics Engineering; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Melikov, Rustamzhon; Srivastava, Shashi Bhushan; Karatüm, Onuralp; Nizamoğlu, Sedat; Doğru-Yüksel, Itır Bakış; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; PhD Student; Researcher; PhD Student; Faculty Member; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; N/A; N/A; 130295; N/A; N/A; 40319Artificial control of neural activity allows for understanding complex neural networks and improving therapy of neurological disorders. Here, we demonstrate that utilization of photovoltaic biointerfaces combined with light waveform shaping can generate safe capacitive currents for bidirectional modulation of neurons. The differential photoresponse of the biointerface due to double layer capacitance facilitates the direction control of capacitive currents depending on the slope of light intensity. Moreover, the strength of capacitive currents is controlled by changing the rise and fall time slope of light intensity. This approach allows for high-level control of the hyperpolarization and depolarization of membrane potential at single-cell level. Our results pave the way toward advanced bioelectronic functionalities for wireless and safe control of neural activity.Publication Open Access Expanding the molecular spectrum of pathogenic SHOC2 variants underlying Mazzanti syndrome(Oxford University Press (OUP), 2022) Motta, Marialetizia; Solman, Maja; Bonnard, Adeline; Kuechler, Alma; Pantaleoni, Francesca; Priolo, Manuela; Chandramouli, Balasubramanian; Coppola, Simona; Pizzi, Simone; Zara, Erika; Ferilli, Marco; Onesimo, Roberta; Leoni, Chiara; Brinkmann, Julia; Vial, Yoann; Kamphausen, Susanne B.; Thomas-Teinturier, Cecile; Guimier, Anne; Cordeddu, Viviana; Mazzanti, Laura; Zampino, Giuseppe; Chillemi, Giovanni; Zenker, Martin; Cave, Helene; Hertog, Jeroen; Tartaglia, Marco; Kayserili, Hülya; Undergraduate Student; PhD Student; School of Medicine; Koç University Hospital; 7945We previously molecularly and clinically characterized Mazzanti syndrome, a RASopathy related to Noonan syndrome that is mostly caused by a single recurrent missense variant (c.4A?>?G, p.Ser2Gly) in SHOC2, which encodes a leucine-rich repeat-containing protein facilitating signal flow through the RAS-mitogen-associated protein kinase (MAPK) pathway. We also documented that the pathogenic p.Ser2Gly substitution causes upregulation of MAPK signaling and constitutive targeting of SHOC2 to the plasma membrane due to the introduction of an N-myristoylation recognition motif. The almost invariant occurrence of the pathogenic c.4A?>?G missense change in SHOC2 is mirrored by a relatively homogeneous clinical phenotype of Mazzanti syndrome. Here, we provide new data on the clinical spectrum and molecular diversity of this disorder and functionally characterize new pathogenic variants. The clinical phenotype of six unrelated individuals carrying novel disease-causing SHOC2 variants is delineated, and public and newly collected clinical data are utilized to profile the disorder. In silico, in vitro and in vivo characterization of the newly identified variants provides evidence that the consequences of these missense changes on SHOC2 functional behavior differ from what had been observed for the canonical p.Ser2Gly change but converge toward an enhanced activation of the RAS-MAPK pathway. Our findings expand the molecular spectrum of pathogenic SHOC2 variants, provide a more accurate picture of the phenotypic expression associated with variants in this gene and definitively establish a gain-of-function behavior as the mechanism of disease.Publication Open Access Maximum likelihood detection with Ligand receptors for diffusion-based molecular communications in internet of bio-nano things(Institute of Electrical and Electronics Engineers (IEEE), 2018) Kuşçu, Murat; Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and EngineeringMolecular Communication (MC) is a bioinspired communication technique that uses molecules as a method of information transfer among nanoscale devices. MC receiver is an essential component having profound impact on the communication system performance. However, the interaction of the receiver with information bearing molecules has been usually oversimplified in modeling the reception process and developing signal detection techniques. In this paper, we focus on the signal detection problem of MC receivers employing receptor molecules to infer the transmitted messages encoded into the concentration of molecules, i.e., ligands. Exploiting the observable characteristics of ligand-receptor binding reaction, we first introduce a Maximum Likelihood (ML) detection method based on instantaneous receptor occupation ratio, as aligned with the current MC literature. Then, we propose a novel ML detection technique, which exploits the amount of time the receptors stay unbound in an observation time window. A comprehensive analysis is carried out to compare the performance of the detectors in terms of bit error probability. In evaluating the detection performance, emphasis is given to the receptor saturation problem resulting from the accumulation of messenger molecules at the receiver as a consequence of intersymbol interference. The results reveal that detection based on receptor unbound time is quite reliable even in saturation, whereas the reliability of detection based on receptor occupation ratio substantially decreases as the receiver gets saturated. Finally, we also discuss the potential methods of implementing the detectors.