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    Bioenergetic shift and proteomic signature induced by lentiviral-transduction of gfp-based biosensors
    (2024) Barakat, Sarah; Çimen, Şeyma; Miri, Seyed Mohammad; Vatandaşlar, Emre; Yelkenci, Hayriye Ecem; San Martín, Alejandro; Beker, Mustafa Çağlar; Kök, Kıvanç; Öztürk, Gürkan; Eroğlu, Emrah
    Fluorescent proteins (FPs) stand as pivotal tools extensively employed across diverse biological research endeavors in various model systems. However, long-standing concerns surround their use due to the numerous side effects associated with their expression. Recent investigations have brought to light the significance of hydrogen peroxide (H2O2) that is associated with the maturation process of green fluorescent protein (GFP) fluorophores. The structural and functional impairments associated with GFP expression are possibly linked to this amount of H2O2. In this study, we assess the impact of the GFP-based HyPer7 biosensor on cellular homeostasis and proteome changes, aiming to identify potential risks related to oxidative stress responses that potentially risks the application of such tools. Cells expressing genome-integrated HyPer7 demonstrated altered mitochondrial membrane potential (MMP), which was alleviated by the addition of antioxidants or culturing cells at physiological normoxia (5 kPa O2). Additionally, HyPer7-expressing cells also exhibited significant impairment in mitochondrial oxidative respiration, suggesting broader mitochondrial dysfunction. Through untargeted proteomics analysis, we identified 26 proteins exhibiting differential expression in HyPer7-expressing cells compared to respective control cells. Functional annotation analysis showed that the list of the delineated proteins is associated with cellular responses to stress and the regulation of antioxidant mechanisms. Our findings underscore the significance of caution and validation in ensuring a thorough comprehension of cellular responses when using fluorescent protein-based tools, thereby enhancing the reliability of the results.
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    Identification of PDE10A related proteins via proteomic analysis
    (İnönü University Faculty of Medicine, 2022) Beker, Mustafa Çağlar; Yelkenci, Hayriye Ecem; Çağlayan, Berrak; Kılıç, Ertuğrul
    Aim: Phosphodiesterase 10A (PDE10A) regulates the expression of secondary messengers of cyclic adenosine monophosphate and cyclic guanosine monophosphate, which control several intracellular signaling pathways. Recently, deactivation of PDE10A has been a notable target for the treatment of neurodegenerative diseases. Herein, we identified the effects of PDE10A inhibition on protein profile using TAK-063 under physiological condi- tions in mice. Materials and Methods: In this study, 8-12 weeks old male C57BL6/J mice were divided into vehicle or 3 mg/kg TAK-063 groups. Thirty minutes after oral delivery of vehicle or TAK-063, animals were sacrificed and liquid chromatography-mass spectrome- try/mass spectrometry (LC-MS/MS) mediated proteomic analyses were performed from tissue samples taken from the striatum region of mice. After the LC-MS/MS analysis, identified proteins were classified based on biological activity, molecular function, and signal transduction pathways using PANTHER (protein annotation through evolutionary relationship, http://www.pantherdb.org/) program. Results: As a result of proteomic analyses, 1873 different proteins were identified. Sixty- one different proteins changed significantly depending on the administration of TAK-063. According to PANTHER classification, a significant part of the identified proteins found to be in the metabolite interconversion enzyme, transporter, and protein modifying enzyme category. The molecular function classification includes the catalytic activity, transporter activity, and binding functions. The signal transduction pathway analysis demonstrated that PDE10A affects ATP synthesis, FGF signaling, EGF receptor signaling, Huntington’s Disease, Parkinson’s Disease, pyrimidine metabolism, and ubiquitin-proteasome signal transduction pathways. Conclusion: TAK-063 mediated PDE10 deactivation is an essential target in the mech- anism of energy metabolism and neurodegenerative diseases.
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    Phosphodiesterase 10A deactivation induces long-term neurological recovery, peri-infarct remodeling and pyramidal tract plasticity after transient focal cerebral ischemia in mice
    (Academic Press Inc., 2022) Beker, Mustafa Çağlar; Pençe, Mahmud Esad; Yağmur, Sümeyya; Çağlayan, Berrak; Çağlayan, Aysun; Kılıç, Ülkan; Yelkenci, Hayriye Ecem; Altıntaş, Mehmet Özgen; Çağlayan, Ahmet Burak; Doeppner, Thorsten Roland; Hermann, Dirk M.; Kılıç, Ertuğrul
    The phosphodiesterase (PDE) superfamily comprises enzymes responsible for the cAMP and cGMP degradation to AMP and GMP. PDEs are abundant in the brain, where they are involved in several neuronal functions. High PDE10A abundance was previously observed in the striatum; however its consequences for stroke recovery were unknown. Herein, we evaluated the effects of PDE10A deactivation by TAK-063 (0.3 or 3 mg/kg, initiated 72 h post-stroke) in mice exposed to intraluminal middle cerebral artery occlusion. We found that PDE10A deactivation over up to eight weeks dose-dependently increased long-term neuronal survival, angiogenesis, and neurogenesis in the peri-infarct striatum, which represents the core of the middle cerebral artery territory, and reduced astroglial scar formation, whole brain atrophy and, more specifically, striatal atrophy. Functional motor-coordination recovery and the long-distance plasticity of pyramidal tract axons, which originate from the contralesional motor cortex and descend through the contralesional striatum to innervate the ipsilesional facial nucleus, were enhanced by PDE10A deactivation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed a set of dopamine receptor-related and neuronal plasticity-related PDE10A targets, which were elevated (e.g., protein phosphatase-1 regulatory subunit 1B) or reduced (e.g., serine/threonine protein phosphatase 1?, ?-synuclein, proteasome subunit ?2) by PDE10A deactivation. Our results identify PDE10A as a therapeutic target that critically controls post-ischemic brain tissue remodeling and plasticity.
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    Vinpocetine ameliorates neuronal injury after cold-induced traumatic brain injury in mice
    (2025) Yelkenci, Hayriye Ecem; Değirmenci, Zehra; Koç, Halil İbrahim; Bayırlı, Sevban; Baltacı, Saltuk Buğra; Altunay, Serdar; Öztekin, Nevin; Koçak, Mehmet; Kılıç, Ertuğrul; Beker, Mustafa Çağlar
    Traumatic brain injury (TBI), also known as intracranial injury, is a common condition with the highest incidence rate among neurodegenerative disorders and poses a significant public health burden. Various methods are used in the treatment of TBI, but the effects of cold-induced traumatic brain injury have not been thoroughly studied. In this context, vinpocetine (VPN), derived from Vinca minor, exhibits notable anti-inflammatory and antioxidant properties. VPN is known for its neuroprotective role and is generally utilized for treating various neurodegenerative disorders. However, the function of VPN after cold-induced TBI needs to be studied in more detail. This study aims to investigate the neuroprotective effects of VPN at varying doses (5 mg/kg or 10 mg/kg) after cold-induced TBI. C57BL/6 mice were sacrificed 2 or 28 days after cold-induced TBI. Results indicate that VPN administration significantly reduces brain infarct volume, brain swelling, blood–brain barrier disruption, and DNA fragmentation in a dose-dependent manner. Additionally, VPN enhances neuronal survival in the ipsilesional cortex. In the long term, VPN treatment (5 mg/kg/day or 10 mg/kg/day, initiated 48 h post-TBI) improved locomotor activity, cell proliferation, neurogenesis, and decreased whole brain atrophy, specifically motor cortex atrophy. We performed liquid chromatography-tandem mass spectrometry (LC–MS/MS) to elucidate the underlying mechanisms to profile proteins and signaling pathways influenced by prolonged VPN treatment post-TBI. Notably, we found that 192 different proteins were significantly altered by VPN treatment, which is a matter of further investigation for the development of therapeutic targets. Our study has shown that VPN may have a neuroprotective role in cold-induced TBI.