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Karadenizli Taşkin S, Şahin D, Dede F, Ünal Halbutoğullari ZS, Sarihan M, Kurnaz Özbek S, Özsoy ÖD, Kasap M, Yazir Y, Ateş N. Endoplasmic reticulum stress produced by Thapsigargin affects the occurrence of spike-wave discharge by modulating unfolded protein response pathways and activating immune responses in a dose-dependent manner. Eur J Pharmacol 2024; 974:176613. [PMID: 38670446 DOI: 10.1016/j.ejphar.2024.176613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 04/28/2024]
Abstract
The Endoplasmic Reticulum (ER) is associated with many cellular functions, from post-transcriptional modifications to the proper folding of proteins, and disruption of these functions causes ER stress. Although the relationship between epileptic seizures and ER stress has been reported, the contribution of ER stress pathways to epileptogenesis is still unclear. This study aimed to investigate the possible effects of ER stress-related molecular pathways modulated by mild- and high-dose Thapsigargin (Tg) on absence epileptic activity, CACNA1H and immune responses in WAG/Rij rats. For this purpose, rats were divided into four groups; mild-dose (20 ng) Tg, high-dose (200 ng) Tg, saline, and DMSO and drugs administered intracerebroventriculary. EEG activity was recorded for 1 h and 24 h after drug administration following the baseline recording. In cortex and thalamus tissues, GRP78, ERp57, GAD153 protein changes (Western Blot), Eif2ak3, XBP-1, ATF6, CACNA1H mRNA expressions (RT-PCR), NF-κB and TNF-α levels (ELISA) were measured. Mild-dose-Tg administration resulted in increased spike-wave discharge (SWD) activity at the 24th hour compared to administration of saline, and high-dose-Tg and it also significantly increased the amount of GRP78 protein, the expression of Eif2ak3, XBP-1, and CACNA1H mRNA in the thalamus tissue. In contrast, high-dose-Tg administration suppressed SWD activity and significantly increased XBP-1 and ATF6 mRNA expression in the thalamus, and increased NF-κB and TNF-α levels. In conclusion, our findings indicate that Tg affects SWD occurrence by modulating the unfolded protein response pathway and activating inflammatory processes in a dose-dependent manner.
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Affiliation(s)
| | - Deniz Şahin
- Physiology Department, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Fazilet Dede
- Physiology Department, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | | | - Mehmet Sarihan
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Sema Kurnaz Özbek
- Department of Histology and Embryology, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Özgür Doğa Özsoy
- Department of Biochemistry, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Murat Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Yusufhan Yazir
- Stem Cell and Gene Therapy Research and Application Center, Kocaeli University, Kocaeli, Turkey; Department of Histology and Embryology, Kocaeli University Medical Faculty, Kocaeli, Turkey.
| | - Nurbay Ateş
- Physiology Department, Kocaeli University Medical Faculty, Kocaeli, Turkey.
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Sarihan M, Kasap M, Akpinar G. Streamlined Biotinylation, Enrichment and Analysis for Enhanced Plasma Membrane Protein Identification Using TurboID and TurboID-Start Biotin Ligases. J Membr Biol 2024; 257:91-105. [PMID: 38289568 DOI: 10.1007/s00232-023-00303-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/23/2023] [Indexed: 04/11/2024]
Abstract
Plasma membrane proteins (PMPs) play pivotal roles in various cellular events and are crucial in disease pathogenesis, making their comprehensive characterization vital for biomedical research. However, the hydrophobic nature and low expression levels of PMPs pose challenges for conventional enrichment methods, hindering their identification and functional profiling. In this study, we presented a novel TurboID-based enrichment approach for PMPs that helped overcoming some of the existing limitations. We evaluated the efficacy of TurboID and its modified form, TurboID-START, in PMP enrichment, achieving efficient and targeted labelling of PMPs without the need for stable cell line generation. This approach resulted reduction in non-specific biotinylation events, leading to improved PMP enrichment and enabled assessment of the subcellular proteome associated with the plasma membrane. Our findings paved the way for studies targeting the dynamic nature of the plasma membrane proteome and aiming to capture transient associations of proteins with the plasma membrane. The novel TurboID-based enrichment approach presented here offers promising prospects for in-depth investigations into PMPs and their roles in cellular processes.
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Affiliation(s)
- Mehmet Sarihan
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
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Yanar S, Sarihan M, Kasap M, Akpinar G, Teke K, Yaprak Bayrak B. GFP Transfection Alters Protein Expression Patterns in Prostate Cancer Cells: A Proteomic Study. J Fluoresc 2024:10.1007/s10895-023-03498-4. [PMID: 38502405 DOI: 10.1007/s10895-023-03498-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 03/21/2024]
Abstract
PURPOSE Green Fluorescent Protein is widely used as a cellular marker tool, but its potential influence on cells has been questioned. Although the potential off-target effects of GFP on tumor cells have been studied to some extent, the findings at the molecular level are insufficient to explain the effect of GFP expression on the tumorigenic capacity of cancer cells. Here, we aimed to investigate the effect of GFP expression on the tumorigenicity of PC3 prostate cancer cells. METHODS Using GFP-expressing and wild-type PC-3 cells, xenograft models were generated in athymic BALB/C mice. To identify differentially expressed proteins, the change in cells proteome was investigated by label-free quantification with nano-high performance liquid chromatography to tandem mass spectrometry (nHPLC-MS/MS). Proteins that showed significantly altered expression levels were evaluated using the bioinformatics tools. RESULTS Unlike the wild-type PC-3 cells, GFP-expressing cells failed to develop tumor. Comparative proteome analysis of GFP-expressing cells with WT PC-3 cells revealed a total of 216 differentially regulated proteins, of which 98 were upregulated and 117 were downregulated. CONCLUSION Upon GFP expression, differential changes in several pathways including the immune system, translational machinery, energy metabolism, elements of cytoskeletal and VEGF signaling pathway were observed. Therefore, care should be taken into account to prevent reporting deceitful mechanisms generated from studies utilizing GFP.
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Affiliation(s)
- Sevinc Yanar
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey.
- Faculty of Medicine, Department of Histology and Embryology, Sakarya University, Korucuk, Sakarya, Turkey.
| | - Mehmet Sarihan
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Kerem Teke
- Faculty of Medicine, Department of Urology, Kocaeli University, Kocaeli, Turkey
| | - Busra Yaprak Bayrak
- Faculty of Medicine, Department of Pathology, Kocaeli University, Kocaeli, Turkey
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Avci IE, Teke K, Gocmez SS, Kasap M, Akpinar G, Yaprak Bayrak B, Celebi G, Sarihan M, Utkan T, Ozkurkcugil C. Therapeutic Effects of AF219 on Interstitial Cystitis/Bladder Pain Syndrome Induced by Cyclophosphamide or Water Avoidance Stress in Rats. Int Urogynecol J 2024; 35:677-688. [PMID: 38376547 DOI: 10.1007/s00192-023-05723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 02/21/2024]
Abstract
INTRODUCTION AND HYPOTHESIS To evaluate the effect of AF219, a P2X3 receptor antagonist, in animal models of interstitial cystitis/bladder pain syndrome (IC/BPS) induced by cyclophosphamide (CYP) or water avoidance stress (WAS). METHODS Thirty-two adult female Wistar albino rats were used in each IC/BPS model. Assessment of nociception and anxiety and severity of inflammation in the bladder were assessed by behavioral experiments and histopathological examinations respectively. The contraction responses of the bladder were evaluated in vitro and protein levels of P2X3, P2X7, Trk-A, TRPV1, and TRPA1 were analyzed by Western blot. RESULTS The IC/BPS groups had shorter response times to noxious stimuli, exhibited more anxiety-like behavior, had higher inflammation-based histological scores, and showed greater increased contraction responses to carbachol, adenosine triphosphate, and electrical field stimulation in in vitro bladder strips than controls for both models (p < 0.05). The improvements in behavioral and bladder contraction responses and inflammation scores in the IC/BPS + AF219 groups were similar to control findings (p > 0.05). Exposure to WAS or CYP increased P2X3 expression in the bladder compared with the controls (p < 0.05). Apart from TRPA1, the levels of P2X7, Trk-A, and TRPV1 were also higher in the IC/BPS groups than in the controls (p < 0.05). No significant differences were observed between IC/BPS + AF219 and controls regarding P2X3, P2X7, Trk-A, and TRPV1 in the WAS model (p > 0.05). Moreover, P2X3 and P2X7 levels were significantly lower in IC/BPS + AF219 than in the AF219-untreated WAS model (p < 0.05). CONCLUSIONS These findings suggest that P2X3 receptors play a significant role in bladder functional responses, nociception, and also the pathogenesis of IC/BPS. AF219 may be a promising therapeutic strategy for IC/BPS. Comparing AF219 with current IC/BPS treatment agents in future studies may yield valuable insights into its efficacy.
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Affiliation(s)
- Ibrahim Erkut Avci
- Department of Urology, Kocaeli University School of Medicine, 41001, Kocaeli, Turkey
| | - Kerem Teke
- Department of Urology, Kocaeli University School of Medicine, 41001, Kocaeli, Turkey
| | - Semil Selcen Gocmez
- Department of Pharmacology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Busra Yaprak Bayrak
- Department of Pathology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Gulsen Celebi
- Department of Pharmacology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Mehmet Sarihan
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Tijen Utkan
- Department of Pharmacology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Cuneyd Ozkurkcugil
- Department of Urology, Kocaeli University School of Medicine, 41001, Kocaeli, Turkey.
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Melekoglu R, Yasar S, Colak C, Kasap M, Dogan UK, Yologlu S, Yilmaz E, Shazly S. Determination of biomarker candidates for the placenta accreta spectrum by plasma proteomic analysis. Sci Rep 2024; 14:2803. [PMID: 38307924 PMCID: PMC10837117 DOI: 10.1038/s41598-024-53324-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/31/2024] [Indexed: 02/04/2024] Open
Abstract
Placenta accreta spectrum (PAS) presents a significant obstetric challenge, associated with considerable maternal and fetal-neonatal morbidity and mortality. Nevertheless, it is imperative to acknowledge that a noteworthy subset of PAS cases remains undetected until the time of delivery, thereby contributing to an augmented incidence of morbidity among the affected individuals. The delayed identification of PAS not only hinders timely intervention but also exacerbates the associated health risks for both the maternal and fetal outcomes. This underscores the urgency to innovate strategies for early PAS diagnosis. In this study, we aimed to explore plasma proteins as potential diagnostic biomarkers for PAS. Integrated transcriptome and proteomic analyses were conducted to establish a novel diagnostic approach. A cohort of 15 pregnant women diagnosed with PAS and delivering at Inonu University Faculty of Medicine between 01/04/2021 and 01/01/2023, along with a matched control group of 15 pregnant women without PAS complications, were enrolled. Plasma protein identification utilized enzymatic digestion and liquid chromatography-tandem mass spectrometry techniques. Proteomic analysis identified 228 plasma proteins, of which 85 showed significant differences (P < 0.001) between PAS and control cases. We refined this to a set of 20 proteins for model construction, resulting in a highly accurate classification model (96.9% accuracy). Notable associations were observed for proteins encoded by P01859 (Immunoglobulin heavy constant gamma 2), P02538 (Keratin type II cytoskeletal 6A), P29622 [Kallistatin (also known as Serpin A4)], P17900 (Ganglioside GM2 activator Calmodulin-like protein 5), and P01619 (Immunoglobulin kappa variable 3-20), with fold changes indicating their relevance in distinguishing PAS from control groups. In conclusion, our study has identified novel plasma proteins that could serve as potential biomarkers for early diagnosis of PAS in pregnant women. Further research and validation in larger PAS cohorts are necessary to determine the clinical utility and reliability of these proteomic biomarkers for diagnosing PAS.
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Affiliation(s)
- Rauf Melekoglu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey.
| | - Seyma Yasar
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey
| | - Cemil Colak
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Umran Karabulut Dogan
- Clinic of Obstetrics and Gynecology, Malatya Education and Research Hospital, Malatya, Turkey
| | - Saim Yologlu
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey
| | - Ercan Yilmaz
- Department of Obstetrics and Gynecology, Faculty of Medicine, Inonu University, 44280, Malatya, Turkey
| | - Sherif Shazly
- Department of Obstetrics and Gynecology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Yanar S, Kanli A, Kasap M, Bal Albayrak MG, Eskiler GG, Ozkan AD. Synergistic effect of a nonsteroidal anti-inflammatory drug in combination with topotecan on small cell lung cancer cells. Mol Biol Rep 2024; 51:145. [PMID: 38236451 DOI: 10.1007/s11033-023-09055-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/23/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND The topoisomerase I inhibitor topotecan (TPT) is used in the treatment of recurrent small cell lung cancer (SCLC). However, the drug has a limited success rate and causes distress to patients due to its side effects, such as hematologic toxicities, including anemia and thrombocytopenia. Due to these pharmacokinetic limitations and undesirable side effects of chemotherapeutic drugs, the development of combination therapies has gained popularity in SCLC. Meclofenamic acid (MA), a nonsteroidal anti-inflammatory drug, has demonstrated anticancer effects on various types of cancers through different mechanisms. This study aims to investigate the potential synergistic effects of MA and TPT on the small cell lung cancer cell line DMS114. METHODS AND RESULTS To assess the cytotoxic and apoptotic effects of the combined treatment of MA and TPT, trypan blue exclusion assay, Annexin V, acridine orange/propidium iodide staining, western blot, and cell cycle analysis were conducted. The results demonstrated that the combination of MA and TPT elicited synergistic effects by enhancing toxicity in DMS114 cells (P < 0.01) without causing toxicity in healthy epithelial lung cells MRC5. The strongest synergistic effect was observed when the cells were treated with 60 µM MA and 10 nM TPT for 48 h (CI = 0,751; DRI = 10,871). CONCLUSION This study, for the first time, furnishes compelling evidence that MA and TPT synergistically reduce cellular proliferation and induce apoptosis in SCLC cells. Combinations of these drugs holds promise as a potential therapeutic strategy to improve efficacy and reduce the side effects associated with TPT.
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Affiliation(s)
- Sevinc Yanar
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey.
- Faculty of Medicine, Department of Histology and Embryology, Sakarya University, Korucuk, Sakarya, 54290, Turkey.
| | - Aylin Kanli
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Faculty of Medicine, Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | | | - Gamze Guney Eskiler
- Faculty of Medicine, Department of Medical Biology, Sakarya University, Sakarya, Turkey
| | - Asuman Deveci Ozkan
- Faculty of Medicine, Department of Medical Biology, Sakarya University, Sakarya, Turkey
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Yılmaz Tuğan B, Sarıhan M, Kasap M, Akpınar G, Karabaş L, Şahin N, Yüksel N, Bayrak YE, Sönmez HE. Is tear proteome profile a predictor of developing uveitis in ANA-positive patients with oligoarticular juvenile idiopathic arthritis? Graefes Arch Clin Exp Ophthalmol 2024; 262:211-221. [PMID: 37773290 DOI: 10.1007/s00417-023-06251-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023] Open
Abstract
PURPOSE Although less than one-third of anti-nuclear antibody (ANA) positive patients with oJIA develop uveitis, ANA positivity is still the most well-known marker for assessing the risk of uveitis in oligoarticular JIA (oJIA). Therefore, novel biomarkers are needed to better assess the risk of developing uveitis. For this purpose, we performed a comparative tear proteome analysis of uveitis patients to reveal the identity of differentially regulated proteins. DESIGN Tear samples were collected using the Schirmer strips in 7 oJIA and 7 oJIA patients with uveitis (oJIA-U). All oJIA-U patients had developed bilateral anterior uveitis and were inactive and topical treatment-free. METHODS The nHPLC LC-MS/MS system was used for protein identification and label-free proteome comparisons. The PANTHER and STRING analyses were carried out using UniProt accession numbers of the identified proteins. RESULTS Patient characteristics, e.g., age, gender, disease duration, and treatments were similar. For protein identification, three different databases were searched. Twenty-two, 147, and 258 database searches, respectively. Of these, 15 were common to all three proteome databases. Of these 15 proteins, 10 proteins were upregulated, and 2 were downregulated, based on the twofold regulation criteria. The upregulated proteins were, namely, cystatin-S, secretoglobin family 1D member, opiorphin prepropeptide, mammaglobin-B, lysozyme C, mesothelin, immunoglobulin kappa constant, extracellular glycoprotein lacritin, beta-2-microglobulin, and immunoglobulin J chain. The downregulated proteins were dermcidin and prolactin-inducible protein. Among the differentially regulated proteins, cystatin-S was the most regulated protein with an 18-fold upregulation ratio in tear samples from uveitis patients. CONCLUSION Here, the identities and regulation ratios of several proteins were revealed when tear samples from uveitis patients were compared to patients without uveitis. These proteins are putative biomarkers for assessing uveitis risk and require further attention.
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Affiliation(s)
- Büşra Yılmaz Tuğan
- Department of Ophthalmology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey.
| | - Mehmet Sarıhan
- Department of Basic Medical Sciences, Medical Biology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Basic Medical Sciences, Medical Biology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Gürler Akpınar
- Department of Basic Medical Sciences, Medical Biology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Levent Karabaş
- Department of Ophthalmology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Nihal Şahin
- Department of Pediatrics, Division of Pediatric Rheumatology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Nurşen Yüksel
- Department of Ophthalmology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Yunus Emre Bayrak
- Department of Pediatrics, Division of Pediatric Rheumatology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Hafize Emine Sönmez
- Department of Pediatrics, Division of Pediatric Rheumatology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
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Simsek T, Bal Albayrak MG, Akpinar G, Canturk NZ, Kasap M. Downregulated GPD1 and MAGL protein levels as potential biomarkers for the metastasis of triple‑negative breast tumors to axillary lymph nodes. Oncol Lett 2024; 27:34. [PMID: 38108074 PMCID: PMC10722549 DOI: 10.3892/ol.2023.14167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
Glycerol-3-phosphate dehydrogenase (GPD1) and monoacylglycerol lipase (MAGL) levels are known to be significantly downregulated in both the tissue and serum samples of patients with triple-negative breast cancer (TNBC), compared with other BC subtypes and healthy controls. As such, the association between GPD1 and MAGL levels and lymph node metastasis was evaluated in the present study. Utilizing western blotting, lymph node protein extracts from metastasized BC subtypes were analyzed and a significant downregulation of GPD1 and MAGL protein expression levels in the lymph node metastases was demonstrated in the TNBC subtype, compared with healthy controls. This finding further highlighted the potential use of these two proteins in early BC onset and metastasis detection.
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Affiliation(s)
- Turgay Simsek
- Department of General Surgery, Kocaeli University Medical School, 41001 Kocaeli, Turkey
| | | | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Medical School, 41001 Kocaeli, Turkey
| | - Nuh Zafer Canturk
- Department of General Surgery, Kocaeli University Medical School, 41001 Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Medical School, 41001 Kocaeli, Turkey
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Kizilkaya S, Akpinar G, Sesal NC, Kasap M, Gokalsin B, Kayhan FE. Using proteomics, q-PCR and biochemical methods complementing as a multiapproach to elicit the crucial responses of zebrafish liver exposed to neonicotinoid pesticide. Comp Biochem Physiol Part D Genomics Proteomics 2023; 47:101103. [PMID: 37399785 DOI: 10.1016/j.cbd.2023.101103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/10/2023] [Accepted: 06/10/2023] [Indexed: 07/05/2023]
Abstract
Pesticides enter the environment through runoff and leaching and this raises public concern about effects on non-target organisms. Imidacloprid (IMI) a synthetic pesticide, has an unstable half-life, metabolized in minutes to weeks in the water. To evaluate the effects of IMI on the zebrafish liver, we conducted proteomic, molecular and biochemical analysis in a multi-level approach, to highlight the complementary features regarding the results of each method. Adult zebrafish were exposed to 60 mg/L IMI for 48 h and were evaluated using nLC-MS/MS for proteins, q-PCR analysis for expression of cat, gpx, pxr, ache, along with CAT and AChE enzyme activities and GSH and MDA assays. Based on proteomics, the regulation of antioxidant and immune responses, as well as gene transcription were significant processes affected. Apoptosis and ER stress pathways were upregulated and there was a down-regulation of cat and gpx genes. There was also elevated CAT activity and GSH and decreased MDA. Additionally, elevated AChE activity and up regulation of ache expression was observed. The multi-approach results included regulators of antioxidant, xenobiotic response and neuro-protective related proteins (genes and enzymes), which overall reflected harmful effects of IMI. Consequently, this study highlights the effects of IMI on zebrafish liver and reveals new potential biomarkers. In this respect, evaluated outcomes reveal the complementary features emphasizing the importance of studying chemicals using several methods. Our study provides deeper insights for future work in ecotoxicological studies regarding IMI and contribute to existing toxicity literature.
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Affiliation(s)
- Seyma Kizilkaya
- Marmara University Institute of Pure and Applied Sciences, Istanbul 34722, Turkiye.
| | - Gurler Akpinar
- Kocaeli University Faculty of Medicine, Department of Medical Biology, Kocaeli 41001, Turkiye
| | - Nuzhet Cenk Sesal
- Marmara University Faculty of Science, Department of Biology, Istanbul 34722, Turkiye
| | - Murat Kasap
- Kocaeli University Faculty of Medicine, Department of Medical Biology, Kocaeli 41001, Turkiye
| | - Baris Gokalsin
- Marmara University Faculty of Science, Department of Biology, Istanbul 34722, Turkiye
| | - Figen Esin Kayhan
- Marmara University Faculty of Science, Department of Biology, Istanbul 34722, Turkiye
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Toprak M, Yuksel N, Akpinar G, Kasap M, Pirhan D, Tugan BY. Comparative Proteomic Analysis of the Aqueous Humor from Patients with Pseudoexfoliation Syndrome. J Curr Glaucoma Pract 2023; 17:118-125. [PMID: 37920371 PMCID: PMC10618601 DOI: 10.5005/jp-journals-10078-1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 09/04/2023] [Indexed: 11/04/2023] Open
Abstract
Purpose The goal of this study was to pinpoint potential molecular pathways that may have contributed to the onset of pseudoexfoliation syndrome (PEX), a systemic illness associated with aging that has no known cause and is brought on by the deposition of fibrillary white flaky debris in ocular tissues. Materials and methods Protein pools representing each group were created using two-dimensional gel electrophoresis (2DE) in conjunction with a matrix-assisted laser desorption ionization-time of flight/time of flight (MALDI-TOF/TOF) mass spectrometer. Aqueous humor (AH) from patients with PEX and cataracts was also collected for a comprehensive study of the data; ingenuity pathway analysis (IPA) was used for the discovered proteins. Results In comparison to controls, 2DE showed that 10 sites in PEX patients had differently altered gene expression. Two of these proteins, transthyretin (TTR) and apolipoprotein A4 (ApoA4) were significantly overexpressed in PEX patients, but the remaining proteins were only mildly altered. The liver X receptor (LXR) and the retinoid X receptors (RXR) may play a crucial role in the pathophysiology of PEX according to IPA employing these 10 proteins. Conclusion The altered proteins, particularly ApoA4 and TTR, may be important in revealing the molecular process behind PEX, as anticipated by IPA. How to cite this article Toprak M, Yuksel N, Akpinar G, et al. Comparative Proteomic Analysis of the Aqueous Humor from Patients with Pseudoexfoliation Syndrome. J Curr Glaucoma Pract 2023;17(3):118-125.
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Affiliation(s)
- Muge Toprak
- Ophthalmology Clinic/Dunya Goz Tıp Merkezi, Pendik/Istanbul, Turkey
| | - Nursen Yuksel
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Murat Kasap
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Dilara Pirhan
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Busra Yilmaz Tugan
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
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11
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Hemşinlioğlu C, Aslan ES, Taştan C, Çakırsoy D, Turan RD, Seyis U, Elek M, Sır Karakuş G, Günaydın ÖS, Abanuz S, Kançağı DD, Yurtsever B, Yalçın K, Kasap M, Ovalı E. In Vitro FVIII-Encoding Transgenic Mesenchymal Stem Cells Maintain Successful Coagulation in FVIII-Deficient Plasma Mimicking Hemophilia A. Turk J Haematol 2023; 40:118-124. [PMID: 37022209 DOI: 10.4274/tjh.galenos.2023.2022-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
Objective Hemophilia A is an X-linked recessive bleeding disorder caused by a deficiency of plasma coagulation factor VIII (FVIII), and it accounts for about 80%-85% of all cases of hemophilia. Plasma-derived therapies or recombinant FVIII concentrates are used to prevent and treat the bleeding symptoms along with FVIII-mimicking antibodies. Recently, the European Medicines Agency granted conditional marketing approval for the first gene therapy for hemophilia A. The aim of this study was to determine the effectiveness of coagulation in correcting FVIII deficiency with FVIII-secreting transgenic mesenchymal stem cells (MSCs). Materials and Methods A lentiviral vector encoding a B domain-deleted FVIII cDNA sequence with CD45R0 truncated (CD45R0t) surface marker was designed to develop a transgenic FVIII-expressing primary cell line by transducing MSCs. The efficacy and functionality of the FVIII secreted from the MSCs was assessed with anti-FVIII ELISA, CD45R0t flow cytometry, FVIII western blot, and mixing test analysis in vitro. Results The findings of this study showed that the transgenic MSCs maintained persistent FVIII secretion. There was no significant difference in FVIII secretion over time, suggesting stable FVIII expression from the MSCs. The functionality of the FVIII protein secreted in the MSC supernatant was demonstrated by applying a mixing test in coagulation analysis. In the mixing test analysis, FVIII-deficient human plasma products were mixed with either a saline control or FVIII-secreted MSC supernatant. The mean FVIII level of the saline control group was 0.41±0.03 IU/dL, whereas the mean level was 25.41±33.38 IU/dL in the FVIII-secreting MSC supernatant mixed group (p<0.01). The mean activated partial thromboplastin time (aPTT) of the saline control group was 92.69±11.38 s, while in the FVIII-secreting MSC supernatant mixed group, the mean aPTT level decreased to 38.60±13.38 s (p<0.001). Conclusion The findings of this in vitro study suggest that the new method presented here is promising as a possible treatment for hemophilia A. Accordingly, a study of FVIII-secreting transgenic MSCs will next be initiated in a FVIII-knockout animal model.
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Affiliation(s)
- Cansu Hemşinlioğlu
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Biruni University, Department of Molecular Biology and Medical Genetics, İstanbul, Türkiye
| | - Elif Sibel Aslan
- Biruni University, Department of Molecular Biology and Medical Genetics, İstanbul, Türkiye
| | - Cihan Taştan
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Üsküdar University, Department of Molecular Biology and Genetics, İstanbul, Türkiye
- Üsküdar University, Transgenic Cell Technologies and Epigenetic Application and Research Center (TRGENMER), İstanbul, Türkiye
| | - Didem Çakırsoy
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Institute of Karolinska, Department of Medicine, Stockholm, Sweden
| | - Raife Dilek Turan
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Yeditepe University, Department of Biotechnology, İstanbul, Türkiye
- Yeditepe University, Cell and Gene Therapy Center of Excellence, İstanbul, Türkiye
| | - Utku Seyis
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
| | - Muhammer Elek
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Yeditepe University, Department of Biotechnology, İstanbul, Türkiye
| | | | | | - Selen Abanuz
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Acıbadem Mehmet Ali Aydınlar University, Department of Medical Biochemistry, İstanbul, Türkiye
| | | | - Bulut Yurtsever
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
| | - Koray Yalçın
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Medical Park Göztepe Hospital, Pediatric Bone Marrow Transplantation Unit, İstanbul, Türkiye
- Acıbadem Mehmet Ali Aydınlar University, Department of Medical Biotechnology, İstanbul, Türkiye
| | - Murat Kasap
- Kocaeli University Medical School, Department of Medical Biology, Kocaeli, Türkiye
| | - Ercüment Ovalı
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
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12
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Okcu A, Yazir Y, Şimşek T, Mert S, Duruksu G, Öztürk A, Kiliç KC, Akpinar G, Kasap M. Investigation of the effect of pancreatic decellularized matrix on encapsulated Islets of Langerhans with mesenchymal stem cells. Tissue Cell 2023; 82:102110. [PMID: 37235912 DOI: 10.1016/j.tice.2023.102110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
OBJECTIVE In this study, it was aimed to provide a therapeutic approach for T1DM by encapsulating the pancreatic islets with mesenchymal stem cells and decellularized pancreatic extracellular matrix to support the survival of islets while maintaining their cellular activity. METHOD Pancreatic extracellular matrix was decellularized using different concentrations of detergent series. After the preparation of the protein-based tissue extracellular matrix was shown to be free of cells or any genetic material by molecular, immunofluorescence and histochemical techniques. Following the homogenization of the decellularized pancreatic extracellular matrix and the analysis of its protein composition by LC-MS, the matrix proteins were incorporated with pancreatic islets and rat adipose tissue-derived MSCs (rAT-MSCs) in alginate microcapsules. Glucose-stimulated insulin secretion property of the islet cells in the microbeads was evaluated by insulin ELISA. The gene expression profile of the encapsulated cells was analyzed by Real-Time PCR. RESULTS Unlike the protein composition of whole pancreatic tissue, the decellularized pancreas matrix was free of histone proteins or proteins originated from mitochondria. The protein matrix derived from pancreatic tissue was shown to support the growth and maintenance of the islet cells. When compared to the non-encapsulated pancreatic islet, the encapsulated cells demonstrate to be more efficient in terms of insulin expression. CONCLUSION The extracellular pancreatic matrix obtained in this study was directly used as supplementary in the alginate-based microcapsule enhancing the cell survival. The tissue matrix protein and alginate had a synergistic effect on total insulin secretion, which might have the potential to overcome the insulin deficiency. Despite the improvement in the cell viability and the number, the efficiency of the insulin secretion in response to glucose stimulation from the alginate microcapsules did not meet the expectation when compared with the non-encapsulated pancreatic islets.
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Affiliation(s)
- Alparslan Okcu
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Yusufhan Yazir
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Department of Histology and Embryology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey.
| | - Turgay Şimşek
- Department of General Surgery, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Serap Mert
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Department of Chemistry and Chemical Processing Technology, Kocaeli University, Turkey; Department of Polymer Science and Technology, Kocaeli University, Kocaeli, Turkey
| | - Gökhan Duruksu
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Ahmet Öztürk
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Kamil Can Kiliç
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Gürler Akpinar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
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13
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Hemşinlioğlu C, Aslan ES, Taştan C, Çakırsoy D, Turan RD, Seyis U, Elek M, Karakuş GS, Günaydın ÖS, Abanuz S, Kançağı DD, Yurtsever B, Yalçın K, Kasap M, Ovalı E. In Vitro FVIII Encoding Transgenic Mesenchymal Stem Cells Maintain A Successful Coagulation in FVIII- Deficient Plasma Mimicking Hemophilia A. Turk J Haematol 2023. [PMID: 37022209 DOI: 10.4274/tjh.galenos.2023.2022.0318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Objective Hemophilia A is an X-linked recessive bleeding disorder caused by deficiency of plasma coagulation factor VIII (FVIII), and accounts for about 80-85% of patients with hemophilia. Plasma-derived therapies or recombinant factor VIII concentrates and also FVIII mimicking antibodies are used to prevent and treat the bleeding symptoms. Recently, EMA granted a conditional marketing approval for the first gene therapy of Hemophilia A. Aim of this study was to determine the effectiveness of coagulation in correcting FVIII deficiency with FVIII secreting transgenic mesenchymal stem cells (MSC). Materials and Methods A lentiviral vector encoding B-domain-deleted Factor VIII cDNA sequence with CD45 R0 truncated (CD45R0t) surface marker was designed to develop a transgenic FVIII expressing primary cell line by transducing MSC. Efficacy and functionality of secreted FVIII from MSCs was assessed with anti- FVIII ELISA, CD45R0t flow cytometry, FVIII Western Blot and Mixing Test analysis in vitro. Results Results of this study showed that the transgenic MSCs maintain a persistent FVIII secretion. There was no significant difference in FVIII secretion over time, suggesting stable FVIII expression from the MSCs. Functionality of FVIII protein secreted in MSC supernatant was demonstrated by using Mixing Test in coagulation analysis. In the Mixing Test analysis, FVIIIdeficient human plasma products were mixed either with saline control or FVIII-secreted MSC supernatant. Mean FVIII levels of saline control group were 0.41±0.03 IU/dL whereas mean FVIII levels were 25.41±33.38 IU/dL (p<0.01) in FVIII-secreting MSC supernatant mixed group. Mean activated partial thromboplastin time (aPTT) of saline control group was 92.69±11.38 seconds whereas in FVIII-secreting MSC supernatant mixed group, mean aPTT levels were decreased to 38.60±13.38 seconds (p<0.001). Conclusion Findings of this in vitro study shows a promising new method applicable to treat Hemophilia A. Accordingly, a FVIII secreting transgenic mesenchymal stem cell study will be initiated in FVIII knock-out animal model.
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Affiliation(s)
- Cansu Hemşinlioğlu
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Molecular Biology and Medical Genetics Department, Biruni University, İstanbul, Türkiye
| | - Elif Sibel Aslan
- Molecular Biology and Medical Genetics Department, Biruni University, İstanbul, Türkiye
| | - Cihan Taştan
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Molecular Biology and Genetics Department, Üsküdar University, İstanbul, Türkiye
- Transgenic Cell Technologies and Epigenetic Application and Research Center (TRGENMER), Uskudar University, İstanbul, Türkiye
| | - Didem Çakırsoy
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Medicine Department, Institute of Karolinska, Stockholm, Sweden
| | - Raife Dilek Turan
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Biotechnology Department, Yeditepe University, İstanbul, Türkiye
- Cell and Gene Therapy Center of Excellence, Yeditepe University, İstanbul, Türkiye
| | - Utku Seyis
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
| | - Muhammer Elek
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Biotechnology Department, Yeditepe University, İstanbul, Türkiye
| | | | | | - Selen Abanuz
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Medical Biochemistry Department, Acibadem Mehmet Ali Aydinlar University, İstanbul, Türkiye
| | | | - Bulut Yurtsever
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
| | - Koray Yalçın
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
- Medical Park Goztepe Hospital, Pediatric Bone Marrow Transplantation Unit, İstanbul, Türkiye
- Medical Biotechnology Department, Acıbadem Mehmet Ali Aydinlar University, İstanbul, Türkiye
| | - Murat Kasap
- Department of Medical Biology, Medical School of Kocaeli University, Kocaeli, Türkiye
| | - Ercüment Ovalı
- Acıbadem Labcell Cellular Therapy Laboratory, İstanbul, Türkiye
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14
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Sarihan M, Bal Albayrak MG, Kasap M, Akpinar G, Kocyigit E. An experimental workflow for enrichment of low abundant proteins from human serum for the discovery of serum biomarkers. J Biol Methods 2023; 10:e99010001. [PMID: 37007981 PMCID: PMC10062475 DOI: 10.14440/jbm.2023.394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Serum contains proteins that possess important information about diseases and their progression. Unfortunately, these proteins, which carry the information in the serum are in low abundance and are masked by other serum proteins that are in high abundance. Such masking prevents their identification and quantification. Therefore, removal of high abundance proteins is required to enrich, identify, and quantify the low abundance proteins. Immunodepletion methods are often used for this purpose, but there are limitations in their use because of off-target effects and high costs. Here we presented a robust, reproducible and cost-effective experimental workflow to remove immunoglobulins and albumin from serum with high efficiency. The workflow did not suffer from such limitations and enabled identification of 681 low abundance proteins that were otherwise undetectable in the serum. The identified low abundance proteins belonged to 21 different protein classes, namely the immunity-related proteins, modulators of protein-binding activity, and protein-modifying enzymes. They also played roles in various metabolic events, such as integrin signalling, inflammation-mediated signalling, and cadherin signalling. The presented workflow can be adapted to remove abundant proteins from other types of biological material and to provide considerable enrichment for low-abundance proteins.
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15
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Avci I, Teke K, Gocmez S, Kasap M, Akpinar G, Yaprak Bayrak B, Celebi G, Sarihan M, Utkan T, Ozkurkcugil C. Therapeutic effects of AF219 on interstitial cystitis/bladder pain syndrome induced by cyclophosphamide and water avoidance stress in rats. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00810-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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16
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Yanar S, Kasap M, Kanli A, Akpinar G, Sarihan M. Proteomics analysis of meclofenamic acid‐treated small cell lung carcinoma cells revealed changes in cellular energy metabolism for cancer cell survival. J Biochem Mol Toxicol 2022; 37:e23289. [PMID: 36536497 DOI: 10.1002/jbt.23289] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/03/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Small cell lung carcinoma (SCLC) is a highly aggressive cancer with low survival rate. Although initial response to chemotherapy in SCLC patients is well-rated, the treatments applied after the disease relapses are not successful. Drug resistance is accepted to be one of the main reasons for this failure. Therefore, there is an urgent need for new treatment strategies for SCLC. Meclofenamic acid, a nonsteroidal anti-inflammatory drug, has been shown to have anticancer effects on various types of cancers via different mechanisms. The aim of this study was to investigate the alterations that meclofenamic acid caused on a SCLC cell line, DMS114 using the tools of proteomics namely two-dimensional gel electrophoresis coupled to MALDI-TOF/TOF and nHPLC coupled to LC-MS/MS. Among the proteins identified by both methods, those showing significantly altered expression levels were evaluated using bioinformatics databases, PANTHER and STRING. The key altered metabolism upon meclofenamic acid treatment appeared to the cellular energy metabolism. Glycolysis was suppressed, whereas mitochondrial activity and oxidative phosphorylation were boosted. The cells underwent metabolic reprogramming to adapt into their new environment for survival. Metabolic reprogramming is known to cause drug resistance in several cancer types including SCLC. The identified differentially regulated proteins in here associated with energy metabolism hold value as the potential targets to overcome drug resistance in SCLC treatment.
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Affiliation(s)
- Sevinc Yanar
- Department of Medical Biology, Faculty of Medicine Kocaeli University Kocaeli Turkey
- Department of Histology and Embryology, Faculty of Medicine Sakarya University Sakarya Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine Kocaeli University Kocaeli Turkey
| | - Aylin Kanli
- Department of Medical Biology, Faculty of Medicine Kocaeli University Kocaeli Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Faculty of Medicine Kocaeli University Kocaeli Turkey
| | - Mehmet Sarihan
- Department of Medical Biology, Faculty of Medicine Kocaeli University Kocaeli Turkey
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17
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Albayrak MGB, Simsek T, Kasap M, Akpinar G, Canturk NZ, Guler SA. Tissue proteome analysis revealed an association between cancer, immune system response, and the idiopathic granulomatous mastitis. Med Oncol 2022; 39:238. [PMID: 36175807 DOI: 10.1007/s12032-022-01845-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Idiopathic Granulomatous Mastitis (IGM) is a disease that clinically mimics breast cancers with symptoms of pain, edema, erythema, nipple discharge, nipple retraction, and fistula. Although IGM is considered to be formed by autoimmune responses or infections, the molecular mechanism behind formation and progress is unknown. Therefore, in this study, we aimed to investigate molecular mechanisms underlying IGM formation, progress, and recurrence by monitoring the changes at the proteome level. Protein extracts prepared from IGM (n = 15) and within-control tissues (n = 15) were subjected to nHPLC followed by LC-MS/MS proteomic analysis. Label-free quantitation analysis revealed that sixty differentially regulated between the two groups. Those proteins were classified based on their role in metabolic pathways using bioinformatics tools. Based on DAVID analysis, 16 of the differently regulated proteins were associated with the immune system, while 17 proteins were involved in cancer metabolism. STRING analysis showed that five of the differentially regulated proteins were associated with combined immune deficiency which were PNP, TAP1, ITGAL, PRKDC, and PTPRC while the other proteins were involved in insulin response and neutrophil degranulation. This study is one of the very few studies that investigated the changes in protein expressions of IGM tissues compared to controls. For the first time, we have shown the relationship of IGM with the immune system at the protein level and also underlined the cancer-like behavior of the disease. Furthermore, the proteins that were pointed out as combined immune deficiency-related proteins may have value as diagnostic markers for idiopathic granulomatous mastitis although further studies are needed to shed more light on the pathogenesis of the disease.
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Affiliation(s)
| | - Turgay Simsek
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical School, Kocaeli University, 41001, Kocaeli, Turkey.
| | - Nuh Zafer Canturk
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Sertac Ata Guler
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
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18
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Saglam BS, Kanli A, Yanar S, Kasap M, Akpinar G. Investigation of the effect of meclofenamic acid on the proteome of LNCaP cells reveals changes in alternative polyadenylation and splicing machinery. Med Oncol 2022; 39:190. [PMID: 36071279 DOI: 10.1007/s12032-022-01795-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/09/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the most common type of cancer among men, and there is still no definitively effective drug treatment. Thus, the search for novel drug agents that may be used for the effective treatment continues. Meclofenamic acid (MA), a non-steroidal anti-inflammatory drug, with anti-tumor effects in various types of cancers was used to investigate its effects on LNCaP cells, a prostate cancer cell line, at the proteome level. The cells were treated with 80 µM MA for 24 h and a comparative proteomic analysis was performed with their untreated control cells. Proteins were extracted from the cells and then were subjected to two-dimensional gel electrophoresis. Protein spots displaying changes in their regulation ratios for more than two-fold were excised from the gels and identified with MALDI-TOF/TOF mass spectrometry. Bioinformatics analysis of the differentially regulated proteins that we identified showed that they were all associated with and took part in related pathways. Glycolytic pathway, cytoskeletal formation, transport activity, protein metabolism, and most notably an mRNA processing pathway were affected by the MA treatment. In addition to presenting a detailed information for what is happening inside the cells upon MA treatment, the proteins affected by MA treatment hold the potential to be novel targets for prostate cancer treatment provided that further in vivo experiments are carried out.
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Affiliation(s)
- Busra Sahinoz Saglam
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey.
| | - Sevinc Yanar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
- Department of Histology and Embryology, Faculty of Medicine, Sakarya University, Serdivan, Sakarya, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
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Maraş Genç H, Akpınar G, Kasap M, Uyur Yalçın E, Üstek D, Aslanger AD, Kara B. Proteomic Analysis of m.8296A>G Variation in the Mitochondrial tRNA Lys Gene. Mol Syndromol 2022; 13:305-317. [PMID: 36158049 PMCID: PMC9421666 DOI: 10.1159/000519526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/07/2021] [Indexed: 01/03/2023] Open
Abstract
Variation in the mitochondrial tRNA Lys gene at position 8296 was previously found to be associated with maternally inherited diabetes mellitus and deafness, hypertrophic cardiomyopathy, myoclonic epilepsy with ragged-red fibers and mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. The pathogenicity of the m.8296A>G variation is unclear. In this study, we aimed to analyze the mitochondrial proteome in a patient with m.8296A>G variation to elucidate the effects of this mutation at the protein level. Whole-exome sequencing and mitochondrial genome analysis were performed in a patient with sensorineural hearing impairment, cognitive impairment, leukodystrophy, migraine-like headaches, and gastrointestinal dysmotility. Mitochondrial genome analysis identified a homoplasmic m.8296A>G variation in the mitochondrial tRNA Lys gene in the proband and unaffected mother. Global mitochondrial proteome analysis was carried out in the muscle mitochondria of the index patient and a control subject. Comparative muscle mitochondrial proteome analysis revealed a total of 13 nuclear-encoded mitochondrial proteins differently expressed with respect to the control. Ten of the 13 proteins were downregulated. Most of the proteins were involved in ATP synthesis and Krebs cycle and have strong interactions with each other. We considered the m.8296A>G variation to be pathogenic with variable penetrance for our patient's phenotype, and this variation led to different expressions of nuclear-encoded proteins involved in energy metabolism.
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Affiliation(s)
- Hülya Maraş Genç
- Department of Pediatrics, Division of Child Neurology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey,*Hülya Maraş Genç,
| | - Gürler Akpınar
- Department of Medical Biology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Emek Uyur Yalçın
- Department of Pediatrics, Division of Child Neurology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Duran Üstek
- Department of Molecular Genetics, Istanbul University Institute of Experimental Medicine, Istanbul, Turkey
| | - Ayça Dilruba Aslanger
- Department of Medical Genetics, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Bülent Kara
- Department of Pediatrics, Division of Child Neurology, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
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20
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Küçükali Cİ, Şengül B, Gezen-Ak D, Dursun E, Erdağ E, Akpınar G, Kasap M, Karaaslan Z, Şirin NG, Tektürk P, Baykan B, Tüzün E. Kv5.1 antibody in epilepsy patients with unknown etiology. Epilepsy Res 2022; 182:106911. [PMID: 35305445 DOI: 10.1016/j.eplepsyres.2022.106911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/26/2022] [Accepted: 03/13/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Neuronal autoantibodies and favorable response to immunosuppressive treatment have been described in patients with chronic epilepsy of unknown cause, suggesting autoimmune etiology. Our aim was to identify novel epilepsy-specific autoantibodies reactive with neuronal surface antigens. METHODS Sera of 172 epilepsy patients with unknown cause and 30 healthy controls were screened with indirect immunofluorescence to identify IgG reacting with primary rat neuronal cultures. Putative target autoantigens were investigated with immunoprecipitation (IP) and liquid chromatography-mass/mass spectrometry (LC-MS/MS) studies using SH-SY5Y cells. Validation of LC-MS/MS results was carried out by IP and immunocytochemistry assays. RESULTS Antibodies to neuronal cell surface antigens were detected in 18 epilepsy patients. LC-MS/MS analysis identified voltage-gated potassium channel modifier subfamily F member 1 (KCNF1, Kv5.1) as the single common cell surface antigen in 4 patients with Lennox-Gastaut syndrome (n = 2), focal epilepsy of unknown cause (n = 1) and mesial temporal lobe epilepsy with hippocampal sclerosis (n = 1). These patients had the common features of early seizure onset and treatment-resistance. IP assays and co-localization (serum IgG and commercial Kv5.1-antibody) studies done with non-fixed Kv5.1-transfected HEK293 cells and primary neuronal cultures confirmed the presence of Kv5.1-antibody in 4 epilepsy patients identified by LC-MS/MS. Similar findings were not obtained by sera of other patients with epilepsy, patients with autoimmune encephalitis and healthy controls. CONCLUSION The herein described novel neuronal surface antibody to Kv5.1 appears to be associated with treatment-resistant epilepsy of unknown cause. Exact clinical and pathogenic significance of this antibody remains to be elucidated.
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Affiliation(s)
- Cem İsmail Küçükali
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Büşra Şengül
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpaşa Faculty of Medicine, Istanbul University, Cerrahpaşa, Istanbul, Turkey
| | - Duygu Gezen-Ak
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpaşa Faculty of Medicine, Istanbul University, Cerrahpaşa, Istanbul, Turkey
| | - Erdinç Dursun
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpaşa Faculty of Medicine, Istanbul University, Cerrahpaşa, Istanbul, Turkey; Department of Neuroscience, Institute of Neurological Sciences, Istanbul University, Cerrahpaşa, Istanbul, Turkey
| | - Ece Erdağ
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Gürler Akpınar
- Medical Biology, Department of Basic Medical Sciences, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Medical Biology, Department of Basic Medical Sciences, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Zerrin Karaaslan
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Nermin Görkem Şirin
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Pınar Tektürk
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Betül Baykan
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey; Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Erdem Tüzün
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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21
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Simsek HU, Albayrak MGB, Kasap M, Simsek T, Akpinar G, Guler SA, Canturk NZ. Elucidation of the changes occurring at the proteome level in ovaries of high-fat diet-induced obese rats. Cell Biochem Funct 2022; 40:278-297. [PMID: 35285971 DOI: 10.1002/cbf.3693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/20/2022]
Abstract
High-fat diet-induced obesity adversely affects the female reproductive system. The metabolic changes that the high-fat diet causes on the ovaries have not been elucidated. Herein, to understand the molecular and cellular mechanisms underlying the effects of long-term high-fat diet-fed, the changes in the global proteomic profile of the rat ovaries were investigated. The female rats were randomly divided into two groups based on their diets: the ones that were fed with the high-fat diet and the other ones that were fed with the control diet for 18 weeks. To identify differentially expressed proteins, the changes in ovary proteomes were investigated by two-dimensional electrophoresis coupled to matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight and label-free quantification with nano-high performance liquid chromatography to tandem mass spectrometry (nHPLC-MS/MS). A total of 80 proteins were differentially regulated. The upregulated proteins were involved in responses to chemical and organic substances, cytokines, external stimuli, and lipids. These proteins were particularly associated with vesicles, microbodies, and cell surface proteins. The downregulated proteins were involved in biological processes associated with cellular respiration. Those proteins created a network consisting of proteins involved in aerobic respiration and energy generation. Our results demonstrated that the mechanisms related to energy production in the ovary tissue were particularly affected by the high-fat diet.
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Affiliation(s)
- Hayal U Simsek
- Department of Obstetrics and Gynecology, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Merve G B Albayrak
- Department of Medical Biology, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Turgay Simsek
- Department of General Surgery, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Sertac A Guler
- Department of General Surgery, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
| | - Nuh Z Canturk
- Department of General Surgery, Kocaeli University Faculty of Medicine, Izmit, Kocaeli, Turkey
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22
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Yoneten KK, Kasap M, Arga KY, Akpinar G, Utkan NZ. Decreased serum levels of glycerol-3- phosphate dehydrogenase 1 and monoacylglycerol lipase act as diagnostic biomarkers for breast cancer. Cancer Biomark 2021; 34:67-76. [PMID: 34657876 DOI: 10.3233/cbm-203093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Breast cancer (BC) is one of the most life-threatening cancer types among women. Despite major developments in medical sciences and technologies, the incidence and mortality rates of BC cases are still increasing. One of the reasons for this increase is the absence of an easy to perform early-diagnostic tool. Although there are defined BC biomarkers routinely used for diagnostic and prognostic purposes, none of these biomarkers is useful for early diagnosis. Therefore, early diagnosis of BC remains an important challenge and there is a great need for the early-diagnostic biomarker(s). OBJECTIVE In this study, we aimed to evaluate the diagnostic and prognostic values of glycerol-3-phosphate dehydrogenase (GPD1) and monoacylglycerol lipase (MAGL) proteins as non-invasive serum biomarkers. METHODS GPD1 and MAGL serum levels were determined by ELISA for BC patients (n= 100) from five different subtypes, and healthy controls (n= 20), and a comparative analysis was performed to determine statistically significant expression differences among the groups. RESULTS The results provided evidence that GPD1 acted as a diagnostic biomarker in distinguishing triple-negative breast cancer (TNBC) patients from other subtypes, and MAGL acted as a diagnostic biomarker in distinguishing healthy individuals from BC patients. CONCLUSION GPD1 and MAGL might be proposed as non-invasive diagnostic biomarkers for BC with high sensitivity and specificity.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Nihat Zafer Utkan
- Department of General Surgery, Medical School, Kocaeli University, Kocaeli, Turkey
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23
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Kara B, Uyguner O, Maraş Genç H, İşlek EE, Kasap M, Toksoy G, Akpınar G, Uyur Yalçın E, Anık Y, Üstek D. BEND4 as a Candidate Gene for an Infection-Induced Acute Encephalopathy Characterized by a Cyst and Calcification of the Pons and Cerebellar Atrophy. Mol Syndromol 2021; 13:12-22. [DOI: 10.1159/000517541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Three siblings born to Turkish parents from the same village had normal brain development until acute neurological deterioration between 12 months and 8 years of age. Consequent loss of all acquired motor, social, and language functions following infections was associated with a pontine cyst, calcification, and cerebellar atrophy. Exome sequencing revealed a homozygous c.1297G>A (p.Gly433Ser) alteration in <i>BEND4</i>, which was predicted to be deleterious in in silico analysis tools and segregated in multiple affected individuals in the family. <i>BEND4</i> has not been associated with any existing disease. Immunofluorescence microscopy analysis of wild-type and mutant BEND4 expressing Vero cells showed nuclear and cytoplasmic localization. Wild-type BEND4 displayed a network-like distribution, whereas mutant BEND4 showed a juxtanuclear distribution pattern. Differential proteome analysis of Vero cells expressing BEND4 revealed that mutant BEND4 expression caused selective increase in reticulocalbin-1 and endoplasmic reticulum resident protein-29. Both proteins are associated with the endoplasmic reticulum and are primarily involved in protein processing and folding pathways. Any defect or stress in protein folding creates stress on cells and may cause chronic damage. This is the first study showing that pathogenic <i>BEND4</i> variants may lead to an infection-induced acute necrotizing encephalopathy as demonstrated in characteristic neuroimaging findings.
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24
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Cerit C, Sarıhan M, Nart Ö, Kasap M, Yaşar H, Akpınar G. Are Mannan-binding Lectine Serin Protease-2 and Alpha-1-microglobulin and Bukinin Precursor the Potential Biomarkers of Manic Episode? A Study via Urinary Proetomic Analysis. Clin Psychopharmacol Neurosci 2021; 19:269-281. [PMID: 33888656 PMCID: PMC8077062 DOI: 10.9758/cpn.2021.19.2.269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/15/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Objective Investigating the molecular basis of bipolar disorder (BD) is crucial in terms of developing effective treatment strategies as well as objective laboratory-based diagnostic tools for the disease. Methods We examined the urine samples of BD patients both in manic episode and after remission and compared their urinary protein profiles with the controls. Twelve patients and twelve controls (C group) included to the study. Urinary samples of patients were first collected during manic episode (M group) and then after remission (R group). Two-dimensional gel electrophoresis (2-DE) coupled to MALDI-TOF/TOF massspectrometry approach and Western blot analysis were used. Results Alphα-1-microglobulin and bukinin precursor (AMBP), Mannan-binding lectine serin protease-2 (MASP-2), and Ig gamma-1-chain displayed significant increases in their abundance in the urine protein pool of M group in comparison to the C and R groups. Alpha-1B glycoprotein and prostaglandin-H2 D-isomerase (PGD2) levels were significantly higher in the urine protein pool of the M and R groups in comparison to the C group. Annexin A1 was downregulated significantly in the urine protein pool of the M group in comparison to the C group. Conclusion Intensities of MASP-2 and AMBP proteins discriminated manic episode from remission period and healthy controls indicating that these proteins may be candidate biomarkers for manic episode. The decrease in Annexin A1 and increase in Ig gamma-1 chain levels appeared to be associated with “Manic Episode” while the increase in PGD2 and alpha-1B glycoprotein levels appeared to be associated with “Bipolar Disorder”.
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Affiliation(s)
- Cem Cerit
- Department of Psychiatry, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Mehmet Sarıhan
- Department of Medical Biology, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Ömer Nart
- Clinic of Psychiatry, Bursa State Hospital, Bursa, Turkey
| | - Murat Kasap
- Department of Medical Biology, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Hilmi Yaşar
- Department of Psychiatry, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Gürler Akpınar
- Department of Medical Biology, School of Medicine, Kocaeli University, Kocaeli, Turkey
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25
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Teke K, Kasap M, Simsek E, Uzunyol A, Uslubas AK, Akpinar G, Culha MM. SERPIN A5 may have a potential as a biomarker in reflecting the improvement of semen quality in infertile men who underwent varicocele repair. Andrologia 2021; 53:e14081. [PMID: 34009669 DOI: 10.1111/and.14081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/20/2021] [Accepted: 04/02/2021] [Indexed: 12/22/2022] Open
Abstract
We aimed to identify proteins that were differentially regulated in spermatozoal samples collected from fertile healthy men (FHM) and infertile patients with varicocele (IFPV) before and after varicocelectomy. Seminal samples were collected from 20 IFPV before and after varicocelectomy and from 14 FHM as controls. Samples underwent seminal examination and proteomic analysis. Extracted spermatozoal proteins were analysed using two-dimensional gel electrophoresis, and differentially regulated spermatozoal proteins (DRSPs) were identified. In particular, attention was placed on those DRSPs in which the concentration changed after varicocelectomy and corrected to approximate levels observed in FHM. Varicocelectomy significantly improved the sperm count and concentration in IFPV (p < 0.05). Proteomic analysis showed that 11 DRSPs were identified when comparisons were made among the three groups. Among these 11 proteins, change in the SERPIN A5 concentrations was notable because it was 100-fold downregulated in pre-operative IFPV samples and nearly resembled to control concentrations following varicocelectomy. Western blot analysis using an anti-SERPIN antibody validated the changes observed in SERPIN A5 levels before and after varicocelectomy operation. Increase in SERPIN A5 after varicocelectomy may be due to improvement in semen quality, suggesting that SERPIN A5 is a potential seminal biomarker for assessment of semen quality in varicocele-related infertility.
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Affiliation(s)
- Kerem Teke
- Department of Urology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Emrah Simsek
- Department of Urology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Ayimgul Uzunyol
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Ali Kemal Uslubas
- Department of Urology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Mustafa Melih Culha
- Department of Urology, Kocaeli University School of Medicine, Kocaeli, Turkey
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26
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Canbek U, Dibek E, Akgun U, Col B, Canbek TD, Aydogan NH, Usmanov N, Kasap M, Akpinar G. Analysis of the fluid biochemistry in patients with prolonged wound drainage after hip hemiarthroplasty. Injury 2021; 52:918-925. [PMID: 33059924 DOI: 10.1016/j.injury.2020.10.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION The origin and content of prolonged wound drainage (PWD) after arthroplasty remain uncertain. In this study, we performed the biochemical, biological and advanced proteomic analysis of the drainage fluid collected from PWD patients following hip hemiarthroplasty (HA). METHODS Data of 28 patients who developed PWD after HA were prospectively analyzed. After examining the biochemical content of the drainage fluid collected on postoperative day 6, to find out if the drainage fluid was transudate or exudate, it was compared with the patient's serum values according to the Light criteria. Subsequently, biological and proteomic analyzes of both drainage fluid and serum were performed. The similarities and differences in terms of protein concentrations, protein identities were examined. In the drainage fluid, we analyzed lymph-specific proteins. RESULTS 16 patients with PWD were male (61.1%), 12 were female (38.9%), and the mean age of all patients was 79.64 ± 8.44 (65-95). Biochemical test results of the drainage fluid / serum were as follows: Total protein: 2.1 / 5.2 g/dl, albumin: 1.3 / 3.1 g/dl, lactate dehydrogenase (LDH): 121/324 U/l, cholesterol: 28/160 mg/dl, triglyceride: 37/122 mg/dl, sodium (Na): 140/ 140mg/dl, potassium (K): 4.1/ 4.1 mg/dl. pH of the drainage fluid was 7.6. According to these biochemical values, drainage fluid was classified as transudate. As a result of protein identification, fibrinogen beta chain, keratin type 1, creatine kinase M-type protein were detected in drainage fluid. Subsequent western analysis revealed that, gliseraldehyde-3-phosphate dehydrogenase (GAPDH) and beta actin antibody were detected in the drainage fluid but not in serum. CONCLUSION Despite the similarity in serum and transudative PWD fluid in terms of biochemical content, we found that when we carried out further proteomic analysis, PWD contains lymph-specific proteins. Unlike PWD, these proteins were not determined in serum. PWD fluid can be also called as lymphorrhea. PWD fluid with abundant proteins may also provide an appropriate environment for the growth of microorganisms.
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Affiliation(s)
- Umut Canbek
- Mugla Sitki Kocman University, Faculty of Medicine, Department of Orthopaedics and Traumatology Mugla, Turkey.
| | - Esra Dibek
- Mugla Sıtkı Koçman University, Faculty of Science, Department of Biology, Mugla, Turkey
| | - Ulas Akgun
- Mugla Sitki Kocman University, Faculty of Medicine, Department of Orthopaedics and Traumatology Mugla, Turkey
| | - Bekir Col
- Mugla Sıtkı Koçman University, Faculty of Science, Department of Biology, Mugla, Turkey
| | - Tugba Dubektas Canbek
- Mugla Sitki Kocman University Training and Research Hospital, Department of Internal Medicine, Mugla, Turkey
| | - Nevres Hurriyet Aydogan
- Mugla Sitki Kocman University, Faculty of Medicine, Department of Orthopaedics and Traumatology Mugla, Turkey
| | - Nosirzhon Usmanov
- Mugla Sitki Kocman University, Faculty of Medicine, Department of Orthopaedics and Traumatology Mugla, Turkey
| | - Murat Kasap
- Kocaeli University, Medical School Department of Medical Biology, Kocaeli, Turkey
| | - Gurler Akpinar
- Kocaeli University, Medical School Department of Medical Biology, Kocaeli, Turkey
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Temiz Karadag D, Cetinarslan B, Kasap M, Canturk NZ, Akpinar G, Canturk Z, Tarkun I, Simsek T, Selek A. Proteomic analysis of thyroid tissue reveals enhanced catabolic activity in Graves' disease compared to toxic multinodular goitre. Cell Biochem Funct 2021; 39:658-666. [PMID: 33728674 DOI: 10.1002/cbf.3632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/08/2022]
Abstract
Graves' disease (GD) and toxic multinodular goitre (TMNG) are the most common thyroid diseases which mainly lead to thyrotoxicosis, however, the underlying mechanism of distinct clinical presentations remains unclear. Protein extracts from the thyroid tissue specimens of the patients with GD and TMNG were subjected to Difference Gel Electrophoresis (DIGE). Differentially regulated protein spots were determined by image analysis, and the spots displaying statistically significant differences were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometer (MALDI-TOF) followed by MASCOT search. Western blot analysis was used to verify changes occurring at the protein levels. The identified proteins were classified based on their functions in metabolic pathways using bioinformatics algorithms. Fifteen proteins showed significant alterations in abundance between the two disease groups. Bioinformatic analysis revealed the differentially regulated proteins were particularly related to catabolism, oxidative stress and especially energy utilization pathways, including glycolysis, proteolysis, ketone body catabolism and other energy metabolism-related pathways. SIGNIFICANCE OF THE STUDY: Previously, GD has been the subject of many studies that performed the proteomics approaches in the orbital tissue samples or tear. This is one of the very few studies that investigate the changes in the proteome of thyroid tissue in GD. We demonstrated mainly the upregulation of catabolic activity-related proteins in patients with GD compared to TMNG. Although it remains to be elucidated, some of these proteins can be used as markers for GD or have a role in the pathogenesis of the disease. Our study contributes the increasing data over time by providing new biomarker candidates for GD.
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Affiliation(s)
- Duygu Temiz Karadag
- Department of Internal Medicine, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Berrin Cetinarslan
- Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology/DEKART Proteomics Laboratory, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Nuh Zafer Canturk
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology/DEKART Proteomics Laboratory, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Zeynep Canturk
- Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Ilhan Tarkun
- Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Turgay Simsek
- Department of General Surgery, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
| | - Alev Selek
- Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine, Kocaeli, Turkey
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28
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Uslubas I, Kanli A, Kasap M, Akpinar G, Karabas L. Effect of aflibercept on proliferative vitreoretinopathy: Proteomic analysis in an experimental animal model. Exp Eye Res 2021; 203:108425. [PMID: 33417914 DOI: 10.1016/j.exer.2020.108425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022]
Abstract
PURPOSE The aim of this study was to monitor inflammatory, proliferative and progressive effects of proliferative vitreoretinopathy (PVR) and aflibercept treatment in dispase induced PVR rat model by proteomic analysis. MATERIAL AND METHODS A total of 35 male Long Evans pigmented rats were divided into three groups, namely, PVR (dispase+saline), PVR+aflibercept (dispase+aflibercept) and control. The PVR group received 2 μl of 0.03 IU/μl dispase and 2 μl saline, the PVR+aflibercept group received 2 μl of 0.03 IU/μl and 2 μl of 40 mg/ml aflibercept at the first day of the experiment. At the end of the 6th week all retina and vitreous specimens were collected by evisceration and transferred to the proteomics laboratory for analysis. Proteomic analysis by 2D gel electrophoresis coupled with MALDI-TOF/TOF was performed. RESULTS In the PVR and PVR+aflibercept group 16 different proteins that were identified to be differentially regulated in comparison to the control group. In the PVR+aflibercept group, ENO1, ENO2, LDH-B, PEBP-1 and GS levels were higher than the PVR group. In addition, the association of proteins such as UCHL, PEBP1, PDHB and ENO1 with PVR has been demonstrated for the first time. CONCLUSION STRING analysis elucidated the functional protein-protein interaction among the differentially regulated proteins and highlighted that those proteins mainly played roles in carbon and nucleotide metabolisms. Functional analysis of the differentially regulated proteins indicated the presence of inflammation, gliosis and retinal damage in the PVR group. Aflibercept treatment had pronounced effect on prevention of inflammation and retinal damage while causing a slight increase in gliosis. However, aflibercept treatment was not effective enough to normalize the levels of differentially regulated proteins of the PVR group. Therefore, we predict that the treatment dose of aflibercept used in this study was below of its ideal concentration and should be increased in the future studies. The differential regulation of these structural proteins in this study should shed some light to the mechanism of glial wound formation in the retina and guide future treatment modalities.
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MESH Headings
- Angiogenesis Inhibitors/therapeutic use
- Animals
- Disease Models, Animal
- Electrophoresis, Gel, Two-Dimensional
- Electrophoresis, Polyacrylamide Gel
- Endopeptidases/toxicity
- Eye Proteins/metabolism
- Male
- Proteome/metabolism
- Proteomics
- Rats
- Rats, Long-Evans
- Receptors, Vascular Endothelial Growth Factor/therapeutic use
- Recombinant Fusion Proteins/therapeutic use
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Vascular Endothelial Growth Factor A/antagonists & inhibitors
- Vitreoretinopathy, Proliferative/chemically induced
- Vitreoretinopathy, Proliferative/drug therapy
- Vitreoretinopathy, Proliferative/metabolism
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Affiliation(s)
- Isil Uslubas
- Kocaeli University School of Medicine, Department of Ophthalmology, Turkey.
| | - Aylin Kanli
- Kocaeli University School of Medicine, Department of Medical Biology, Turkey
| | - Murat Kasap
- Kocaeli University School of Medicine, Department of Medical Biology, Turkey
| | - Gurler Akpinar
- Kocaeli University School of Medicine, Department of Medical Biology, Turkey
| | - Levent Karabas
- Kocaeli University School of Medicine, Department of Ophthalmology, Turkey
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29
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Yıldız M, Terzi H, Yıldız SH, Varol N, Özdemİr Erdoğan M, Kasap M, Akçalı N, Solak M. Proteomic analysis of the anticancer effect of various extracts of endemicThermopsisturcica in human cervical cancer cells. Turk J Med Sci 2020; 50:1993-2004. [PMID: 32682359 PMCID: PMC7775707 DOI: 10.3906/sag-2005-321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background/aim Thermopsisturcica is a perennial species endemic to Turkey and different extracts of T. turcica have an antiproliferative effect on cancer cells, but there has not been any report on HeLa (human cervical cancer) cells. Materials and methods To get a better understanding of the molecular mechanism of anticancer activity of methanolic extracts of leaves (LE) and flowers (FE) of T. turcica, we employed 2-DE-based proteomics to explore the proteins involved in anticancer activity in HeLa cells. Results T. turcica extracts showed a potent cytotoxic effect on HeLa cells with the IC50 values of 1.75 mg/mL for LE and 3.25 mg/mL for FE. The induction of apoptosis by LE and FE was also consistent with increased expression of caspase mRNAs and DNA fragmentation. In terms of the proteomic approach, 27 differentially expressed proteins were detected and identified through MALDI-TOF/TOF mass spectrometry. These altered proteins were involved in cytoskeleton organization and movement, protein folding, proteolysis and translation, cell cycle and proliferation, signal transduction, cell redox homeostasis, and metabolism. Conclusion Up-regulation of protein disulfide isomerases and down-regulation of Rho GDP-dissociation inhibitor, heterogeneous nuclear ribonucleoproteins, and heat shock proteins may contribute to the induction of apoptosis and arresting of the cell cycle in HeLa cells.
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Affiliation(s)
- Mustafa Yıldız
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - Hakan Terzi
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - Saliha Handan Yıldız
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar University of Health Sciences, Afyonkarahisar, Turkey
| | - Nuray Varol
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar University of Health Sciences, Afyonkarahisar, Turkey
| | - Müjgan Özdemİr Erdoğan
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar University of Health Sciences, Afyonkarahisar, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Nermin Akçalı
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar University of Health Sciences, Afyonkarahisar, Turkey
| | - Mustafa Solak
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar University of Health Sciences, Afyonkarahisar, Turkey
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Guney Eskiler G, Yanar S, Akpinar G, Kasap M. Proteomic analysis of talazoparib resistance in triple-negative breast cancer cells. J Biochem Mol Toxicol 2020; 35:e22678. [PMID: 33325624 DOI: 10.1002/jbt.22678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 11/26/2020] [Indexed: 12/21/2022]
Abstract
Talazoparib (TAL) has been effectively used for the treatment of gBRCA1/2-mutated HER2-negative metastatic breast cancer. However, acquired resistance to TAL remains a major challenge that impedes the clinical success of TAL treatment. Therefore, elucidation of proteins and pathways that contribute to or are affected by the TAL resistance is urgently needed to improve the treatment response and provide novel treatment strategies for advanced metastatic breast cancers. Herein, we aimed to investigate the altered protein signatures in TAL-resistant triple-negative breast cancer (TNBC) cells by comparing with the TNBC parental cell line via proteomic analysis. After validation of TAL-resistance by WST-1 and Annexin V analysis, two-dimensional gel electrophoresis (2DE)-based proteomic analysis coupled to matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry was performed to identify differentially regulated proteins. The findings revealed the identities of 10 differentially regulated proteins in TAL-resistant TNBC cells whose bioinformatic analysis predicted changes in EGF/FGF signaling pathways as well as in the AMPK signaling pathway. In addition, phosphorylation/dephosphorylation dynamics were predicted to be altered in TAL-resistant cells. The proteins identified in this study might be the targets to overcome TAL resistance for the treatment of TNBC.
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Affiliation(s)
- Gamze Guney Eskiler
- Department of Medical Biology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Sevinc Yanar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
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Ayimugu A, Sarihan M, Kasap M, Akpinar G. Investigation of the Involvement of Parkin in Parkinson's Disease and Cancer by Monitoring the Changes in SH-SY5Y Cells at the Nuclear Proteome Level. Anticancer Res 2020; 40:3169-3190. [PMID: 32487612 DOI: 10.21873/anticanres.14299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM During the last two decades, Parkinson's disease (PD)-associated genes have been associated with cancer; however, a shared pathogenic mechanism has yet to be discovered. Parkin, an E3 ubiquitin ligase that is involved in early-onset Parkinson's disease, has also been reported to exert tumor suppressor activity. However, the details about the role of Parkin in cancer remain unknown. The present study aimed at identifying differentially regulated nuclear proteins and nuclear phosphoproteins whose levels were affected by Parkin expression. MATERIALS AND METHODS SHS-SY5Y cells expressing either wild-type Parkin or its mutant under tetracycline control were used in this study; cells not expressing Parkin served as control. Nuclear proteins were enriched from Parkin-expressing and control cells to perform a comparative proteomics study using two-dimensional gel electrophoresis (2D) coupled to matrix assisted laser desorption/ionisation-time of flight (MALDI-TOF/TOF) mass spectrometry analysis. Changes in phosphoproteome and nuclear phosphoproteome were also studied by staining the 2D gels with ProQ diamond phosphoprotein stain. The identified proteins were subjected to bioinformatics analysis to elucidate the reactomes and relevant pathways. RESULTS Six nuclear proteins, namely NCL, DDIT3, PARP1, HMGB1, TCTP and TPI were shown to be differentially regulated in cells expressing Parkin protein. Regulations in phosphorylation levels of ENPL, PRDX4, ECHM, ALDOA SET, DHSA, RCC1 and DULRD were also detected. Bioinformatics analysis of differentially regulated proteins highlighted the involvement of Parkin in DNA repair. CONCLUSION Several nuclear protein candidates whose expression or phosphorylation levels were altered in cells expressing Parkin. Bioinformatics analysis of these proteins indicated that the nuclear form of Parkin may play a significant role in DNA repair and contribute to prevention of tumorogenesis via maintaining DNA integrity.
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Affiliation(s)
- Abula Ayimugu
- Kocaeli University Technology Faculty, Department of Biomedical Engineering, Kocaeli, Turkey
| | - Mehmet Sarihan
- Kocaeli University Medical School, Department of Medical Biology, Kocaeli, Turkey
| | - Murat Kasap
- Kocaeli University Medical School, Department of Medical Biology, Kocaeli, Turkey
| | - Gurler Akpinar
- Kocaeli University Medical School, Department of Medical Biology, Kocaeli, Turkey
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Görmüş U, Kasap M, Akpınar G, Tuğtepe H, Kanlı A, Özel K. Comparative Proteome Analyses of Ureteropelvic Junction Obstruction and Surrounding Ureteral Tissue. Cells Tissues Organs 2020; 209:2-12. [PMID: 32259813 DOI: 10.1159/000506736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/23/2020] [Indexed: 12/30/2022] Open
Abstract
Ureteropelvic junction (UPJ) obstruction is a common problem in children, but its etiology remains unclear. In this study, the proteome profiles of the obstructed segment and its surrounding distal and proximal parts were comparatively evaluated. Twelve children younger than 2 years of age with unilateral intrinsic UPJ obstruction were included. The excised operational tissue was divided into three parts immediately after resection: the obstructed part (Obst), the distal normal ureteral part (Dist), and the proximal part of the obstructed segment (Prox). Proteins extracted from the tissue samples were subjected to two-dimensional gel electrophoresis analysis to identify differentially regulated proteins. Spot analysis revealed that four proteins, namely tropomyosin beta and alpha-1 chains, actin and desmin, were upregulated in Obst in comparison to Dist. A similar analysis between Obst and Prox showed that heat shock protein beta-1 and carbonic anhydrase-1 were upregulated in Obst, while tropomyosin alpha 3 chain and ATP synthase beta were upregulated in Prox. The last comparative analysis between Dist and Prox revealed upregulation of annexin-A5 and annexin-A1 in Dist and vimentin, mitochondrial ATP synthase subunit-beta, peroxiredoxin-2, and apolipoprotein-A1 in Prox. Bioinformatics analysis using the STRING server indicated that the differentially regulated proteins, altogether, point to the changes occurring in muscle filament sliding pathway. When regulations occurring in each group were mutually compared, a change in lipase inhibition activity was detected by STRING. This is the first study scrutinizing changes occurring in protein profiles in UPJ.
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Affiliation(s)
- Uzay Görmüş
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Bilim University, Istanbul, Turkey, .,Division of Biochemistry, Department of Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden,
| | - Murat Kasap
- Department of Medical Biology and Genetics/DEKART Proteomics Laboratory, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Gürler Akpınar
- Department of Medical Biology and Genetics/DEKART Proteomics Laboratory, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Halil Tuğtepe
- Division of Pediatric Urology, Department of Pediatric Surgery, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Aylin Kanlı
- Department of Medical Biology and Genetics/DEKART Proteomics Laboratory, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Kerem Özel
- Department of Pediatric Surgery, Faculty of Medicine, Istanbul Bilim University, Istanbul, Turkey
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Yoneten KK, Kasap M, Akpinar G, Gunes A, Gurel B, Utkan NZ. Comparative Proteome Analysis of Breast Cancer Tissues Highlights the Importance of Glycerol-3-phosphate Dehydrogenase 1 and Monoacylglycerol Lipase in Breast Cancer Metabolism. Cancer Genomics Proteomics 2020; 16:377-397. [PMID: 31467232 DOI: 10.21873/cgp.20143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/17/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND/AIM Breast cancer (BC) incidence and mortality rates have been increasing due to the lack of appropriate diagnostic tools for early detection. Proteomics-based studies may provide novel targets for early diagnosis and efficient treatment. The aim of this study was to investigate the global changes occurring in protein profiles in breast cancer tissues to discover potential diagnostic or prognostic biomarkers. MATERIALS AND METHODS BC tissues and their corresponding healthy counterparts were collected, subtyped, and subjected to comparative proteomics analyses using two-dimensional gel electrophoresis (2-DE) and two-dimensional electrophoresis fluorescence difference gel (DIGE) coupled to matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF/TOF) to explore BC metabolism at the proteome level. Western blot analysis was used to verify changes occurring at the protein levels. RESULTS Bioinformatics analyses performed with differentially regulated proteins highlighted the changes occurring in triacylglyceride (TAG) metabolism, and directed our attention to TAG metabolism-associated proteins, namely glycerol-3-phosphate dehydrogenase 1 (GPD1) and monoacylglycerol lipase (MAGL). These proteins were down-regulated in tumor groups in comparison to controls. CONCLUSION GPD1 and MAGL might be promising tissue-based protein biomarkers with a predictive potential for BC.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Abdullah Gunes
- Department of General Surgery, Derince Education and Application Hospital, Kocaeli, Turkey
| | - Bora Gurel
- Department of Pathology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Nihat Zafer Utkan
- Department of General Surgery, Kocaeli University Medical School, Kocaeli, Turkey
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Ceylan Y, Akpınar G, Doger E, Kasap M, Guzel N, Karaosmanoglu K, Kopuk SY, Yucesoy I. Proteomic analysis in endometrial cancer and endometrial hyperplasia tissues by 2D-DIGE technique. J Gynecol Obstet Hum Reprod 2019; 49:101652. [PMID: 31783195 DOI: 10.1016/j.jogoh.2019.101652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To compare the protein expression of complex atypical endometrial hyperplasia, endometrial carcinoma and healthy endometrial tissues, and by this way, to identify proteins that can be used for diagnosis, prognosis and therapeutic targets. METHODS Histopathological examination of the D&C material had reported "benign endometrial changes", "complex atypical endometrial hyperplasia" and "endometrioid adenocarcinoma" and 30 patients ,who underwent surgery with these diagnosis, were studied. Protein profiles of the study groups were detected using 2D-DIGE technique and compared to the control group. Protein spots which showing different expression, were defined by MALDI TOF/TOF-MS method. RESULTS In the present study, significant elevations were observed in the levels of K2C8, UAP56, ENOA, ACTB, GRP78, GSTP1, PSME1, CALR, PPIA, PDIA3 and IDHc proteins when comparisons were made among the cancer cases and the healthy and complex atypical hyperplasia cases. We determined that the induction of CALR activity may be a factor that progresses apoptosis, thus, may be a hope for postoperative new chemotherapy treatment methods. Moreover, when the expressions of the CAH1 and PPIB proteins are compared to complex atypical hyperplasia and endometrial adenocarcinoma stages, we determined that the CAH1 and PPIB levels increased in more advanced stages. Among these indicators, the proteins that had the closest relation to advanced stage cancer were determined as K2C8, UAP56 and GRP78. CONCLUSION We think that it would be useful to determine the diagnosis, prediction of prognosis and identifying therapeutic targets of the highlighted proteins of our study that are K2C8, UAP56, GRP78 and CALR in endometrial cancer.
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Affiliation(s)
- Yasin Ceylan
- Kızıltepe State Hospital, Department of Obstetrics and Gynecology, Mardin, Turkey.
| | - Gurler Akpınar
- Kocaeli University School of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Emek Doger
- Kocaeli University School of Medicine, Department of Obstetrics and Gynecology, Kocaeli, Turkey
| | - Murat Kasap
- Kocaeli University School of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Nil Guzel
- Kocaeli University School of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Kubra Karaosmanoglu
- Kocaeli University School of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Sule Yıldırım Kopuk
- Sağlık Bilimleri University Umraniye Health and Education Hospital, Department of Obstetrics and Gynecology, Istanbul, Turkey
| | - Izzet Yucesoy
- Kocaeli University School of Medicine, Department of Obstetrics and Gynecology, Kocaeli, Turkey
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Senduran F, Mutlu S, Kasap M. The effects of a sixteen-week kickboxing training period on physical and physiological characteristics of young male subjects. MED SPORT 2019. [DOI: 10.23736/s0025-7826.19.03425-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Arkan S, Kasap M, Akman Ö, Akpınar G, Ateş N, Karson A. The lower expression of parvalbumin in the primary somatosensory cortex of WAG/Rij rats may facilitate the occurrence of absence seizures. Neurosci Lett 2019; 709:134299. [DOI: 10.1016/j.neulet.2019.134299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/12/2019] [Accepted: 05/27/2019] [Indexed: 12/29/2022]
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Yoneten KK, Kasap M, Akpinar G, Kanli A, Karaoz E. Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins. J Membr Biol 2019; 252:587-608. [PMID: 31346646 DOI: 10.1007/s00232-019-00084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022]
Abstract
Plasma membrane proteins perform a variety of important tasks in the cells. These tasks can be diverse as carrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating them into intracellular action, and anchoring the cell in a particular location. When these crucial roles of plasma membrane proteins are considered, the need for their characterization becomes inevitable. Certain characteristics of plasma membrane proteins such as hydrophobicity, low solubility, and low abundance limit their detection by proteomic analyses. Here, we presented a comparative proteomics study in which the most commonly used plasma membrane protein enrichment methods were evaluated. The methods that were utilized include biotinylation, selective CyDye labeling, temperature-dependent phase partition, and density-gradient ultracentrifugation. Western blot analysis was performed to assess the level of plasma membrane protein enrichment using plasma membrane and cytoplasmic protein markers. Quantitative evaluation of the level of enrichment was performed by two-dimensional electrophoresis (2-DE) and benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE) from which the protein spots were cut and identified. Results from this study demonstrated that density-gradient ultracentrifugation method was superior when coupled with 16-BAC/SDS-PAGE. This work presents a valuable contribution and provides a future direction to the membrane sub-proteome research by evaluating commonly used methods for plasma membrane protein enrichment.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Erdal Karaoz
- Department of Histology and Embryology, School of Medicine, Istinye University, 34010, Istanbul, Turkey
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Cevik S, Akpinar G, Yildizli A, Kasap M, Karaosmanoglu K, Unyayar S. Comparative physiological and leaf proteome analysis between drought-tolerant chickpea Cicer reticulatum and drought-sensitive chickpea C. arietinum. J Biosci 2019; 44:20. [PMID: 30837371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that drought stress reduced root length, leaf water content, and enhanced free proline content in both species. Effect of drought stress appeared to be greater in C. arietinum compared to C. reticulatum. A total of 24 differently expressed proteins were identified by using MALDI-TOF/ TOF-MS/MS in response to drought. The proteins involved in photosynthesis and energy mechanisms were up-regulated in C. reticulatum and down-regulated in C. arietinum under drought. Our results suggest that the photosynthesis capacity of C. reticulatum is greater than that of C. arietinum under drought stress. Abundance of proline and sucrose biosynthesis related proteins, glutamine synthetase and cyctosolic fructose-bisphosphate aldolase, respectively, also increased in C. reticulatum under drought stress. The findings of this proteome analysis will help in understanding the mechanism of drought resistance in chickpea and may be also helpful in developing drought-resistant transgenic plants.
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Affiliation(s)
- Sertan Cevik
- Vocational School of Mut, Mersin University, Mersin, Turkey,
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Yenihayat F, Altıntaş Ö, Kasap M, Akpınar G, Güzel N, Çelik OS. Comparative proteome analysis of the tear samples in patients with low-grade keratoconus. Int Ophthalmol 2018; 38:1895-1905. [PMID: 28785876 DOI: 10.1007/s10792-017-0672-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/01/2017] [Indexed: 12/12/2022]
Abstract
PURPOSE To elucidate the metabolic processes playing roles in the formation of keratoconus (KC). METHODS Tears samples were collected using capillary glass tubes without stimulation and without prior anesthesia from 17 patients and 16 controls. Proteomic analysis by fluorescent 2D gel electrophoresis (DIGE) coupled with MALDI-TOF/TOF was performed. The identified proteins that were differentially regulated were subjected to Ingenuity Pathway Analysis (IPA). Corneal topography analyses with Sirius topography system (Costruzioni Strumenti Oftalmici, Florence, Italy) were performed on all participants. The steepest keratometry index was lower than 50 diopters in all keratoconus patients. RESULTS DIGE analysis showed changes in abundance of nine proteins. Six of these proteins, namely serum albumin, Keratin Type II Cytoskeletal 1, IgG gamma chain-1, GAPDH, alpha-1 antitrypsin and ApoA-I, were down-regulated in the KC samples in comparison with the controls. In addition, we detected up-regulation of lysozyme C, keratin type I cytoskeletal 10 and lipocalin. The subsequent IPA predicted that NADH repair pathway is activated in the KC patients. This pathway involves generation of NADHX as a by-product via catalysis by GAPDH. NADHX is an inhibitor of several dehydrogenases and must be removed. CONCLUSION The involvement of NADHX repair pathway in KC should be investigated, since preliminary clues obtained in this study point to that direction. In particular, showing the presence of ATP-dependent NAD(P)H-hydrate dehydratase that eliminates NADHX would strengthen our findings and would be a major step toward understanding KC.
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Affiliation(s)
- Fatih Yenihayat
- Department of Ophthalmology, Kocaeli State Hospital, 41100, Kocaeli, Turkey.
| | - Özgül Altıntaş
- Department of Ophthalmology, Medical School, Acıbadem University, Istanbul, Turkey
| | - Murat Kasap
- DEKART Proteomics Laboratory, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Gürler Akpınar
- DEKART Proteomics Laboratory, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Nil Güzel
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Onur Sinan Çelik
- Department of Ophthalmology, Tunceli State Hospital, Tunceli, Turkey
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Yaprak E, Kasap M, Akpinar G, Islek EE, Sinanoglu A. Abundant proteins in platelet-rich fibrin and their potential contribution to wound healing: An explorative proteomics study and review of the literature. J Dent Sci 2018; 13:386-395. [PMID: 30895150 PMCID: PMC6388803 DOI: 10.1016/j.jds.2018.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/01/2018] [Indexed: 01/12/2023] Open
Abstract
Background/purpose It is well-known that diverse types of blood proteins contribute to healing process via different mechanisms. Presence and potential involvements of blood-derived abundant proteins in the platelet-rich fibrin (PRF) to its regenerative capacity have not been sufficiently emphasized in the literature. The aim of this paper was to analyze the abundant proteome content of PRF and summarize previously reported effects of identified proteins on wound healing via a literature review. Materials and methods The PRF samples obtained from non-smoking, systemically healthy volunteers were subjected to 2D gel electrophoresis after extracting the proteins from fibrin matrices. All matching spots were excised from the gels and identified by MALDI TOF/TOF MS/MS analysis. A literature review was conducted to reveal possible contributions of identified proteins to wound healing. Results Totally, thirty-five blood proteins were commonly identified among all studied samples. These proteins included serine protease inhibitors, such as alpha-1-antitrypsin, alpha-1-antichymotrypsin, alpha-1-acid glycoprotein, inter-alpha-trypsin-inhibitor, protease C1 inhibitor, and complement proteins. In addition, abundant presence of immunoglobulin G was observed. The abundance of albumin, haptoglobin, ceruloplasmin vitronectin, fetuin-A, ficolin-3 and transthyretin was also detected. Conclusion The results of this study indicated that PRF abundantly contains blood-origin actors which were previously reported for their direct contribution to wound healing. Further studies exploring the protein content of PRF are needed to reveal its undisclosed potential roles in the healing process.
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Affiliation(s)
- Emre Yaprak
- Kocaeli University, Faculty of Dentistry, Department of Periodontology, Kocaeli, Turkey
- Corresponding author. Kocaeli University, Faulty of Dentistry, Department of Periodontology, Yuvacik, Basiskele, Kocaeli, Turkey. Fax: +90 2623442109.
| | - Murat Kasap
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Gurler Akpinar
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Eylul Ece Islek
- Kocaeli University, Faculty of Medicine, Department of Medical Biology, Kocaeli, Turkey
| | - Alper Sinanoglu
- Kocaeli University, Faculty of Dentistry, Department of Oral and Maxillofacial Radiology, Oral Diagnosis Clinic, Kocaeli, Turkey
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Teke K, Yilmaz H, Uslubas AK, Akpinar G, Kasap M, Mutlu O, Yildiz DK, Guzel N, Dillioglugil O. Histopathologic and molecular comparative analyses of intravesical Aurora kinase-A inhibitor Alisertib with bacillus Calmette-Guérin on precancerous lesions of bladder in a rat model. Int Urol Nephrol 2018; 50:1417-1425. [PMID: 29931492 DOI: 10.1007/s11255-018-1914-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/13/2018] [Indexed: 11/24/2022]
Abstract
PURPOSE Recent studies have shown that Aurora-A expression is associated with bladder cancer initiation and progression. In this study, the effects of intravesical Aurora-A inhibitor Alisertib (ALS) and bacillus Calmette-Guérin (BCG) were compared on bladder carcinogenesis. METHODS Two mg N-Methyl-N-nitrosourea was administered intravesically to forty of Wistar-albino rats every other week for 8 weeks. At week 10, rats were divided into four groups (10/group): No-treatment (vehicle), ALS-alone, BCG-alone, and ALS + BCG. The intravesical treatment of ALS, BCG, and ALS plus BCG was performed once a week for 6 weeks. At week 16, bladders were collected for immunohistopathological and Western blot analysis. The cell cycle regulators p53, p21, Aurora-A, phosphorylated Aurora-A (p-Aurora-A), and apoptotic marker cleavage of poly [ADP-ribose] polymerase (c-PARP) were determined by Western blot. RESULTS Histopathologically relatively healthy urothelium was observed in ALS + BCG group (87.5%) compared to the ALS-alone (50%) and the BCG-alone (50%) groups. The lowest expression of p21 and p53 was detected in the BCG-alone, while the highest level of expression was evident in no-treatment group. The ALS treatment alone caused a slight decrease in Aurora-A while there was a dramatic decrease in p-Aurora-A in comparison to no-treatment group. In overall combined treatment with ALS + BCG significantly increased c-PARP compared to all mono-treatments, and decreased all cell cycle parameters compared to no-treatment group. CONCLUSIONS Although intravesical ALS treatment has similar antiproliferative effects like BCG, ALS + BCG combined treatment led to a best histopathologic and apoptotic response. Consequently, BCG combined with Aurora-A inhibition may provide a new intravesical treatment modality in the prevention of bladder carcinogenesis.
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Affiliation(s)
- Kerem Teke
- Department of Urology, Kocaeli University School of Medicine, 41380, Kocaeli, Turkey.
| | - Hasan Yilmaz
- Department of Urology, Kocaeli University School of Medicine, 41380, Kocaeli, Turkey
| | - Ali Kemal Uslubas
- Department of Urology, Kocaeli University School of Medicine, 41380, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Oguz Mutlu
- Department of Pharmacology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Demir Kursat Yildiz
- Department of Pathology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Nil Guzel
- Department of Medical Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Ozdal Dillioglugil
- Department of Urology, Kocaeli University School of Medicine, 41380, Kocaeli, Turkey
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Sahin D, Karadenizli S, Kasap M, Oztas B, Kir HM, Akpinar G, Ates N. Decreased ERp57 Expression in WAG/Rij Rats Thalamus and Cortex: Possible Correlation with Absence Epilepsy. Protein Pept Lett 2018; 25:398-404. [DOI: 10.2174/0929866525666180207101650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Deniz Sahin
- Department of Physiology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Sabriye Karadenizli
- Department of Physiology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Berrin Oztas
- Sisli Hamidiye Etfal Research and Training Hospital, Department of Biochemistry, Istanbul, Turkey
| | - Hale Maral Kir
- Kocaeli University Medical School, Biochemistry Department, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Nurbay Ates
- Department of Physiology, Kocaeli University Medical School, Kocaeli, Turkey
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Kanli A, Kasap M, Yoneten KK, Akpinar G, Gulkac MD. Identification of differentially regulated deceitful proteins in SH-SY5Y cells engineered with Tet-regulated protein expression system. J Cell Biochem 2018; 119:6065-6071. [PMID: 29600520 DOI: 10.1002/jcb.26804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/23/2018] [Indexed: 01/28/2023]
Abstract
Tetracycline regulated protein expression in mammalian cells is a powerful tool to predict the physiological function, cellular localization, and stability of a protein. In addition, to predict metabolic networks affected by the expression of wild-type or mutant forms of proteins, researchers generally produce a single mammalian cell clone that can express the protein of interest under tetracycline control and study the changes occurring in overall proteome before and after expression of a protein of interest. One limitation of tetracycline regulated clonal cell creation, however, is that it sometimes creates clones with changed protein levels even without the expression of the protein of interest due to the nonspecific insertion of the gene encoding the protein of interest into the genome or disruption of a metabolic pathway due to insertional silencing or activation. The aim of this study was to demonstrate the limitation of tetracycline regulated gene expression by creating clonal cell lines expressing the wild-type or the mutant forms of Fat mass and obesity-associated protein. Comparative proteome analysis of the protein extracts by two-dimensional gel electrophoresis coupled to MALDI-TOF/TOF revealed the presence of eight proteins subjected to differential regulation even in the absence of induction. The identified proteins were 14-3-3 protein Epsilon, Vimentin, Heterogeneous nuclear ribonucleoprotein K, Tubulin beta-2C chain, Heat shock protein HSP 90-alpha, Heat shock protein HSP 90-beta, Alpha-enolase, TATA-binding protein-associated factor 2N. An ultimate care should be taken to prevent reporting of deceitful proteins generated from studies utilizing tetracycline regulated gene expression systems.
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Affiliation(s)
- Aylin Kanli
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Kubra K Yoneten
- Department of Biomedical Engineering, Technology Faculty, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
| | - Mehmet Dogan Gulkac
- Department of Medical Biology, Medical School, Kocaeli University, Kocaeli, Turkey
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44
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Selimoglu SM, Kasap M, Akpinar G, Karadenizli A, Wis AM, Gormus U. Improved Production of Highly Active and Pure Human Creatine Kinase MB. J Mol Microbiol Biotechnol 2018. [PMID: 29539608 DOI: 10.1159/000486716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human creatine kinase MB (hCKMB) is one of the most preferred biomarkers used for the diagnosis of acute coronary syndrome due to its high sensitivity and specificity. The increasing need for highly purified and biologically active hCKMB in the field of diagnostics makes its production valuable. Currently, the production of hCKMB is mainly achieved in methylotrophic yeast, Pichia pastoris, because the production in Escherichia coli is challenging and generally yields an inactive enzyme with a low quantity. With the aim of finding the best way for the high-yield production of active hCKMB in E. coli, an efficient strategy was developed using a construct allowing tandem expression of each subunit with 2 different tags. The strategy allowed the efficient expression and separate characterization of each subunit and 1-step purification of the heterodimeric protein into homogeneity. The heterodimeric protein displayed more than 11-fold greater specific activity than the commercially available one. The production strategy described in this study shows a clear advantage over the currently used ones and can be made available not only for laboratory scale production but also for commercial production. Our study is also a well-suited example for the studies in which novel protein expression strategies are needed to achieve greater yields with higher purities.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Aynur Karadenizli
- Department of Medical Microbiology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Abdul Mounem Wis
- Department of Chemical Engineering, School of Engineering, Kocaeli University, Kocaeli, Turkey
| | - Uzay Gormus
- Department of Medical Biochemistry, Faculty of Medicine, Biruni University, Kocaeli, Turkey
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45
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Yenihayat F, Özkan B, Kasap M, Karabaş VL, Güzel N, Akpınar G, Pirhan D. Vitreous IL-8 and VEGF levels in diabetic macular edema with or without subretinal fluid. Int Ophthalmol 2018. [PMID: 29524030 DOI: 10.1007/s10792-018-0874-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE To determine the cytokine levels in vitreous samples of diabetic macular edema (DME) patients in comparison with nondiabetic patients, and to evaluate the effect of subretinal fluid on the cytokine levels of vitreous samples. METHODS In this prospective case-control study, 11 eyes of 11 patients with DME and subretinal fluid, 11 eyes of 11 patients with DME without subretinal fluid, and 14 eyes of 14 patients who had undergone vitreoretinal surgery for the epiretinal membrane or a macular hole (control group) were evaluated. The blood glycated hemoglobin (HbA1c) level, vitreous vascular endothelial growth factor (VEGF), and interleukin-8 (IL-8) levels were determined. RESULTS The vitreous VEGF level of patients in DME groups was significantly higher than the control group (p < 0.001) without significant difference between DME patients with and without subretinal fluid (p = 0.796). The vitreous IL-8 level of DME patients with subretinal fluid was significantly higher than both control (p = 0.002) and DME without subretinal fluid groups (p = 0.019). The blood HbA1c level was significantly higher in DME group with subretinal fluid than those without subretinal fluid (8.7 ± 1.32 and 7.1 ± 1.13%, respectively, p = 0.010). The only significant correlation was between vitreous VEGF level and blood HbA1c level in DME patients without subretinal fluid (r = 0.813, p = 0.002). CONCLUSIONS IL-8 level in vitreous samples was higher in DME patients with subretinal fluid than those without subretinal fluid, suggesting that inflammation is an important factor in the progression of DME leading to the subretinal fluid formation in diabetic patients.
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Affiliation(s)
- Fatih Yenihayat
- Department of Ophthalmology, Kocaeli State Hospital, 41100, Kocaeli, Turkey.
| | - Berna Özkan
- Department of Ophthalmology, Acıbadem Mehmet Ali Aydınlar University Medical School, Istanbul, Turkey
| | - Murat Kasap
- DEKART Proteomics Laboratory, Kocaeli University Medical School, Kocaeli, Turkey
| | - V Levent Karabaş
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
| | - Nil Güzel
- DEKART Proteomics Laboratory, Kocaeli University Medical School, Kocaeli, Turkey
| | - Gürler Akpınar
- DEKART Proteomics Laboratory, Kocaeli University Medical School, Kocaeli, Turkey
| | - Dilara Pirhan
- Department of Ophthalmology, Kocaeli University Medical School, Kocaeli, Turkey
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46
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Akpinar G, Kasap M, Canturk NZ, Zulfigarova M, Islek EE, Guler SA, Simsek T, Canturk Z. Proteomics Analysis of Tissue Samples Reveals Changes in Mitochondrial Protein Levels in Parathyroid Hyperplasia over Adenoma. Cancer Genomics Proteomics 2018; 14:197-211. [PMID: 28446534 DOI: 10.21873/cgp.20031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND/AIM To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. MATERIALS AND METHODS Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. RESULTS The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. CONCLUSION Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma.
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Affiliation(s)
- Gurler Akpinar
- Department of Medical Biology and Genetics, School of Medicine, Kocaeli University, Kocaeli, Turkey .,DEKART Proteomics Laboratory, Kocaeli University, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology and Genetics, School of Medicine, Kocaeli University, Kocaeli, Turkey.,DEKART Proteomics Laboratory, Kocaeli University, Kocaeli, Turkey
| | - Nuh Zafer Canturk
- Department of General Surgery, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Mehin Zulfigarova
- Department of Medical Biology and Genetics, School of Medicine, Kocaeli University, Kocaeli, Turkey.,DEKART Proteomics Laboratory, Kocaeli University, Kocaeli, Turkey
| | - Eylül Ece Islek
- Department of Medical Biology and Genetics, School of Medicine, Kocaeli University, Kocaeli, Turkey.,DEKART Proteomics Laboratory, Kocaeli University, Kocaeli, Turkey
| | - Sertac Ata Guler
- Department of General Surgery, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Turgay Simsek
- Department of General Surgery, School of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Zeynep Canturk
- Department of Internal Medicine, School of Medicine, Kocaeli University, Kocaeli, Turkey
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Teke K, Guzel N, Uslubas AK, Kasap M, Yilmaz H, Akpinar G, Yildiz DK, Dillioglugil O. Monitoring the response of urothelial precancerous lesions to Bacillus Calmette-Guerin at the proteome level in an in vivo rat model. Cancer Immunol Immunother 2018; 67:67-77. [PMID: 28916862 PMCID: PMC11028241 DOI: 10.1007/s00262-017-2063-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/08/2017] [Indexed: 12/12/2022]
Abstract
Intravesical Bacillus Calmette-Guerin (BCG) is the best treatment modality for progression of non-muscle invasive bladder cancer. We aimed to monitor changes at the proteome level to identify putative protein biomarkers associated with the response of urothelial precancerous lesions to intravesical BCG treatment. The rats were divided into three groups (n = 10/group): control, non-treated, and BCG-treated groups. The non-treated and BCG-treated groups received N-methyl-N-nitrosourea intravesically. BCG Tice-strain was instilled into bladder in BCG-treated group. At the endpoint of experiment, all surviving rat bladders were collected and equally divided into two portions vertically from dome to neck. Half of each bladder was assessed immunohistopathologically and the other half was used for 2D-based comparative proteomic analysis. Differentially expressed proteins were validated by Western blot analysis. Precancerous lesions of bladder cancer were more common in non-treated group (77.8%) than in BCG-treated group (50%) and the control group (0%). Greater than twofold changes occurred in the expression of a number of proteins. Among them, Rab-GDIβ, aldehyde dehydrogenase 2 (ALDH2) and 14-3-3 zeta/delta were important since they were previously reported to be associated with cancer and their expression levels were found to be lower in BCG-treated group in comparison to the non-treated group. ALDH2 and 14-3-3 zeta/delta were also found to be highly expressed in the non-treated group compared to the control group. The down-regulation of these proteins and Rab-GDIβ was achieved with BCG; this result indicates that they may be used as putative biomarkers for monitoring changes in bladder carcinogenesis in response to BCG immunotherapy.
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Affiliation(s)
- Kerem Teke
- Department of Urology, Kocaeli University School of Medicine, Umuttepe Campus, 41380, Kocaeli, Turkey.
| | - Nil Guzel
- Department of Molecular Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Ali Kemal Uslubas
- Department of Urology, Kocaeli University School of Medicine, Umuttepe Campus, 41380, Kocaeli, Turkey
| | - Murat Kasap
- Department of Molecular Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Hasan Yilmaz
- Department of Urology, Kocaeli University School of Medicine, Umuttepe Campus, 41380, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Molecular Biology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Demir Kursat Yildiz
- Department of Pathology, Kocaeli University School of Medicine, Kocaeli, Turkey
| | - Ozdal Dillioglugil
- Department of Urology, Kocaeli University School of Medicine, Umuttepe Campus, 41380, Kocaeli, Turkey
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Subasi S, Altintas O, Kasap M, Guzel N, Akpinar G, Karaman S. Comparative proteomic analysis of amnion membrane transplantation and cross-linking treatments in an experimental alkali injury model. Int Ophthalmol 2017; 38:2563-2574. [PMID: 29170974 DOI: 10.1007/s10792-017-0770-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/16/2017] [Indexed: 11/28/2022]
Abstract
PURPOSE In this study, by using a two-dimensional (2D) electrophoresis-based experimental approach, we aimed at understanding the nature of alkali injuries and the underlying mechanisms. A secondary aim was to compare the effects of cross-linking (CXL) and amnion membrane transplantation (AMT) on corneal protein compositions at the end of the early repair phase after injured with alkali. METHOD The right corneas of 24 rabbits were injured with a 1 N solution of NaOH. Groups were formed based on the adjuvant therapies as (1) healthy group, (2) control group, (3) CXL group, (4) AMT group. In addition to the therapies, a conventional medical treatment was applied to all groups. Left eyes were used as within-subject healthy corneas (1). The corneas were excised at day 21, and a comparative proteomic analysis was performed using 2D gel electrophoresis coupled with MALDI-TOF/TOF. RESULT 2D gel electrophoresis revealed the presence seven protein spots whose abundance changed among the groups. Those proteins were SH3 domain-binding protein, plant homeodomain finger protein 23, S100 calcium binding protein A-11(S100 A11), keratin type 2 cytoskeletal 1 and 2, transketolase and glyceraldehyde 3-phosphate dehydrogenase. Ingenuity pathway analysis predicted that the observed changes may be linked to a central metabolic pathway, transforming growth factor beta 1. Canonical pathway analysis focused our attention to two different pathways, namely nicotinamide adenine dinucleotide repair pathway and non-oxidative branch of pentose phosphate pathway. CONCLUSION Our results shed some light onto the molecular mechanisms affected by alkali injury and adjuvant treatments. Further research is needed to propose medically significant target molecules that may be used for novel drug developments for alkali injury.
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Affiliation(s)
- Sevgi Subasi
- Department of Ophthalmology, Körfez State Hospital, Kocaeli, Turkey.
| | - Ozgul Altintas
- Department of Ophthalmology, Medical Faculty, Acıbadem University, Istanbul, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Nil Guzel
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Suleyman Karaman
- Department of Ophthalmology, Talya Medical Center, Antalya, Turkey
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49
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Akpinar G, Simsek T, Guler A, Kasap M, Canturk NZ. Elucidation of a Conserved Proteomic Pattern of Breast Cancer Tissue and Metastatic Axillary Lymph Node. Chirurgia (Bucur) 2017; 112:443-448. [PMID: 28862121 DOI: 10.21614/chirurgia.112.4.443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Breast cancer is one of the most devastating cancer types affecting women. For critical decision making regarding the fate of cancerous breast tissue, the assessment of axillary lymph node (ALN) involvement is required. However, such ALN involvement is difficult to predict without surgical intervention. Therefore, an easy predictive test using protein markers may be a desirable approach. In this study, we performed a whole proteome analysis to reveal the presence of a putative biomarker panel using primary breast tumor tissue. Materials and Methods: Proteins were extracted from tumor tissues and were subjected to two dimensional (2D) gel electrophoresis. The resulting gel images were used for inter-gel spot comparisons using PDQuest Advance software. The paterns thus obtained were used for differentiating invasive tumor types from non-invasive ones. Results: The analysis of 2D gel images revealed the presence of 24 conserved protein spots whose intensities were moderately regulated high on the gels. Those protein spots were used to create a conserved 2D pattern spanning a pH range of 4 to 8. CONCLUSION Protein spots generating a preserved model among pattern between primary breast cancer and its axillary lymph node indicated that a robust and highly reliable proteomic approach, e.g., 2DE may be used to differentiate metastatic forms of breast cancer from non-metastatic ones.
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Tombulturk FK, Kasap M, Tuncdemir M, Polat E, Sirekbasan S, Kanli A, Kanigur-Sultuybek G. Effects of Lucilia sericata on wound healing in streptozotocin-induced diabetic rats and analysis of its secretome at the proteome level. Hum Exp Toxicol 2017. [DOI: 10.1177/0960327117714041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of Lucilia sericata larvae on the healing of wounds in diabetics has been reported. However, the role of the excretion/secretion (ES) products of the larvae in treatment of diabetic wounds remains unknown. This study investigated whether application of the ES products of L. sericata on the wound surface could improve the impaired wound healing in streptozotocin-induced diabetic rats. Additional analysis was performed to understand proteome content of L. sericata secretome to understand ES contribution at the molecular level. For this purpose, full-thickness skin wounds were created on the backs of diabetic and control rats. A study was conducted to assess the levels of the ES-induced collagen I/III expression and to assay nuclear factor κB (NF-κB) (p65) activity in wound biopsies and ES-treated wounds of diabetic rat skin in comparison to the controls. The expression levels of collagen I/III and NF-κB (p65) activity were determined at days 3, 7, and 14 after wounding using immunohistological analyses and enzyme-linked immunosorbent assay technique. The results indicated that treatment with the ES extract increased collagen I expressions of the wound control and diabetic tissue. But the increase in collagen I expression in the controls was higher than the one in the diabetics. NF-κB (p65) activity was also increased in diabetic wounds compared to the controls, whereas it was decreased in third and seventh days upon ES treatment. The results indicated that ES products of L. sericata may enhance the process of wound healing by influencing phases such as inflammation, NF-κB (p65) activity, collagen synthesis, and wound contraction. These findings may provide new insights into understanding of therapeutic potential of ES in wound healing in diabetics.
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Affiliation(s)
- FK Tombulturk
- Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
- Medical Laboratory Techniques, Vocational School of Health Services, Istinye University, Istanbul, Turkey
| | - M Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical Faculty, Kocaeli, Turkey
| | - M Tuncdemir
- Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - E Polat
- Department of Medical Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - S Sirekbasan
- Department of Medical Microbiology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
- Department of Biotherapy Research and Development Laboratory, Istanbul University, Istanbul, Turkey
| | - A Kanli
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical Faculty, Kocaeli, Turkey
| | - G Kanigur-Sultuybek
- Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
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