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Karaca C, Demir Karaman E, Leblebici A, Kurter H, Ellidokuz H, Koc A, Ellidokuz EB, Isik Z, Basbinar Y. New treatment alternatives for primary and metastatic colorectal cancer by an integrated transcriptome and network analyses. Sci Rep 2024; 14:8762. [PMID: 38627442 PMCID: PMC11021540 DOI: 10.1038/s41598-024-59101-8] [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: 01/23/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Metastatic colorectal cancer (CRC) is still in need of effective treatments. This study applies a holistic approach to propose new targets for treatment of primary and liver metastatic CRC and investigates their therapeutic potential in-vitro. An integrative analysis of primary and metastatic CRC samples was implemented for alternative target and treatment proposals. Integrated microarray samples were grouped based on a co-expression network analysis. Significant gene modules correlated with primary CRC and metastatic phenotypes were identified. Network clustering and pathway enrichments were applied to gene modules to prioritize potential targets, which were shortlisted by independent validation. Finally, drug-target interaction search led to three agents for primary and liver metastatic CRC phenotypes. Hesperadin and BAY-1217389 suppress colony formation over a 14-day period, with Hesperadin showing additional efficacy in reducing cell viability within 48 h. As both candidates target the G2/M phase proteins NEK2 or TTK, we confirmed their anti-proliferative properties by Ki-67 staining. Hesperadinin particular arrested the cell cycle at the G2/M phase. IL-29A treatment reduced migration and invasion capacities of TGF-β induced metastatic cell lines. In addition, this anti-metastatic treatment attenuated TGF-β dependent mesenchymal transition. Network analysis suggests IL-29A induces the JAK/STAT pathway in a preventive manner.
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Affiliation(s)
- Caner Karaca
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Demir Karaman
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, Izmir, Turkey
| | - Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hasan Kurter
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
| | - Altug Koc
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Department of Gastroenterology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Zerrin Isik
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, Izmir, Turkey.
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey.
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Edizer DT, Leblebici A, Ergun U, Yilmaz F, Koc A, Basbinar Y, Ellidokuz EB. Effects of VDR and CYP24A1 gene polymorphisms on the outcome of supraglottic larynx cancer. Eur Rev Med Pharmacol Sci 2024; 28:2168-2178. [PMID: 38567579 DOI: 10.26355/eurrev_202403_35720] [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] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
OBJECTIVE Vitamin D has been demonstrated to play a protective role in carcinogenesis. Polymorphisms of the vitamin D receptor (VDR) genes and 24-α-hydroxylase (encoded by CYP24A1) may affect the outcome of some cancers. This study examines the effects of the VDR gene and CYP24A1 single nucleotide polymorphisms on the outcome of supraglottic larynx cancer. PATIENTS AND METHODS Patients diagnosed with supraglottic larynx cancer between 2017 and 2022 were enrolled. Single nucleotide polymorphisms of the VDR gene (rs2228570, rs731236, rs7975232, rs11574113, rs11168267 and rs11168266) and CYP24A1 gene (rs4809960, rs6022999, rs6068816, rs2259735 and rs2296241) were investigated. All patients were followed up for any evidence of local recurrence, regional recurrence, distant metastasis, and second primary tumor development. Cox regression analysis was performed to evaluate the prognostic value of single-nucleotide polymorphisms (SNPs). Kaplan-Meier method was used for survival analysis. RESULTS 87 patients were included. The mean follow-up time was 45.02±24.47 months. Cox regression analysis for locoregional recurrence revealed that the hazard ratio of rs731236 GG was 2.098 (95% CI, range: 1.047-4.202, p=0.037). Locoregional recurrence for rs731236 AA, AG, and GG were 38.6%, 23.1%, and 53.3%, respectively. In the presence of rs731236 GG polymorphism, disease-specific survival was significantly shorter (47.63±7.48 months, p=0.015), and disease-free survival (45.71±6.3 months) was significantly shorter (p=0.040). Rates of metastases and second primary tumors were not significantly different between SNPs. CONCLUSIONS This study has demonstrated the possible effects of VDR rs731236 SNP on the locoregional recurrence and prognosis of supraglottic larynx cancer.
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Affiliation(s)
- D T Edizer
- Department of Translational Oncology, Dokuz Eylul University, Institute of Health Sciences, Izmir, Turkey.
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Leblebici A, Sancar C, Tercan B, Isik Z, Arayici ME, Ellidokuz EB, Basbinar Y, Yildirim N. In Silico Approach to Molecular Profiling of the Transition from Ovarian Epithelial Cells to Low-Grade Serous Ovarian Tumors for Targeted Therapeutic Insights. Curr Issues Mol Biol 2024; 46:1777-1798. [PMID: 38534733 DOI: 10.3390/cimb46030117] [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: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
This paper aims to elucidate the differentially coexpressed genes, their potential mechanisms, and possible drug targets in low-grade invasive serous ovarian carcinoma (LGSC) in terms of the biologic continuity of normal, borderline, and malignant LGSC. We performed a bioinformatics analysis, integrating datasets generated using the GPL570 platform from different studies from the GEO database to identify changes in this transition, gene expression, drug targets, and their relationships with tumor microenvironmental characteristics. In the transition from ovarian epithelial cells to the serous borderline, the FGFR3 gene in the "Estrogen Response Late" pathway, the ITGB2 gene in the "Cell Adhesion Molecule", the CD74 gene in the "Regulation of Cell Migration", and the IGF1 gene in the "Xenobiotic Metabolism" pathway were upregulated in the transition from borderline to LGSC. The ERBB4 gene in "Proteoglycan in Cancer", the AR gene in "Pathways in Cancer" and "Estrogen Response Early" pathways, were upregulated in the transition from ovarian epithelial cells to LGSC. In addition, SPP1 and ITGB2 genes were correlated with macrophage infiltration in the LGSC group. This research provides a valuable framework for the development of personalized therapeutic approaches in the context of LGSC, with the aim of improving patient outcomes and quality of life. Furthermore, the main goal of the current study is a preliminary study designed to generate in silico inferences, and it is also important to note that subsequent in vitro and in vivo studies will be necessary to confirm the results before considering these results as fully reliable.
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Affiliation(s)
- Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ceren Sancar
- Department of Gynecology and Obstetrics, Faculty of Medicine, Ege University, 35340 Izmir, Turkey
| | - Bahar Tercan
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Zerrin Isik
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Mehmet Emin Arayici
- Department of Public Health, Faculty of Medicine, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ender Berat Ellidokuz
- Department of Internal Medicine, Faculty of Medicine, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Nuri Yildirim
- Department of Gynecology and Obstetrics, Faculty of Medicine, Ege University, 35340 Izmir, Turkey
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Goksel T, Özgür S, Vardarlı AT, Koç A, Karakuş HS, Özdemir TR, Erdoğan KM, Aldağ C, Veral A, Komurcuoglu B, Gursoy P, Arayici ME, Leblebici A, Yiğitbaşı T, Ellidokuz H, Basbinar Y. Prognostic and predictive role of liquid biopsy in lung cancer patients. Front Oncol 2024; 13:1275525. [PMID: 38304031 PMCID: PMC10830640 DOI: 10.3389/fonc.2023.1275525] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction Lung cancer (LC) is a leading cause of cancer-related mortality worldwide. Approximately 80% of LC cases are of the non-small cell lung cancer (NSCLC) type, and approximately two-thirds of these cases are diagnosed in advanced stages. Only systemic treatment methods can be applied to patients in the advanced stages when there is no chance of surgical treatment. Identification of mutations that cause LC is of vital importance in determining appropriate treatment methods. New noninvasive methods are needed to repeat and monitor these molecular analyses. In this regard, liquid biopsy (LB) is the most promising method. This study aimed to determine the effectiveness of LB in detecting EGFR executive gene mutations that cause LC. Methods One hundred forty-six patients in stages IIIB and IV diagnosed with non-squamous cell non-small cell LC were included. Liquid biopsy was performed as a routine procedure in cases where no mutation was detected in solid tissue or in cases with progression after targeted therapy. Liquid biopsy samples were also obtained for the second time from 10 patients who showed progression under the applied treatment. Mutation analyses were performed using the Cobas® EGFR Test, a real-time PCR test designed to detect mutations in exons 18, 20, and 21 and changes in exon 19 of the EGFR gene. Results Mutation positivity in paraffin blocks was 21.9%, whereas it was 32.2% in LB. Solids and LB were compatible in 16 patients. Additionally, while no mutation was found in solid tissue in the evaluation of 27 cases, it was detected in LB. It has been observed that new mutations can be detected not only at the time of diagnosis, but also in LB samples taken during the follow-up period, leading to the determination of targeted therapy. Discussion The results showed that "liquid biopsy" is a successful and alternative non-invasive method for detecting cancer-causing executive mutations, given the limitations of conventional biopsies.
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Affiliation(s)
- Tuncay Goksel
- Department of Pulmonary Medicine, Ege University Faculty of Medicine, Izmir, Türkiye
- EgeSAM-Ege University Translational Pulmonary Research Center, Izmir, Türkiye
| | - Su Özgür
- EgeSAM-Ege University Translational Pulmonary Research Center, Izmir, Türkiye
| | - Aslı Tetik Vardarlı
- EgeSAM-Ege University Translational Pulmonary Research Center, Izmir, Türkiye
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Türkiye
| | - Altuğ Koç
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Türkiye
| | - Haydar Soydaner Karakuş
- Department of Pulmonary Medicine, Ege University Faculty of Medicine, Izmir, Türkiye
- EgeSAM-Ege University Translational Pulmonary Research Center, Izmir, Türkiye
| | - Taha Reşid Özdemir
- Department of Medical Genetics, Health Sciences University, Izmir Tepecik Research and Training Hospital, Izmir, Türkiye
| | - Kadri Murat Erdoğan
- Department of Medical Genetics, Health Sciences University, Izmir Tepecik Research and Training Hospital, Izmir, Türkiye
| | - Ceyda Aldağ
- EgeSAM-Ege University Translational Pulmonary Research Center, Izmir, Türkiye
- Department of Biology, Ege University Faculty of Science, Izmir, Türkiye
| | - Ali Veral
- Department of Medical Pathology, Faculty of Medicine, Ege University, Izmir, Türkiye
| | - Berna Komurcuoglu
- Health Sciences University, Dr. Suat Seren Training and Research Hospital of Chest Diseases and Surgery, Izmir, Türkiye
| | - Pınar Gursoy
- Department of Medical Oncology, Faculty of Medicine, Ege University, Izmir, Türkiye
| | - Mehmet Emin Arayici
- Department of Cancer Epidemiology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Türkiye
| | - Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Türkiye
| | - Türkan Yiğitbaşı
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Türkiye
| | - Hülya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Türkiye
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Türkiye
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Arayıcı ME, Korkut-Uysal SO, Leblebici A, Akcali Z, Edizer DT, Kabul S, Cimrin D, Ellidokuz EB. Evaluation of 25-hydroxyvitamin D (25(OH)D) levels before and during the COVID-19 pandemic: A cross-sectional study and trend analysis involving 86,772 samples. PLoS One 2023; 18:e0284647. [PMID: 37195911 DOI: 10.1371/journal.pone.0284647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/04/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND The aim of this paper was to evaluate the change in 25-hidroxyvitamin D (25(OH)D) levels before and during the COVID-19 pandemic. METHODS In this retrospective, cross-sectional and methodological study included 86,772 patients (18-75 years) samples who were admitted to the Izmir Dokuz Eylul University Hospital (latitude and longitude (Turkey): 27 E 09; 38 N 25, respectively) for various reasons and whose 25(OH)D levels were measured in the biochemistry unit between 2019-2020 and 2020-2021 (before and during the COVID-19 outbreak). A time series analysis of monthly averages for 25(OH)D was performed. For the purpose of seasonal study, the mean levels of 25(OH)D are grouped by years. Data were modeled in terms of 25(OH)D levels using the MATLAB Curve Fitting Toolbox. RESULTS There was no significant difference between the sexes according to 25(OH)D levels (p>0.05). 25(OH)D levels were significantly higher in the summer months and lower in the winter months (p<0.001). When comparing the spring months, 25(OH)D levels in 2020 (18 ± 10) were found to be significantly lower than in 2019 (22 ± 12) (p<0.001); on the contrary, when examined based on the summer, autumn, and winter months, it was determined that 25(OH)D levels increased in 2020 (summer: 25 ± 13, autumn: 25 ± 14, and winter: 19 ± 10) compared to 2019 (summer: 23 ± 11, autumn: 22 ± 10, and winter: 19 ± 11) (p<0.001). In the estimates curve obtained with an error margin of 11% in the time series analysis, it was estimated that the 25(OH)D averages after the pandemic would be similar to those before the pandemic. CONCLUSIONS Restrictions, partial or complete closures, and curfews can significantly affect individuals' 25(OH)D levels during the COVID-19 outbreak. There is a need for multicenter studies with larger populations covering different regions to strengthen and support our results.
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Affiliation(s)
- Mehmet Emin Arayıcı
- Department of Preventive Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Sila Ovgu Korkut-Uysal
- Faculty of Engineering and Architecture, Department of Engineering Sciences, Izmir Katip Celebi University, Izmir, Turkey
| | - Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Zeynep Akcali
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Deniz Tuna Edizer
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Seher Kabul
- Faculty of Medicine, Department of Biochemistry, Dokuz Eylul University, Izmir, Turkey
| | - Dilek Cimrin
- Department of Medical Services and Techniques, Medical Laboratory Techniques Program, Vocational School of Health Services, Dokuz Eylul University, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Faculty of Medicine, Department of Gastroenterology, Division of Internal Medicine, Dokuz Eylul University, Izmir, Turkey
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Pakdemirli A, Karaca C, Sever T, Daşkin E, Leblebici A, Yiğitbaşi T, Başbinar Y. Carvacrol alters soluble factors in HCT-116 and HT-29 cell lines. Turk J Med Sci 2020; 50:271-276. [PMID: 31742371 PMCID: PMC7080355 DOI: 10.3906/sag-1907-173] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Background/aim Natural products are popular insights for researchers to investigate promising anti-cancer agents since some of these substances have lesser adverse effects restricting the treatment than traditional chemotherapeutic agents. A well-known monoterpene Carvacrol, widely consumed in Mediterranean cuisine and lower risks of cancer, has efficient anticancer effects. However, the mechanism of action is yet to be discovered. Materials and methods The investigation aims to illuminate a new perceptive in the role of this substance on colorectal cancer treatment, by the means of differences in a well-defined range of soluble factors. Carvacrol effect on both HT-29 and HCT-116 cell lines was evaluated on proliferation and the IC50 values were calculated by the RTCA xCELLigence device. Then MAGPIX assay was performed to obtain the changes in soluble factors of the cell lines. Results The Multiplexing assay suggests some of these factors were altered in favor of surviving and proliferation in aggressive cell line HCT-116 whereas they were altered against these characters in HT-29, were correlated with the increased IC50 concentration of HCT- 116 in carvacrol treatment. Conclusion The current study indicates that differences in the levels of these soluble factors could modulate the anticancer effect related to carvacrol.
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Affiliation(s)
- Ahu Pakdemirli
- Department of First and Emergency Aid, Vocational School of Health Services, Dokuz Eylül University, İzmir, Turkey
| | - Caner Karaca
- Department of Basic Oncology, Institute of Health Sciences, Dokuz Eylül University, İzmir, Turkey
| | - Tolga Sever
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylül University, İzmir, Turkey
| | - Ezgi Daşkin
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylül University, İzmir, Turkey
| | - Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylül University, İzmir, Turkey
| | - Türkan Yiğitbaşi
- Department of Biochemistry, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkey
| | - Yasemin Başbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey
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Pakdemirli A, Leblebici A. AI in Medicine versus AI in Prehospital. Med-Science 2020. [DOI: 10.5455/medscience.2020.09.9186] [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: 11/03/2022] Open
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Uncu B, Leblebici A, Kocal GC, Isik Z, Baskin Y. PO-510 Investigation of potential therapeutic targets by using in silico methods in glioblastoma. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.525] [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: 11/04/2022] Open
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