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Yanar K, Atayik MC, Horozoğlu C, Demirkol Ş, Simsek B, Verim A, Küçükhüseyin Ö, Aydın S, Yaylım İ, Çakatay U. Significance of Intercellular adhesion molecule-1 Lys496Glu gene polimorphism on plasma redox status regulation in laryngeal carcinoma. J Cancer Res Ther 2023; 19:1781-1787. [PMID: 38376278 DOI: 10.4103/jcrt.jcrt_1081_21] [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: 06/06/2021] [Accepted: 12/24/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Intercellular adhesion molecule-1 (ICAM-1) is a surface glycoprotein important for tumor invasion and angiogenesis. The present research is conducted to investigate whether specific gene polymorphism of ICAM-1 K469E (rs5498) and plasma redox status could be associated with laryngeal cancer (LC) development. Since there is no clear evidence which investigates the relationship between ICAM-1 polymorphism and ROS-mediated plasma protein oxidation in LC, our study is the first significant contribution for investigating the relationship. METHODS The study covered patients with primary LC and their age-matched healthy control subjects. Evaluation of ICAM-1 K469E (rs5498) gene polymorphism was performed by polymerase chain reaction-restriction fragment length polymorphism. Plasma redox status was assessed with spectrophotometric methods. RESULTS In the current paper, we found that LC patients with GG genotype had a decreasing trend for the plasma oxidative damage biomarker levels when compared with all allele genotypes (AA and AG). CONCLUSION We concluded that G allele of the ICAM-1 K469E gene plays a significant role in the optimal regulation of plasma redox homeostasis in patients with LC.
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Affiliation(s)
- Karolin Yanar
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehmet Can Atayik
- Medical Program, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Cem Horozoğlu
- Department of Medical Services and Techniques, Istanbul Gelişim University, Istanbul, Turkey
| | - Şeyda Demirkol
- Vocational School of Health Services, Biruni University, Istanbul, Turkey
| | - Bahadir Simsek
- Center for Coronary Artery Disease Minneapolis Heart Institute Foundation Minneapolis United States
| | - Aysegul Verim
- Department of Otorhinolaryngology/Head and Neck Surgery, Haydarpasa Numune Education and Research Hospital, Istanbul, Turkey
| | - Özlem Küçükhüseyin
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey
| | - Seval Aydın
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - İlhan Yaylım
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey
| | - Ufuk Çakatay
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
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Cakmak A, Ayaz H, Arıkan S, Ibrahimzada AR, Demirkol Ş, Sönmez D, Hakan MT, Sürmen ST, Horozoğlu C, Doğan MB, Küçükhüseyin Ö, Cacına C, Kıran B, Zeybek Ü, Baysan M, Yaylım İ. Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models. Med Biol Eng Comput 2023; 61:243-258. [PMID: 36357628 DOI: 10.1007/s11517-022-02707-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022]
Abstract
This study explores the machine learning-based assessment of predisposition to colorectal cancer based on single nucleotide polymorphisms (SNP). Such a computational approach may be used as a risk indicator and an auxiliary diagnosis method that complements the traditional methods such as biopsy and CT scan. Moreover, it may be used to develop a low-cost screening test for the early detection of colorectal cancers to improve public health. We employ several supervised classification algorithms. Besides, we apply data imputation to fill in the missing genotype values. The employed dataset includes SNPs observed in particular colorectal cancer-associated genomic loci that are located within DNA regions of 11 selected genes obtained from 115 individuals. We make the following observations: (i) random forest-based classifier using one-hot encoding and K-nearest neighbor (KNN)-based imputation performs the best among the studied classifiers with an F1 score of 89% and area under the curve (AUC) score of 0.96. (ii) One-hot encoding together with K-nearest neighbor-based data imputation increases the F1 scores by around 26% in comparison to the baseline approach which does not employ them. (iii) The proposed model outperforms a commonly employed state-of-the-art approach, ColonFlag, under all evaluated settings by up to 24% in terms of the AUC score. Based on the high accuracy of the constructed predictive models, the studied 11 genes may be considered a gene panel candidate for colon cancer risk screening.
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Affiliation(s)
- Ali Cakmak
- Department of Computer Engineering, Istanbul Technical University, Ayazaga Campus, Reşitpaşa, 34467, Sarıyer, Istanbul, Turkey.
| | | | - Soykan Arıkan
- Başakşehir Çam and Sakura City Hospital, Istanbul, Turkey
| | | | | | - Dilara Sönmez
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet T Hakan
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime T Sürmen
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | | | - Mehmet B Doğan
- Istanbul Research and Training Hospital, Istanbul, Turkey
| | - Özlem Küçükhüseyin
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Canan Cacına
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | | | - Ümit Zeybek
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet Baysan
- Department of Computer Engineering, Istanbul Technical University, Ayazaga Campus, Reşitpaşa, 34467, Sarıyer, Istanbul, Turkey
| | - İlhan Yaylım
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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Ay EN, Demirkol Ş, Hakan MT, Horozoğlu C, Arıkan S, Doğan MB, Akyüz F, Hepokur CÖ, Yaylım İ. Investigation of possible associations between tryptophan/kynurenine status and FOXP3 expression in colorectal cancer. Scand J Clin Lab Invest 2022; 82:185-191. [PMID: 35452343 DOI: 10.1080/00365513.2022.2040050] [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] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tryptophan metabolism in the tumor microenvironment exerts immunosuppressive effects by affecting the anti-tumor functions of immune cells. The immunosuppressive roles of tryptophan and tryptophan metabolites and their effects on the FOXP3 gene, highly expressed in regulatory T cells (Tregs), are remarkable. Our study aimed to investigate the relation between tryptophan metabolism and the transcription factor FOXP3 gene in colorectal cancer (CRC). Patients with CRC (n = 159) and controls (n = 112) were included in the study. The FOXP3 rs3761548 variant genotyping from the isolated genomic DNA was performed by PCR-RFLP. FOXP3 gene expression was determined by Q-PCR in RNAs isolated from resected tissues at the same time. Serum tryptophan, kynurenine, kynurenic acid levels of the cases were determined by HPLC. In serum samples with CRC, tryptophan level was 14.32 ± 1.09 μmol/L, kynurenine level was 1.33 ± 0.02 μmol/L, and the kynurenic acid level was 0.01 ± 0.001 μmol/L. The level of tryptophan was found to be low in CRC compared to control (p < .001). In cases with CRC, CC genotype (p = .048) and C allele (p = .012) frequency for FOXP3 rs3761548 were higher than the control group. It was found that the expression level of the FOXP3 gene was approximately 44 times higher in the advanced tumor stage (T3 + T4) than in the early tumor stage (T1 + T2) (p = .021).We suggest that there may be a possible relationship among serum TRP, TRP metabolites (KYN, KYNA) levels, FOXP3 gene expression, and FOXP3 gene variants in CRC pathogenesis.
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Affiliation(s)
- Ebru Nur Ay
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey.,Department of Medical Services and Techniques, Vocational School of Health Services, Istinye University, Istanbul, Turkey
| | - Şeyda Demirkol
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey.,Department of Molecular Biology and Genetics, Biruni University, Istanbul, Turkey
| | - Mehmet Tolgahan Hakan
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey
| | - Cem Horozoğlu
- Department of Biochemistry, Biruni University Medical Faculty, İstanbul, Turkey
| | - Soykan Arıkan
- General Surgery Clinic, Cam and Sakura City Hospital, Istanbul, Turkey
| | - Mehmet Baki Doğan
- General Surgery Clinic, Istanbul Training and Research Hospital, Istanbul, Turkey
| | - Filiz Akyüz
- Department of Gastroenterology, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Ceylan Özsoy Hepokur
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - İlhan Yaylım
- Department of Molecular Medicine, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Turkey
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Küçük U, Demirkol Ş, Balta Ş, Küçuk H, Işcen S, Çelik T, Iyisoy A, Yokuşoğlu M, Barçin C. PP-022 THREE DIMENTIONAL ECHOCARDIOGRAPHIC IMAGING OF BIVENTRICULAR FALSE TENDONS MIMICKING HYPERTROPHIC CARDIOMYOPATHY. Int J Cardiol 2012. [DOI: 10.1016/s0167-5273(12)70259-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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