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Article ; Online: Investigation of Long Non-coding RNAs H19 and LINC00675 in Colorectal Cancers in Terms of Histopathological Features and Correlations With Plasma Markers.

Nacarkahya, Gulper / Borazan, Ersin / Horozoglu, Cem / Yaylim, Ilhan

2022 Volume 42, Issue 3, Page(s) 1301–1306

Abstract: Background/aim: Functional and bioinformatic studies provide strong evidence that long non-coding RNAs (lncRNAs) can alter the molecular mechanisms of cancer through their interactions with DNA, RNAs, and proteins. This study aimed to evaluate the role ... ...

Abstract	Background/aim: Functional and bioinformatic studies provide strong evidence that long non-coding RNAs (lncRNAs) can alter the molecular mechanisms of cancer through their interactions with DNA, RNAs, and proteins. This study aimed to evaluate the role of H19 and LINC00675 lncRNAs in colorectal cancers (CRCs) in terms of clinicopathological features. Materials and methods: Tumor and tumor-free surrounding tissue samples were obtained from 51 CRC cases. Total RNA isolation and cDNA synthesis were performed. qPCR was performed using the TaqMan non-coding lncRNA assay specific for H19 and LINC00675. Preoperative levels of plasma markers, lncRNA expression, and clinicopathological characteristics of the cases were evaluated statistically. Results: Expression of H19 in tumor tissue was found to be 2.11 times higher than that of tumor-free surrounding tissue (p<0.001). LINC00675 levels were found to be approximately three times higher in colon tumors than tumors with rectal involvement (p=0.019). There was a correlation between H19 expression and creatinine (r=0.408; p=0.003). In addition, correlations were detected between LINC00675 with albumin (r=0.303; p=0.03), and between LINC00675 with globulin (r=0.332; p=0.02). Conclusion: H19 is a candidate biomarker that can be evaluated in terms of prognosis and antineoplastic treatment response, while LINC00675 may be an important marker of the microenvironment of advanced stage tumors, especially in tumors with rectal involvement.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Colonic Neoplasms/blood ; Colonic Neoplasms/genetics ; Colonic Neoplasms/pathology ; Colonic Neoplasms/surgery ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Middle Aged ; Prognosis ; RNA, Long Noncoding/genetics ; Rectal Neoplasms/blood ; Rectal Neoplasms/genetics ; Rectal Neoplasms/pathology ; Rectal Neoplasms/surgery ; Up-Regulation
Chemical Substances	Biomarkers, Tumor ; H19 long non-coding RNA ; RNA, Long Noncoding ; long non-coding RNA Linc00675, human
Language	English
Publishing date	2022-02-22
Publishing country	Greece
Document type	Comparative Study ; Journal Article
ZDB-ID	604549-2
ISSN	1791-7530 ; 0250-7005
ISSN (online)	1791-7530
ISSN	0250-7005
DOI	10.21873/anticanres.15597
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Article ; Online: Plasma Levels of Kynurenine, Soluble OX40 and Mir-138-5p Are Associated With Tumor-infiltrating Lymphocytes in Colorectal Cancer: An Exploratory Study.

Zor, Dilara Sönmez / Hakan, Mehmet Tolgahan / Özgür, Emre / Horozoglu, Cem / Yörüker, Ebru Esin / Kulle, Cemil Burak / Gezer, Ugur / Yaylim, Ilhan

Anticancer research

2023 Volume 43, Issue 7, Page(s) 3281–3288

Abstract: Background/aim: Colorectal cancer (CRC) is one of leading cancers in terms of incidence and mortality. Interaction of tumor cells with the surrounding microenvironment plays a crucial role in the development and progression of CRC. Many pathways such as ...

Abstract	Background/aim: Colorectal cancer (CRC) is one of leading cancers in terms of incidence and mortality. Interaction of tumor cells with the surrounding microenvironment plays a crucial role in the development and progression of CRC. Many pathways such as the kynurenine pathway, OX40/OX40L-mediated signaling and microRNAs targeting PD-L1 may be involved in CRC development by affecting T cell activation, thus creating an immune-deficient microenvironment. Herein, our goal was to assess the association between plasma levels of tryptophan (TRP), kynurenine (KYN), KYN/TRP ratio, soluble OX40 (sOX40) and PD-L1-targeting miR-138-5p and CRC risk. Patients and methods: Plasma concentrations of TRP and KYN were determined by HPLC; sOX40 was measured by ELISA whereas circulating miR-138-5p was measured by quantitative PCR in pathologically confirmed CRC patients and colonoscopy-verified CRC-free controls without polyps (control group 1) and with polyps (control group 2). Results: We found significantly lower plasma levels of TRP in CRC patients compared to control groups which resulted in significantly higher KYN/TRP ratio in CRC patients than in the controls (p=0.007). Plasma levels of sOX40 did not significantly differ between groups. The levels of circulating miR-138-5p were significantly lower in CRC patients (relative median value 0.02) than in the control groups (relative median values 0.2 and 4.29, respectively) (p=0.03). Plasma levels of KYN and sOX40 were considerably higher in patients with no tumor-infiltrating lymphocytes (TILs) than those with TILs whereas circulating miR-138-5p had opposite expression pattern in plasma. Conclusion: The kynurenine pathway and miR-138-5p are associated with CRC risk and plasma levels of KYN, sOX40 and miR-138-5p are related to TILs, making them possible target molecules in possible immunotherapeutic targets for CRC.
MeSH term(s)	Humans ; Kynurenine ; B7-H1 Antigen ; MicroRNAs/metabolism ; Tryptophan ; Colorectal Neoplasms ; Lymphocytes/pathology ; Tumor Microenvironment
Chemical Substances	Kynurenine (343-65-7) ; B7-H1 Antigen ; MicroRNAs ; Tryptophan (8DUH1N11BX) ; MIRN138 microRNA, human
Language	English
Publishing date	2023-06-23
Publishing country	Greece
Document type	Journal Article
ZDB-ID	604549-2
ISSN	1791-7530 ; 0250-7005
ISSN (online)	1791-7530
ISSN	0250-7005
DOI	10.21873/anticanres.16503
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Article ; Online: lncRNA NORAD, soluble ICAM1 and their correlations may be related to the regulation of the tumor immune microenvironment in laryngeal squamous cell carcinoma (LSCC).

Horozoglu, Cem / Bal, Görkem / Kabadayı, Batuhan / Hakan, Mehmet Tolgahan / Sönmez, Dilara / Nacarkahya, Gulper / Verim, Aysegul / Yaylım, İlhan

Pathology, research and practice

2023 Volume 246, Page(s) 154494

Abstract: NORAD, non-coding RNA activated by DNA damage, is a Long non-coding RNA (lncRNA) transcript that modulates genome stability and has been reported to be dysregulated in different cancers. Although it has been reported to be upregulated in tumor cells ... ...

Abstract	NORAD, non-coding RNA activated by DNA damage, is a Long non-coding RNA (lncRNA) transcript that modulates genome stability and has been reported to be dysregulated in different cancers. Although it has been reported to be upregulated in tumor cells mostly for solid organ cancers, it has also been reported to be downregulated in some cancers. Although the pathophysiological mechanism is not fully understood, a negative correlation between NORAD and intercellular cell adhesion molecule-1 (ICAM-1) has been shown in experimental models, but this situation has not been evaluated in terms of cancer. We aimed to evaluate the potential roles of these two biomarker candidates together and separately in the clinicopathological axis in Laryngeal squamous cell carcinoma (LSCC) in a case-control study setting. The interactions of NORAD and ICAM1 at the RNA level were evaluated interactively by the RIblast program. sICAM1 (soluble intercellular cell adhesion molecule-1) levels were determined by ELISA in one hundred and five individuals (forty-four LSCC, sixty-one control) and lncRNA NORAD expression in eighty-eight tissues (forty-four LSCC tumors, forty-four tumor-free surrounding tissues) was determined by Real-time PCR. While the energy treesholud was - 16 kcal/mol between NORAD and ICAM1, the total energy was 176.33 kcal/mol, and 9 base pair pairings from 4 critical points were detected. NORAD expression level was found to be higher in tumor surrounding tissue compared to tumor tissue, and sICAM1 was higher in the control group compared to LSCC (p = 0.004; p = 0.02). NORAD discreminte tumor surrounding tissue from tumor (AUC: 0.674; optimal sensitivity:87.50%; optimal specificity 54.55%; cut-off point as >1.58 fold change; P = 0.034). The sICAM1 level was found to be higher in the control (494,814 ± 93.64 ng/L) than LSCC (432.95 ± 93.64 ng/L) (p = 0.02). sICAM1 discreminte control group from LSCC (AUC: 0.624; optimal sensitivity 68,85%; optimal specificity 61,36%; cut-off point ≤115,0 ng/L; (p = 0.033). A very strong negative correlation was found between NORAD expression and patients' sICAM1 levels (r = -.967; n = 44; p = 0.033). sICAM1 levels were found to be 1.63 times higher in NORAD downregulated subjects compared to upregulated ones (p = 0.031). NORAD was 3.63 times higher in those with alcohol use, and sICAM 1 was 5.77 times higher in those without distant organ metastasis (p = 0.043; 0.004). The increased NORAD expression in the tumor microenvironment in LSCC, the activation of T cells via TCR signaling, and the decrease of sICAM in the control group in correlation with NORAD suggests that ICAM1 may be needed as a membrane protein in the tumor microenvironment. NORAD and ICAM1 may be functionally related to tumor microenvironment and immune control in LSCC.
MeSH term(s)	Humans ; Carcinoma, Squamous Cell/pathology ; Case-Control Studies ; Cell Adhesion Molecule-1/metabolism ; Cell Line, Tumor ; Cell Proliferation ; Gene Expression Regulation, Neoplastic ; Head and Neck Neoplasms/genetics ; Intercellular Adhesion Molecule-1/metabolism ; Laryngeal Neoplasms/pathology ; MicroRNAs/genetics ; RNA, Long Noncoding/genetics ; Squamous Cell Carcinoma of Head and Neck/genetics ; Tumor Microenvironment
Chemical Substances	Cell Adhesion Molecule-1 ; ICAM1 protein, human ; Intercellular Adhesion Molecule-1 (126547-89-5) ; MicroRNAs ; RNA, Long Noncoding ; NORAD long non-coding RNA, human
Language	English
Publishing date	2023-04-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2023.154494
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Article ; Online: Impact of calcitriol and an AKT inhibitor, AT7867, on survival of rat C6 glioma cells

Kucukhuseyin, Ozlem / Cakiris, Aris / Hakan, Mehmet Tolgahan / Horozoglu, Cem / Tüzün, Erdem / Yaylim, Ilhan

Biotechnology & Biotechnological Equipment. 2021 Jan. 1, v. 35, no. 1 p.731-739

2021

Abstract: Glioma is the most prevalent and lethal type of primary tumor of central nervous system. The regulatory role of calcitriol, the active form of vitamin D3, has been determined in various cellular processes including cell survival and apoptosis. To study ... ...

Abstract	Glioma is the most prevalent and lethal type of primary tumor of central nervous system. The regulatory role of calcitriol, the active form of vitamin D3, has been determined in various cellular processes including cell survival and apoptosis. To study the impact of AKT-pathway inhibition with or without calcitriol combination on glioma cell viability, the effects of AT7867 (AKT-pathway inhibitor) and calcitriol on cell viability and apoptosis were investigated in glioma C6 cell-line. Optimal doses of calcitriol and AT7867 were determined by MTT- and xCELLigence-assays. Both agents (alone/in combination) effectively suppressed the proliferation of C6 cells. While AT7867 inhibited glioma cell viability more effectively than calcitriol, this inhibitory action of AT7867 was not significantly increased by calcitriol combination. The expression levels of vitamin D receptor(VDR)-triggered molecules, AKT-pathway components and apoptosis factors were compared between calcitriol-, AT7867- and calcitriol + AT7867-treated and non-treated cells. CYP24A1 gene was upregulated and DBP, CYP1A1, CYP27B1, EGFRvIII, AKT-pathway (AKT1, MTOR, CREB, PTEN), apoptosis (BAD, CYC-C, CASP3, APAF-1, BCL2) and MMP3 genes were downregulated by calcitriol treatment.AT7867 treatment induced CYP27B1 upregulation, reduced VDR and AKT-pathway (PI3K, MTOR, CREB, PTEN) gene expression levels but showed a relatively less pronounced effect on apoptosis-related gene levels. The combination of calcitriol and AT7867 treatment generated an effect that was similar to that induced by calcitriol alone. Our results demonstrate that calcitriol and AT7867 have differing actions on AKT- and apoptotic-pathways of C6 glioma cell-line. Calcitriol has a lesser viability reducing impact than AT7867 putatively due to its apoptosis inhibiting action. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1912641 .
Keywords	apoptosis ; biotechnology ; calcitriol ; cell viability ; central nervous system ; cholecalciferol ; equipment ; gene expression ; genes ; glioma ; phosphatidylinositol 3-kinase ; rats ; AKT pathway ; AT7867 ; C6 cell line
Language	English
Dates of publication	2021-0101
Size	p. 731-739.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	1214963-9
ISSN	1314-3530 ; 0205-2067 ; 1310-2818
ISSN (online)	1314-3530
ISSN	0205-2067 ; 1310-2818
DOI	10.1080/13102818.2021.1912641
Database	NAL-Catalogue (AGRICOLA)

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Article: The role of galectin-3 and its genetic variants in tumor risk and survival of patients with surgically resected early-stage non-small cell lung cancer.

Terzioğlu-Uşak, Şule / Horozoğlu, Cem / Demirkol, Şeyda / Turna, Akif / Yaylım, İlhan

Turk gogus kalp damar cerrahisi dergisi

2021 Volume 29, Issue 2, Page(s) 212–222

Abstract: Background: The aim of this study was to investigate the possible relationship between galectin-3 gene variants, serum level, gene expression level, and the risks and survivals of resectable non-small cell lung cancer patients.: Methods: The rs4644 ... ...

Abstract	Background: The aim of this study was to investigate the possible relationship between galectin-3 gene variants, serum level, gene expression level, and the risks and survivals of resectable non-small cell lung cancer patients. Methods: The rs4644 and rs4652 variants of galectin-3 were genotyped by TaqMan single nucleotide polymorphism assay using genomic deoxyribonucleic acid isolated from the peripheral blood of 65 (54 males, 11 females; mean age: 60.1±11.9 years; range, 34 to 83 years) with Stage IA-IIIA non-small cell lung cancer who underwent primary surgical treatment and 95 healthy individuals (48 males, 47 females; mean age: 53.9±13.5 years; range, 32 to 87 years) between March 2017 and September 2018. Circulating galectin-3 levels in serum samples of the patient and control groups were assessed by enzyme-linked immunosorbent assay. Messenger ribonucleic acid expression of galectin-3 in tumor and surrounding tissues of the patient group was examined by real-time quantitative polymerase chain reaction. Both predictive and prognostic significance of the results were analyzed. Results: The presence of angiolymphatic invasion was significant in the patients with rs4652 AA genotype (p=0.04). Serum galectin-3 levels were significantly higher in the patients than the controls (p<0.0001). The patients with rs4644 CA/CC (p<0.0001 and p<0.0001) and rs4652 AA/AC (p=0.001 and p<0.0001) genotypes had higher serum galectin-3 levels than their corresponding controls. Serum galectin-3 levels increased in the presence of vascular invasion in patients with both rs4644 AC (p=0.03) and rs4652 AC (p=0.019) genotypes. The receiver operating characteristic curve suggested serum galectin-3 level as a strong predictive marker for the patient group with a cut-off value of 17.089 ng/mL (area under the curve: 0.910±0.04; 95% confidence interval: 0.832-0.988; p<0.001). Univariate analysis revealed the association of lower serum galectin-3 levels with better survival (p=0.048). Multivariate survival analysis showed that only high serum galectin-3 levels tended to be related to survival of the patients (hazard ratio: 5.106; 95% confidence interval: 0.956-27.267; p=0.056). Conclusion: The presence of galectin-3 gene variants may lead to histopathological differences among patients with non-small cell lung cancer. Serum galectin-3 level may be a valuable diagnostic biomarker and be associated with survival of these patients.
Language	English
Publishing date	2021-04-26
Publishing country	Turkey
Document type	Journal Article
ISSN	1301-5680
ISSN	1301-5680
DOI	10.5606/tgkdc.dergisi.2021.20141
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Article ; Online: Investigation of possible associations between tryptophan/kynurenine status and FOXP3 expression in colorectal cancer.

Ay, Ebru Nur / Demirkol, Şeyda / Hakan, Mehmet Tolgahan / Horozoğlu, Cem / Arıkan, Soykan / Doğan, Mehmet Baki / Akyüz, Filiz / Hepokur, Ceylan Özsoy / Yaylım, İlhan

Scandinavian journal of clinical and laboratory investigation

2022 Volume 82, Issue 3, Page(s) 185–191

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 ... ...

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 (
MeSH term(s)	Colorectal Neoplasms/genetics ; Forkhead Transcription Factors/genetics ; Humans ; Kynurenic Acid ; Kynurenine/metabolism ; Tryptophan ; Tumor Microenvironment
Chemical Substances	FOXP3 protein, human ; Forkhead Transcription Factors ; Kynurenine (343-65-7) ; Tryptophan (8DUH1N11BX) ; Kynurenic Acid (H030S2S85J)
Language	English
Publishing date	2022-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	3150-1
ISSN	1502-7686 ; 0036-5513
ISSN (online)	1502-7686
ISSN	0036-5513
DOI	10.1080/00365513.2022.2040050
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Article ; Online: Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models

Çakmak, Ali / Ayaz, Huzeyfe / Arıkan, Soykan / Ibrahimzada, Ali R. / Demirkol, Şeyda / Sönmez, Dilara / Hakan, Mehmet T. / Sürmen, Saime T. / Horozoğlu, Cem / Doğan, Mehmet B. / Küçükhüseyin, Özlem / Cacına, Canan / Kıran, Bayram / Zeybek, Ümit / Baysan, Mehmet / Yaylım, İlhan

Med Biol Eng Comput 2023 Jan., v. 61, no. 1, p. 243-258

2023 , Page(s) 243–258

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 ... ...

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.
Keywords	DNA ; biopsy ; colorectal neoplasms ; computed tomography ; data collection ; genes ; genomics ; genotype ; models ; public health ; risk
Language	English
Dates of publication	2023-01
Size	p. 243-258
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	282327-5
ISSN	1741-0444 ; 0025-696X ; 0140-0118
ISSN (online)	1741-0444
ISSN	0025-696X ; 0140-0118
DOI	10.1007/s11517-022-02707-9
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Article ; Online: Potential role of immune cell genetic variants associated with tumor microenvironment response in laryngeal squamous cell carcinoma (LSCC) in terms of clinicopathological features.

Horozoglu, Cem / Sonmez, Dilara / Demirkol, Seyda / Hakan, Mehmet Tolgahan / Kaleler, Islim / Hepokur, Ceylan / Verim, Aysegul / Yaylim, Ilhan

Pathology, research and practice

2021 Volume 228, Page(s) 153665

Abstract: Immunomodulatory signals regulate the self-tolerance, activation, priming and survival processes of T cells. Programmed cell death protein 1 (PD1), Programmed death-ligand 1 (PD-L1) inhibitory signals and CD27, CD28 costimulators have been detected for ... ...

Abstract	Immunomodulatory signals regulate the self-tolerance, activation, priming and survival processes of T cells. Programmed cell death protein 1 (PD1), Programmed death-ligand 1 (PD-L1) inhibitory signals and CD27, CD28 costimulators have been detected for many solid organ cancers in tumor-infiltrating T cells. It was aimed to investigate the immune cell-based regulatory genetic variants in laryngeal squamous cell carcinoma (LSCC) in terms of clinicopathological features. Genotyping was performed by PCR-RFLP method for PD-1 rs2227981, PD-L1 rs2890658, CD28 rs3116496, CD27 rs2267966 genetic variants from genomic DNAs extracted from peripheral blood samples in One Hundred Thirty-Six individuals (Sixty-one LSCC and seventy-five controls). Analysis of SNPs was carried out according to multiple inheritance models (co-dominant, dominant, recessive, over-dominant and log-additive). There was no difference between LSCC and control groups in genotype/allele distribution for PD-1 and PD-L1 (p > 0.05). In the PD-1 overdominant model, the CT genotype was found to be high (p = 0.036) in those without a family history. The frequency of C allele (AC+CC) in the PD-L1 dominant model was higher in alcohol users and those with reflux (p = 0.024; p = 0.001 respectively). In the Dominant model for PD-L1, the AA genotype was lower in moderately and well-differentiated tumors than in poorly differentiated tumors (p = 0.02). CD27 AT and CD28 CT genotypes were found to be higher in LSCC patients compared to the control group (p = 0.009; p = 0.01 respectively), while linkage disequilibrium (LD) was detected between CD27 and CD28 (p = 0.02). In the CD28 dominant model, C allele (CT+CC) carriage was found to be high in those with family history and in those without reflux and perineural invasion (p = 0.01; p = 0.01; p = 0.03 respectively). In LSCC, PD-L1 rather than PD-1 has a prognostic effect in terms of clinicopathology, and the LD and clinicopathological relationships detected between CD28 and CD27 genotypes suggest that the hereditary immune checkpoint-dependent T cell traffic may be pathophysiologically important.
MeSH term(s)	Aged ; B7-H1 Antigen/genetics ; CD28 Antigens/genetics ; Female ; Genotype ; Head and Neck Neoplasms/genetics ; Head and Neck Neoplasms/immunology ; Head and Neck Neoplasms/pathology ; Humans ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Programmed Cell Death 1 Receptor/genetics ; Squamous Cell Carcinoma of Head and Neck/genetics ; Squamous Cell Carcinoma of Head and Neck/immunology ; Squamous Cell Carcinoma of Head and Neck/pathology ; Tumor Microenvironment/immunology ; Tumor Necrosis Factor Receptor Superfamily, Member 7/genetics
Chemical Substances	B7-H1 Antigen ; CD274 protein, human ; CD28 Antigens ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Tumor Necrosis Factor Receptor Superfamily, Member 7
Language	English
Publishing date	2021-10-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2021.153665
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Article ; Online: Significance of Intercellular adhesion molecule-1 Lys496Glu gene polimorphism on plasma redox status regulation in laryngeal carcinoma.

Yanar, Karolin / Atayik, Mehmet Can / Horozoğlu, Cem / Demirkol, Şeyda / Simsek, Bahadir / Verim, Aysegul / Küçükhüseyin, Özlem / Aydın, Seval / Yaylım, İlhan / Çakatay, Ufuk

Journal of cancer research and therapeutics

2022 Volume 19, Issue 7, Page(s) 1781–1787

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 ...

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.
MeSH term(s)	Humans ; Alleles ; Carcinoma ; Intercellular Adhesion Molecule-1/genetics ; Laryngeal Neoplasms/genetics ; Oxidation-Reduction
Chemical Substances	Intercellular Adhesion Molecule-1 (126547-89-5) ; ICAM1 protein, human
Language	English
Publishing date	2022-04-27
Publishing country	India
Document type	Journal Article
ZDB-ID	2187633-2
ISSN	1998-4138 ; 0973-1482
ISSN (online)	1998-4138
ISSN	0973-1482
DOI	10.4103/jcrt.jcrt_1081_21
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Article ; Online: Predicting the predisposition to colorectal cancer based on SNP profiles of immune phenotypes using supervised learning models.

Cakmak, Ali / Ayaz, Huzeyfe / Arıkan, Soykan / Ibrahimzada, Ali R / Demirkol, Şeyda / Sönmez, Dilara / Hakan, Mehmet T / Sürmen, Saime T / Horozoğlu, Cem / Doğan, Mehmet B / Küçükhüseyin, Özlem / Cacına, Canan / Kıran, Bayram / Zeybek, Ümit / Baysan, Mehmet / Yaylım, İlhan

Medical & biological engineering & computing

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.
Language	English
Publishing date	2022-11-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	282327-5
ISSN	1741-0444 ; 0025-696X ; 0140-0118
ISSN (online)	1741-0444
ISSN	0025-696X ; 0140-0118
DOI	10.1007/s11517-022-02707-9
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