Browsing by Author "Yaylim, Ilhan"

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Citation Count: 12
An application of raman spectroscopy in combination with machine learning to determine gastric cancer spectroscopy marker
(Elsevier Ireland Ltd, 2023) Guleken, Zozan; Sönmez, Deniz; Paja, Wieslaw; Pancerz, Krzysztof; Wosiak, Agnieszka; Yaylim, Ilhan; Depciuch, Joanna; İşletme / Business Administration
Background and Objective: Globally, gastric carcinoma (Gca) ranks fifth in terms of incidence and third in terms of mortality. Higher serum tumor markers (TMs) than those from healthy individuals, led to TMs clinical application as diagnostic biomarkers for Gca. Actually, there is no accurate blood test to diagnose Gca. Methods: Raman spectroscopy is applied as an efficient, credible, minimally invasive technique to evalu-ate the serum TMs levels in blood samples. After curative gastrectomy, serum TMs levels are important in predicting the recurrence of gastric cancer, which must be detected early. The experimentally assesed TMs levels using Raman measurements and EL ISA test were used to develop a prediction model based on machine learning techniques. A total of 70 participants diagnosed with gastric cancer after surgery ( n = 26) and healthy ( n = 44) were comrpised in this study. Results: In the Raman spectra of gastric cancer patients, an additional peak at 1182 cm -1 was observed and, the Raman intensity of amide III, II, I, and CH2 proteins as well as lipids functional group was higher. Furthermore, Principal Component Analysis (PCA) showed, that it is possible to distinguish between the control and Gca groups using the Raman range between 800 and 1800 cm -1, as well as between 2700 and 30 0 0 cm -1. The analysis of Raman spectra dynamics in gastric cancer and healthy patients showed, that the vibrations at 1302 and 1306 cm -1 were characteristic for cancer patients. In addition, the selected machine learning methods showed classification accuracy of more than 95%, while obtaining an AUROC of 0.98. Such results were obtained using Deep Neural Networks and the XGBoost algorithm. Conclusions: The obtained results suggest, that Raman shifts at 1302 and 1306 cm -1 could be spectro-scopic markers of gastric cancer.(c) 2023 Elsevier B.V. All rights reserved.
Citation Count: 31
Assessment of structural protein expression by FTIR and biochemical assays as biomarkers of metabolites response in gastric and colon cancer
(Elsevier, 2021) Guleken, Zozan; Sönmez, Deniz; İnal Gültekin, Güldal; Arikan, Soykan; Yaylim, Ilhan; Hakan, Mehmet Tolgahan; Depciuch, Joanna; İşletme / Business Administration; Fizyoloji / Physiology
Colon and gastric cancers are the widespread benign types of cancers which are synchronous and metachronous neoplasms. In terms of the progression and progress of the disease, metabolic processes and differentiation in protein structures have an important role in for treatment of the disease. In this study we proposed to investigate the metabolic process and the differentiation of protein secondary structure among colon and gastric cancer as well as healthy controls using biochemistry and Fourier Transform InfraRed spectroscopy (FTIR) methods. For this purpose, we measured blood serum of 133 patients, which were conducted upon oncology department (45 colon cancer, 45 gastric cancer and 43 control individuals). The obtained spectroscopic results and biochemical assays showed significant reduction in the amount of functional groups in cancer groups contrary with total protein measurements and structure of protein differences between colon and gastric cancers. Differentiations were visible in serum levels of CEA, CA-125, CA-15-3, CA-19-9 AFP (Alpha fetoprotein) of gastric and colon cancer patients as well as in amide III and secondly described amide I regions. Our findings suggest that amide I bonds in colon cancer cells can be helpful in diagnosis of colon cancer. Indeed, our results showed that metabolic processes were higher in gastric cancer group than in colon cancer. Hence, FTIR spectroscopy and curve-fitting analysis of amide I profile can be successfully applied as tools for identifying quantitative and qualitative changes of proteins in human cancerous blood serum. However, what is very important, in PCA analysis we see, that the scatter plot of PC1 (variability 80%) and PC2 (variability 15%) show that the data related to the control and two cancer groups are clustered together with different magnitudes and directions.
Citation Count: 0
Determining the expression levels of circulating tumour cell markers in canine mammary tumours
(veterinarni A Farmaceuticka Univerzita Brno, 2021) İnal Gültekin, Güldal; Kahraman, Ozlem Timirci; Gultekin, Guldal Inal; Degirmencioglu, Sevgin; Yaylim, Ilhan; Guvenc, Kazim; Fizyoloji / Physiology
Detection of the circulating tumour cells (CTC) in dogs with a mammary tumour is a useful tool to reveal the micrometastases long before metastases are recognised clinically. The aim of this study was to evaluate the association of the epidermal growth factor receptor (EGFR), claudin 7 (CLND7) and epithelial cell adhesion molecule (EPCAM) with the clinical indices and to reveal the diagnostic importance of these biomarkers in canine mammary tumours (CMTs). Peripheral blood (PB) samples were collected from 45 bitches (group MT) which had single mass with malignant epithelial tumours and 9 healthy bitches (group H). Real time PCR (rt-PCR) was performed to determine the expression levels of EGFR, CLDN7, and EPCAM. Mean values of EGFR and CLDN7 expressions were significantly higher in group MT compared to group H (P < 0.01 and P < 0.001, respectively). The expression level of CLDN7 was positively correlated with EGFR and EPCAM (P < 0.001 and P < 0.05, respectively). The EPCAM expression was associated with increased tumour size (P < 0.05) and EPCAM tended to decrease in the presence of skin ulceration on tumour (P = 0.05). Furthermore, expression levels of EGFR in intact dogs were significantly higher compared to spayed dogs in group MT (P < 0.01). The EGFR expression was significantly higher in the presence of metastases (P < 0.05). Also, increased EGFR was determined in grade 2 compared to grade 1 (P < 0.05). In conclusion, these results show that EGFR, CLDN7, EPCAM markers are measureable in PB and they may provide valuable information about the clinical pathophysiology of CMT.
Citation Count: 0
Six potential biomarkers for bladder cancer: key proteins in cell-cycle division and apoptosis pathways
(Springer, 2022) Gultekin, Guldal Inal; İnal Gültekin, Güldal; Isbilen, Murat; Durmus, Saliha; Cakir, Tunahan; Yaylim, Ilhan; Isbir, Turgay; Fizyoloji / Physiology
Background: The bladder cancer (BC) pathology is caused by both exogenous environmental and endogenous molecular factors. Several genes have been implicated, but the molecular pathogenesis of BC and its subtypes remains debatable. The bioinformatic analysis evaluates high numbers of proteins in a single study, increasing the opportunity to identify possible biomarkers for disorders. Methods: The aim of this study is to identify biomarkers for the identification of BC using several bioinformatic analytical tools and methods. BC and normal samples were compared for each probeset with T test in GSE13507 and GSE37817 datasets, and statistical probesets were verified with GSE52519 and E-MTAB-1940 datasets. Differential gene expression, hierarchical clustering, gene ontology enrichment analysis, and heuristic online phenotype prediction algorithm methods were utilized. Statistically significant proteins were assessed in the Human Protein Atlas database. GSE13507 (6271 probesets) and GSE37817 (3267 probesets) data were significant after the extraction of probesets without gene annotation information. Common probesets in both datasets (2888) were further narrowed by analyzing the first 100 upregulated and downregulated probesets in BC samples. Results: Among the total 400 probesets, 68 were significant for both datasets with similar fold-change values (Pearson r: 0.995). Protein-protein interaction networks demonstrated strong interactions between CCNB1, BUB1B, and AURKB. The HPA database revealed similar protein expression levels for CKAP2L, AURKB, APIP, and LGALS3 both for BC and control samples. Conclusion: This study disclosed six candidate biomarkers for the early diagnosis of BC. It is suggested that these candidate proteins be investigated in a wet lab to identify their functions in BC pathology and possible treatment approaches.