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    A detailed in-silico analysis of potential gastric cancer molecular marker genes in the literature
    (Inderscience Enterprises Ltd, 2021) Aktas, Sedef Hande; Akin-Bali, Dilara Fatma; Yazici, Ozan
    Genes found extremely important for the diagnosis and prognosis of Gastric Cancer (GC) in the literature between 2015 and 2020 were analysed in detail by in-silico methods. Thereby, broadly-based analysis of the genes was performed for future studies of GC. For this purpose, expression, pathological stage, Overall Survival (OS) and Disease Free Survival (DFS) plots were carried out with GEPIA web tool. PolyPhen-2 and SNAP tools were used to detect pathogenic impact of the mutations. As a result, COL10A1, SOX9, MTBP, CCL5, PSMB8 and PBK genes were found significant to distinguish individuals with GC from healthy individuals. PCDH9 and HGF genes were found significant for both OS and DFS. METTL3, COL10A1, USP3, CCL5, IMP3, CXCR6, PBK, HGF, MRC1, CD163, SSP1 genes were found correlated with the stage of GC. Effect of the mutations of PCDH9 and HGF genes, especially on the Kringle domain of HGF gene, were found pathogenic.
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    Survivin As an Immunohistochemical Prognostic Biomarker in Colorectal Cancer: A Meta-Analysis
    (Kare Publ, 2022) Aktas, Sedef Hande; Emir, Busra; Akin Bali, Dilara Fatma; Yazici, Ozan
    OBJECTIVE Genome-level research qualities survivin as the fourth-best transcriptorne for colon, lung, brain, breast, and melanoma cancers. To date, it has been stated as a prognostic marker and therapeutic target in colorectal cancer (CRC). However, researchers on survivin expression in CRC are heterogeneous. Our current study aimed to reveal prognostic importance of survivin by investigating all CRC articles up to January 2021 that have performed analysis of survivin by immunohistochernical staining method. METHODS A comprehensive literature search for relevant studies published up to January 2021 was performed using SCOPUS and Pubmed databases. Only articles in which survivin was detected by IHC staining were included in the study. All analyses were conducted by using Comprehensive Meta-Analysis. Eight articles and data of 1535 patients were included in the study. Me hazard Ratio was used to examine the relationship between CRC and survivin protein, for the relative weights of each research article. HR and 95% confidence interval values and general summary HR were calculated and forest plot graph was obtained. RESULTS Statistical heterogeneity Cochrane Q test statistics 24.156; p=0.004 and I-2 value was obtained as 62,742. In line with the assumption that the data consisted of different populations, the HR and 95% CI values were calculated as 1.446 (1.1(13-1.897) using the Dersimonian and Laird random effects model. In order to evaluate the risk of publication bias, funnel plots were obtained, including log HR and standard error values on the x and y axes, respectively. CONCLUSION The lite analyzes obtained suggest that survivin overexpression in CRC is associated with poor prognosis. (HR=1.446; 95% CI: 1.103-1.897).
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    Tumor-Infiltrating Lymphocytes (TIL), Tertiary Lymphoid Structures (TLS), and Expression of PD-1, TIM-3, LAG-3 on TIL in Invasive and In Situ Ductal Breast Carcinomas and Their Relationship with Prognostic Factors
    (Cig Media Group, Lp, 2022) Acar, Elif; Esendagli, Guldal; Yazici, Ozan; Dursun, Ayse
    We wanted to evaluate the expression of immune checkpoint receptors in pathology samples to support research on whether the immune response against breast cancer can be used for treatment. For this purpose, we studied 312 invasive and 68 in situ breast cancers. We found that PD-1 and stromal TIL were associated with survival. Determination of PD-1 expression on stromal TIL can provide information about whether the patient can benefit from immunotherapy. Introduction: Immunotherapy has been determined as an important choice in breast carcinomas, especially in tumors with markedly inflammatory response. About this promising subject, tumor-infiltrating lymphocytes (TIL) and the expression of immune control point receptors on TIL have gained importance. Materials and Methods: In this study, stromal TIL and tertiary lymphoid structures (TLS) were determined in tumor tissues of 312 invasive and 68 in situ breast cancer patients. Expression rates of PD-1, LAG-3, and TIM-3 on intratumoral and stromal TIL were immunohistochemically evaluated. Results: In invasive breast carcinomas, stromal TIL was found to be significantly associated with lymph node metastasis, HR and HER2 expression, and basal-like phenotype, as the presence of TLS with neoadjuvant therapy, recurrence, death, and expression of HR and HER2. PD-1, LAG-3, and TIM-3 expressions were found to be associated with HR and HER2 status, stromal TIL rates, and TLS. In multivariate analysis, high stromal TIL and PD-1 expression in intratumoral TIL were found to be independent prognostic factors in terms of overall survival and disease-free survival. Conclusion: Evaluation of TIL and immune control point receptor expressions in breast cancer is particularly important in terms of planning the therapeutic approaches based on immunotherapy protocols.