Yazar "Karabay, Umut" seçeneğine göre listele

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    Bioinformatic assessment of the relationship between breast cancer and autophagy-related protein Ambra1 mutation
    (Kare Publishing, 2024) Karabay, Umut; Ayan, Durmus
    Objectives: Autophagy protein 1, regulated by Beclin 1 (Ambra1), promotes tumor formation and development by modulating autophagy. Therefore, in situ intervention in autophagy is a promising new strategy for tumor therapy. We aimed to evaluate the possible effects of changes in the Ambra1 gene on breast cancer (BC) treatment in the BRCA cohort. Methods: The gene profile of a total of 996 patients with BC was examined using data obtained from the Cancer Genome Atlas database via cBioPortal. The effects of mutations on proteins were examined by scoring the Polymor-phism Phenotyping v2, Mutation Assessor, and Sorting Intolerant from Tolerant databases. The association of genes with other genes was determined with the STRING database. Kaplan-Meier Plot database was used by evaluating the overall survival (OS). The promoter methylation was evaluated by the UALCAN database. Results: Eleven mutations were detected. Four of these mutations were truncated proteins. Ambra1 tissue expression levels were upregulated compared to healthy tissue in the BRCA cohort; this was not statistically significant (p>0.05). Decreased Ambra1 expression levels were associated with a shorter OS (p=0.038). Ambra1 promoter region hyperme-thylation was significant in the BRCA cohort compared to healthy tissue (p<0.001). Conclusion: To our best knowledge, our study is the first to examine the relationship between BC and Ambra1 using bioinformatic tools. Ambra1 may be a candidate target molecule within the treatment strategy due to the mutations evaluated in the BRCA cohort, hypermethylation status, and the association of Ambra1 with shorter OS. However, these situations need to be confirmed by further studies. © 2024, Kare Publishing. All rights reserved.
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    Bioinformatic Investigation of Genetic Changes in Paraoxonase Genes in Breast Cancer and Breast Cancer Subtypes
    (Galenos Publ House, 2024) Ayan, Durmus; Gul, Mehmet Ali; Karabay, Umut; Bulut, Seyyid Mehmet
    Objective: Among women, breast cancer (BC) is the most prevalent form of cancer. Many molecular targets have been discovered for BC prognosis and treatment. However, new markers still need to be identified, as cancer pathogenesis is triggered by different mechanisms. The aim of this study was to examine the changes in the paraoxonase genes ( PON1 , PON2 , and PON 3 ) involved in the pathogenesis of BC. Materials and Methods: The characteristics of the mutations were evaluated with the Cbioportal database. Kaplan-Meier Plot evaluated recurrence-free survival (RFS). The UALCAN database determined the promoter methylation. Gene expression was evaluated by GEPIA2.0 database. Results: PON1 harbored the most mutations. There was a significant decrease in PON3 expression levels in BC samples compared with healthy samples. PON1 and PON2 expression levels did not differ between BC tissue and normal adjacent tissue. Elevated expression levels of PON1 and PON2 genes were correlated with longer RFS, whereas reduced expression of the PON2 gene showed an association with longer RFS. Moreover, the promoter regions of PON1 and PON 3 were found to be hypermethylated, while the promoter region of PON 2 was found to be hypomethylated. The PON3 promoter region was significantly hypermethylated in luminal and human epidermal growth factor receptor 2 (HER2) + BC subtypes. However, the PON3 promoter region was significantly hypomethylated in the triple negative breast cancer (TNBC) subtype. Conclusion: These results suggest that methylation and expression status of PON3 in BC and BC subtypes (TNBC, luminal and HER2) may indicate a poor prognosis. The PON3 gene could be a negative prognostic marker in BC. However, the results should be supported by prospective studies.
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    NÖTROFİL/LENFOSİT ORANI PREDİYABETİK HASTALARDA İNSÜLİN DİRENCİ TAHMİNİNDE HOMA-IR İNDEKSİNE ALTERNATİF BİR BELİRTEÇ OLABİLİR Mİ?: BİR RETROSPEKTİF ÇALIŞMA
    (2023) Ayan, Durmus; Balcı, Tevfik; Aydoğan, Kader Zeybek; Özmen, Esma; Karabay, Umut
    Amaç: Çalışmamızda prediyabet ve diyabet olmayan hastalarda HOMA-IR indeksi ile Trigliserid/Glukoz (TyG) indeksi, LDL-K/HDL-K oranını, Trigliserid/ HDL-K oranını ve Nötrofil/ Lenfosit Oranını (NLO) bir biri ile karşılaştırmayı amaçladık. Gereç ve Yöntem: Çalışmamıza Niğde Ömer Halisdemir Üniversitesi Eğitim ve Araştırma Hastanesine 2019-2021 yılları arasında başvuran 18-75 yaş arasında 673’ü kadın 890’ü erkeklerden oluşan toplam 1433 hasta dahil edilmiştir. HOMA-IR indeksi, TyG indeksi, LDL-K/HDL-K oranı, Trigliserid/ HDL-K oranı, NLO hesaplamaları analizi yapılan testler vasıtasıyla yapılmış tır. Bulgular: Bulgularımıza göre diyabetik olmayan grupta Trigliserid/HDL-K oranının ve pre-diyabetik grupta NLO’nun rutinde kullanılan yöntem olan HOMA-IR indeksine göre hem de IR tahmininde kullanılan diğer indekslere göre duyarlılığı ve özgüllüğünün daha yüksek olduğu tespit edildi. Ayrıca diyabetik olmayan grupta Trigliserid/HDL-K oranı ile HOMA-IR indeksi arasında pozitif anlamlı bir korelasyon sonucuna ulaşılırken (r=0,219; p<0,001), pre-diyabetik grupta NLO ile HOMA-IR indeksi arasında anlamlı bir korelasyon sonucu bulunamadı (r=0,034; p=0,290). Sonuç: Sonuç olarak, NLO pre-diyabetik hastalarda IR tahmininde HOMA IR yerine alternatif bir parametre olabilir. Ancak bunun referans yöntem ile verifikasyonu yapılan prospektif çalışmalar ile doğrulanması gerektiği düşüncesindeyiz.