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    Beta-lactam antibiotic-induced thrombocytopenia: MYH9 & TUBB1 genes
    (Bayrakol Medical Publisher, 2022) Ozkan, Didem; Akisin, Yasemin Ardicoglu; Bali, Dilara Fatma Akin; Akar, Nejat
    Aim: Macrothrombocytopenia is a congenital autosomal-dominant blood disorder characterized by increased platelet size and a decreased number of circulating platelets. In this study, it was aimed to show the MYH9 and TUBB1 gene changes, which are the genes associated with the disease, in a patient with thrombocytopenia receiving beta-lactam antibiotic therapy. Material and Methods: In this study, coagulation parameters and platelet aggregation tests were performed after ingestion of a beta-lactam antibiotic in an 8-year-old boy with thrombocytopenia, the MYH9 and TUBB1 genes were scanned by PCR and DNA sequencing, and the results were subsequently analyzed using bioinformatics tools. Results: We found previously described TUBB1 polymorphisms, p.R307H , p.Q43P, p.T178T and the novel mutation p.K64A in the MYH9 gene in a boy and his mother. Changes in genes important for thrombocytopenia in a boy after taking beta-lactam antibiotics prompted us to study the same genes in the mother, since her mother had macrothrombocytopenia, and we found a new mutation in her mother Discussion: Determination of gene changes after beta-lactam antibiotic use in bleeding patients is important in terms of helping the clinic in the treatment.
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    Epidermal Growth Factor-Like Repeats and Discoidin I-Like Domains 3 is a Novel Regulator of Epithelial-Mesenchymal Transition in Clear Cell Renal Cell Carcinoma: In Silico Analysis
    (Erciyes Univ Sch Medicine, 2021) Sagkan, Rahsan Ilikci; Bali, Dilara Fatma Akin
    Objective: Epithelial-mesenchymal transition (EMT) contributes to cancer metastasis and recurrence, which are major obstacles in changing the course of cancer. However, studies on the mutational and gene expression profiles of epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3) that reveal the relationship between clear cell renal cell carcinoma (ccRCC) and EMT markers are limited. The aim of our study was to reveal the correlation between tumor and EMT markers (E-cadherin and vimentin) and EDIL3 expression. Additionally, we evaluated target gene expression levels and mutational profiles in kidney cancer tissue and normal tissue. Materials and Methods: We investigated the mutational profile and mRNA expression of EDIL3 and compared them with that of VIM and CDH1 in 523 patients with ccRCC using validated bioinformatics analysis. Additionally, Polymorphism Phenotyping v2 (PolyPhen-2), Screening for NonAcceptable Polymorphisms (SNAP) were used to predict and confirm the pathogenicity of the mutations detected. Studies were performed in silico using bioinformatics tools. Results: EDIL3 and VIM expression was statistically significantly higher in the healthy group and exhibited a positive correlation in patients with ccRCC. Patients with elevated VIM and CDH1 expression and low EDIL3 expression had prolonged survival time. In addition, 7 mutations were detected in the evaluated genes, 6 of which had potential pathogenic features. Conclusion: Our study provides insights for further experimental studies. EDIL3 can be used as a diagnostic or prognostic indicator of cancer development to help cure renal clear cell cancer.
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    Identification of relationships among EDIL3, angiogenesis and inflammation in colorectal cancer: In-silico analysis
    (Bayrakol Medical Publisher, 2021) Sagkan, Rahsan Ilikci; Bali, Dilara Fatma Akin
    Aim: The relationship between inflammation and the development of colorectal adenocarcinoma has been described for a number of years. In this cancer, chronic inflammation causes cellular damage and DNA mutations responsible for the proliferation of transformed cells. Epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3/DEL-1) were anti-inflammatory protein, especially in epithelial cells. Our study, it was aimed to clarify the link of among IL-17A, EDIL3/DEL1, and the main angiogenic factor VEGFA/B in colorectal cancer. Materials and Methods: We investigated EDIL3, IL-17, and VEFGA/B mutations profile and levels of m-RNA expressions in 594 colorectal cancer patients using bioinformatics analysis for the revealing relationship among these molecules. Additionally, PolyPhen-2 and SNAP tools were used to predict and confirm the pathogenicity of the detected mutations. Results: In colorectal cancer patients, the IL-17 and EDIL3 expressions were inversely correlated but the low correlation coefficient was statistically significant. EDIL3 and VEGFB m-RNA levels were found to be statistically significantly lower in the patient group than in the healthy group. Furthermore, 10 mutations were identified in the EDIL3. The study predicted the potential pathological effect of eight mutations in the EDIL3. Discussion: Low expression of EDIL3 might contribute to anti-inflammation, supporting extravasation of leukocytes to inflammatory area by increased IL-17 expression. Although further studies to clarify the mechanisms explaining the role of EDIL3 in tumor angiogenesis in terms of VEGF gene, and the interaction between IL-17 and EDIL3 are required, the results indicate that EDIL3 may be a good novel molecular target gene in inflammatory pathways for colorectal cancer.
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    Mutations and Expression Profile of EDIL3 and Correlation with HIF1A and Tumor-Associated Carbonic Anhydrases in Pancreatic Cancer
    (Marmara Univ, Inst Health Sciences, 2021) Bali, Dilara Fatma Akin; Sagkan, Rahsan Ilikci
    Objective: Epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3) expression is upregulated in some types of cancer which means that it can be used as a candidate tumor marker. The expression level of EDIL3 as a marker of the hypoxic microenvironment of pancreatic cancer was assessed by studying its relationship with the expression of tumor-associated carbonic anhydrases (CA IX and CA XII) and Hypoxia-inducible factor-1 (HIF-1) in tumor development. Methods: Gene expression and mutation profiles of pancreatic cancer patients and healthy tissue samples were downloaded The Cancer Genome Atlas (TCGA), and the genetic alterations and expression levels of the EDIL3, HIF-1 alpha, CA IX and CA XII genes were analyzed. Additionally, PolyPhen-2 and SNAP tools were used to prediction and confirmation of detected alterations pathogenicity and survival analysis was performed. Results: Expression levels of EDIL3, HIF-1 alpha and CA IX were found to be statistically significant higher in the patient compared to healthy group and we showed also positive correlation between EDIL3 and HIF-1 alpha gene expression. Furthermore, low CA IX and CA XII expression levels were found effective on overall survival (p<0.05). Additionally, 8 missense mutations were detected in the coding region of studied genes. Conclusion: We suggested that relationship between EDIL3 and HIF-1 alpha in pancreatic cancer and EDIL3 is a novel molecule cancer development in pancreatic cancer.
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    Pathogenic Ala303Val Mutation in the PROS1 Gene is Associated with the Pathogenesis of Deep Vein Thrombosis
    (Erciyes Univ Sch Medicine, 2022) Bali, Dilara Fatma Akin; Eroglu, Tamer; Ozkan, Didem Torun
    Objective: The aim of this study was to predict the functional impact of pathogenic mutations and the mRNA expression profiles of the platelet endothelial aggregation receptor 1 (PEAR1), protein S (alpha) (PROS1), and adrenoceptor alpha 2A (ADRA2A) genes in deep vein thrombosis (DVT), as well as to examine the effects of these genes on the pathogenesis of DVT. Materials and Methods: Patients diagnosed with DVT were selected for the study and healthy individuals were used as controls. Mutations in the PEAR1, PROS1, and ADRA2A genes were determined by DNA sequencing analysis and gene expressions were determined using quantitative real-time polymerase chain reaction testing. Polymorphism Phenotyping v2 (Polyphen-2: http://genetics.bwh.harvard.edu/pph2/), SNAP2 (https://rostlab.org/services/snap2web/) and MutationTaster (https://www.mutationtaster.org/) software were used to define the pathogenic effects of mutations detected by sequencing the selected genes in hotspot regions. Mutation and gene expression analyses were noted in the results and clinical data. Results: A total of 27 patients with DVT and 10 healthy individuals were included in the study. Twenty-one mutations were detected in the 27 patients, most often in the PROS1 gene. A p.Ala303Val mutation is located on the human sex hormone-binding globulin (SHBG) domain of mutation PROS1 and is pathogenic. A p.A303V mutation is associated with premature termination in codon 303 of the SHBG domain. Examination of the effect on the mRNA expression level of wild-type versus mutant genotypes revealed that the mutant PROS1 p.A303V expression was significantly lower (p=0.041). Conclusion: A p.A303V mutation in PROS1 might be an independent risk factor for DVT, which could provide helpful insight into the pathogenesis of DVT.
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    The Effect of Sex-Specific Genetic Factors on the Host Immune Response to COVID-19: A Pilot Study
    (Erciyes Univ Sch Medicine, 2022) Bali, Dilara Fatma Akin; Gulen, Tugba Arslan; Ozmen, Esma; Yuce, Zeynep Ture; Yildiz, Orhan; Turunc, Tuba; Kayabas, Uner
    Objective: The aim of this study was to investigate the impact of sex-specific genetic factors in the pathogenesis and prog-nosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2)-induced macrophage activation syndrome (MAS), independent of age and comorbidity presence.Materials and Methods: Patients aged 18-50 years who had been diagnosed with coronavirus 2019 (COVID-19), the disease caused by the SARS-CoV2 virus, were enrolled in a prospective, case-control, multi-center study. Genetic alterations and messenger RNA (m-RNA) expression levels of the TLR7, TLR8, ACE2, CD40L, CXCR3, and TASL genes were determined using DNA sequencing analysis, and gene expression was determined using quantitative reverse transcriptase polymerase chain reaction testing. PolyPhen-2 (Polymorphism Phenotyping v2; Adzhubei et al., 2010) and SNAP2 (Rostlab, Munich, Germany) genetic analysis tools were used to define the pathogenic effects of detected mutations by sequencing the selected genes in hotspot regions.Results: The study group consisted of 80 patients diagnosed with COVID-19 and was divided into groups based on sex and MAS status. Twenty-nine mutations were detected in 6 genes. Among the alterations, 15 were identified in this study for the first time and 9 were pathogenic. Pathogenic missense mutations in the TLR7, TLR8, ACE2, and TASL genes were detected in the MAS (+) group. In males, decreased TLR7, TLR8, and CXCR3 expression was statistically significant in the MAS (+) group (p<0.050). CXCR3 expression was lower in the female and male MAS (+) groups compared with the MAS (-) groups (p<0.050).Conclusion: In the absence of major risk factors for COVID-19, the TLR7/8, ACE2, and CXCR3 variants and decreased m-RNA expression levels associated with genetic susceptibility may be independent prognostic risk factors for COVID-19.