Browsing by Author "Karadeniz, Sedat"

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Citation - WoS: 1
The association of HLA-DRB1 alleles and MBL2 gene variant in pediatric acute lymphoblastic leukemia patients
(Elsevier, 2024) Oguz, Rustu; Ciftci, Hayriye Senturk; Gokce, Muge; Ogret, Yeliz; Karadeniz, Sedat; Pehlivan, Sacide; Ayd, Filiz
Introduction: Epidemio logic studies on pediatric acute lymphoblastic leukemias (ALL) have been conducted to evaluate the possible risk factors including genetic, infectious and environmental factors with the objective of idenfying the etiology. Mannose-binding lectin 2 (MBL2) plays an important role in first-line immune defense. HLA DRB1 alleles play a role in presentation of peptides to T cells and in activation of the adaptive immune response. Objective: In our study, we aimed to investigate both the MBL2 gene variant and HLA-DRB1 alleles in pediatric ALL patients. Materials: In this study, 86 high-risk ALL patients and 100 controls were included. Polymerase Chain Reaction (PCR)-Restriction Fragment Length Polymorphism (PCR-RFLP) and PCRsequence specific primer (SSP) methods were used for detection of polymorphism of the MBL2 and HLA-DRB1 alleles, respectively. Results: The frequency of the MBL2 AB genotype was lower in female ALL patients, compared to male ALL patients (p = 0.034). An association was found between the MBL2 BB genotype and DRB1*07 and among patients with the MBL2 BB genotype; those who also carried the DRB1*07 and *04 alleles were significantly higher than those without the DRB1*07 and *04 alleles. (p = 0.048, p = 0.022, respectively). Conclusion: This is the first study suggesting that the MBL2 BB genotype in association with the DRB1*07 or co-inheritance of the HLA-DRB1*04 and HLA DRB1*07 may have an impact on the etiopathogenesis of the disease. (c) 2023 Associa & ccedil;& atilde;o Brasileira de Hematologia, Hemoterapia e Terapia Celular. Published by Elsevier Espa & ntilde;a, S.L.U. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Citation - WoS: 0
Citation - Scopus: 0
Investigation of the Potential Effect of Complement 5 on Transplantation Outcome by Bioinformatics Tools
(Iranian Soc Nephrolgy, 2025) Oguz, Suleyman Rustu; Kivanc, Demet; Ozdilli, Kursat; Karadeniz, Sedat; Kluge, Ekin Ece Gurer; Ciftci, Hayriye Senturk
Introduction. Activation of the complement system following transplantation may result in allograft rejection. Our study aimed to evaluate the potential relationship between factors affecting kidney transplant success and complement 5 (C5) using bioinformatic tools. Methods. GenCards and Genemania were used to provide the genetic functional information belonging to the C5 gene, and genomic browsers of STRING, UCSC, KEGG were used to reveal interactions with other genes and various pathways. MiRDB was used to specify the miRNAs that were associated with the C5 gene. The UniProt database was used to determine the tissues that expressed the C5 gene using protein-protein interactions. Results. In the bioinformatic analyses performed, high levels of C5 gene expression were found in the naiive kidney. Twenty-five genes were found to be strongly associated with C5. Fifty-four miRNAs targeting the C5 gene were specified. The C5 gene was found to be involved in biologic processes such as complement activation (FDR = 6.46e-22), complement binding (FDR = 2.20e-06), cytolysis (FDR = 4.82e-14), regulation of complement activation (FDR = 4.08e24), positive regulation of vascular endothelial growth factor production (FDR = 0.0430), regulation of macrophage chemotaxis (FDR = 0.0447), activation of the immune response (FDR = 1.26e13), leukocyte-mediated immunity (FDR = 1.41e-09), innate immune response (FDR = 3.05e-09), allograft rejection (FDR = 2.40e-12), oxidative injury response (FDR = 0.00016), and trigerring of the beginning of the complement cascade (FDR = 0.0244). Conclusions. The data obtained in this study will be used to guide future experimental investigations in the field of transplantation, and these data will give physicians with insight into allograft status following transplantation.
Citation - WoS: 0
Uncommon Hla Alleles Observed in a Population of Istanbul Province
(Pera Yayincilik Hizmetleri, 2024) Ogret, Yeliz Duvarcı; Oguz, Rustu; Karadeniz, Sedat; Cıftcı, Hayriye Senturk; Kıvanc, Demet; Kıvanc, Demet; Oguz, Fatma Savran
Objective: New polymorphisms are formed in human leucocyte antigen (HLA) genes with point mutations, gene conversions, and duplication, and the diversity continues to increase. Various new HLA alleles have significant roles in transplantation, and epidemiologic and population studies. The aim of our study was to determine the status of HLA alleles in the Turkish population, which is uncommon, well-defined, and non-defined in the world population according to the international ImMunoGeneTics information system® (IMGT) database. Methods: We performed HLA-A, -B, -C, -DQB1, and DRB1 loci at the four-field resolution level, using Sanger- sequence-based typing (SBT) for 5592 healthy, unrelated bone marrow donor volunteers from Istanbul Province. The uncommon alleles were also confirmed using high-throughput next-generation sequencing (NGS). Results: Uncommon alleles were determined at five loci as follows: HLA-A*01:155, 02:66, 02:90, 02:110, 02:343, 03:82, 24:28, 24:146, 24:276, 24:356, 31:23,33:33, 68:38; HLA-B *07:240, 18:19, 35:193, 40:303, 51:69, 51:169; HLA-C*04:39, 06:40, 07:93, 12:149, 15:73; HLA-DRB1*11:149, 13:14:02 and HLA-DQB1*03:27. All alleles were arranged according to the common and well documented (CWD) 3.0.0 catalog. Conclusion: This is the first study to show uncommon alleles in our population. These reported data increase the knowledge of HLA polymorphisms in the Turkish population and provide a basis for further studies in population genetics. This information may also be useful in determining whether a matched, unrelated donor is unlikely to be found so that a mismatch strategy, an extended family search, or alternate therapy, can be pursued, thus saving time and cost for patients.