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    HRM method for identification of TP53 exon 5 and 8 mutations in human prostate cancer patients
    (Elsevier, 2022) Özmerdiven, Çağdaş Gökhun; Dirican, Ebubekir; Ayan, Semih; Tatar, Zeynep; Çakır, Sami; Güler, Yavuz; Karadağ, Abdullah; Soydaş, Tuğba; Karabulut Uzunçakmak, Sevgi; Aru, Melek; Kanigur, Gönül; İlvan, Ahmet
    Background: The purpose of the present study was to perform a high-resolution melting (HRM) analysis to discover mutations in gene exons 5-8 of tumor protein p53 (TP53), as well as the relationships of these mutations to clinical parameters in prostate cancer (PC).& nbsp;Methods: Genomic DNA was extracted from 50 formalin-fixed paraffin-embedded (FFPE) tissues with PC. Mutations in exons 5 and 8 of TP53 were analyzed using the HRM method. Sanger sequencing was used to describe mutations.& nbsp;Results: According to the HRM analysis results, 21 (42%) PC samples had different normalized and shifted melting curves from other samples. Mutations in TP53 exons 5 and8 were observed in 12 (24%) patients by the Sanger method. The detection sensitivity of the HRM method in exon 5 and exon 8 mutations was 66.7% and 50%, respectively. PSA levels of PC patients with TP53 mutation were found to be lower than that of patients with no mutation (p = 0.8270). However, we did not find any correlations between TP53 mutations and clinical parameters (p > 0.05).& nbsp;Conclusions: HRM analysis is a simple, rapid, and efficient mutation-scanning method for known/unknown mutations in TP53 exons 5and8, as well as an attractive method for detection of mutations and their analysis in FFPE tissues. Additional studies with larger patient populations are warranted to confirm the correlation between the TP53 mutations and PC risk.
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    Investigating associations between hla-dr genotype, h. pylori infection, and anti-caga iga seropositivity in a turkish gastritis cohort
    (2024) Karataş, Lokman; Tatar, Zeynep; James, Eddie A.; Çolakoğulları, Mukaddes
    Helicobacter pylori (H. pylori) is associated with gastric inflammation and mucosal antibodies against its cytotoxin-associated gene A (CagA) are protective. Vaccine-elicited immunity against H. pylori requires MHC class II expression, indicating that CD4+ T cells are protective. We hypothesized that the HLA-DR genotypes in human populations include protective alleles that more effectively bind immunogenic CagA peptide fragments and susceptible alleles with an impaired capacity to present CagA peptides. We recruited patients (n = 170) admitted for gastroendoscopy procedures and performed high-resolution HLA-DRB1 typing. Serum anti-CagA IgA levels were analyzed by ELISA (23.2% positive) and H. pylori classified as positive or negative in gastric mucosal tissue slides (72.9% positive). Pearson Chi-square analysis revealed that H. pylori infection was significantly increased in DRB1*11:04-positive individuals (p = 0.027). Anti-CagA IgA was significantly decreased in DRB1*11:04 positive individuals (p = 0.041). In contrast, anti-CagA IgA was significantly increased in DRB1*03:01 positive individuals (p = 0.030). For these HLA-DRB1 alleles of interest, we utilized two in silico prediction methods to compare their capacity to present CagA peptides. Both methods predicted increased numbers of peptides for DRB1*03:01 than DRB1*11:04. In addition, both alleles preferred distinctively different CagA 15mer peptide sequences for high affinity binding. These observations suggest that DRB1*11:04 is a susceptible genotype with impaired CagA immunity, whereas DRB1*03:01 is a protective genotype that promotes enhanced CagA immunity.