TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs(Galenos Publ House, 2025-01-02) Duran, Gizem Ayna; Duran, Assist. Prof. Dr. Gizem AynaObjective: The prevalence of breast cancer and gynaecological cancers is high, and these cancer types can occur consecutively as secondary cancers. The aim of our study is to determine the genes commonly expressed in these cancers and to identify the common hub genes and drug components. Materials and Methods: Gene intensity values of breast cancer, gynaecological cancers such as cervical, ovarian and endometrial cancers were used from the Gene Expression Omnibus database Affymetrix Human Genome U133 Plus 2.0 Array project. Using the linear modelling method included in the R LIMMA package, genes that differ between healthy individuals and cancer patients were identified. Hub genes were determined using cytoHubba in Cytoscape program. “ShinyGo 0.80” tool was used to determine the disease-specific biological KEGG pathways. Drug.MATADOR from the ShinyGo 0.80 tool was used to predict drug-target relationships. Results: The RecQ Like Helicase 4 and Family with Sequence Similarity 13 Member C genes were found to be similarly expressed in breast cancer and gynaecological cancers. Upon KEGG pathway analyses with hub genes, Drug.MATADOR analysis with hub genes related to cancer related pathways was performed. We have determined these gene/drug interactions: NBN (targeted by Hydroxyurea), EP300 (targeted by Acetylcarnitine) and MAPK14 (targeted by Salicylate and Dibutyryl cyclic AMP). Conclusion: The drugs associated with hub genes determined in our study are not routinely used in cancer treatment. Our study offers the opportunity to identify the target genes of drugs used in breast and gynaecological cancers with the drug repurposing approach.Article Citation - WoS: 2Differences in the Differential Expression of Micrornas Between Patients With Familial Multiple Sclerosis and Those With Sporadic Multiple Sclerosis(Galenos Publ House, 2023-12-28) Güllüoğlu, Halil; Uysal, Hasan Armağan; Poyraz, Turan; Altun, Zekiye; Kaya, Derya; Özcelik, Pınar; İdiman, Egemen; Poyraz, TuranObjective: Multiple sclerosis (MS) is a heterogeneous disease with clinical and immunological features. Most MS cases occur sporadically, but a considerable proportion of patients have a family history of MS. The etiology and pathophysiology of MS remain unclear. Recent epidemiological and gene expression studies have indicated that dysregulation of microRNAs (miRNAs) may play a role in MS pathogenesis. This study aimed to evaluate the differential expression of miRNAs in sporadic MS (sMS) and familial MS Materials and Methods: This cross-section, single-center study was conducted in 20 FMS and 10 sMS patients and 8 healthy controls. The patients were in the remission. In total, 2,549 miRNA genes were screened in the blood mononuclear cells from the whole blood samples of MS patients depending on miRBase 21. Differential expression of miRNAs in MS patients was identified compared with the control group, and miRNAs with a fold change >= 2 were validated using reverse transcription-polymerase chain reaction. Differentially expressed miRNAs were then compared between FMS and sMS patients. Results: Initial findings showed that miR-5100 and hsa-miR-16-2-3p were increased and miR-432-3p was decreased in FMS compared with sMS, whereas miR-548-aa, hsa-miR-142-3p, and miR-451-b were increased in both sMS and FMS, but miR-548-v was increased only in sMS. Some miRNAs showed the same expression patterns in both groups. Conclusion: Differential expression of certain miRNAs may be a useful biomarker in the diagnosis of MS. This study showed that miRNAs may discriminate between FMS and sMS cases and MS subtypes, as indicated in earlier studies.Article New Lymph Node Parameters and a Comparison With the American Joint Committee on Cancer N-Stages in Breast Cancer(Galenos Publ House, 2023-08-01) Eliyatkin, Nuket Ozkavruk; Başkır, İnci; İşlek, Akif; Zengel, BahaBACKGROUND/AIMS: The N-stage of TNM systems considers only the number of metastatic lymph nodes (NMLN) in breast cancer (BC). However, new lymph node parameters refer to the number of harvested lymph nodes (NHLN) and negative lymph nodes (NNLN), which have had an increasing significance in the current literature. This study aimed to compare NHLN, NNLN, lymph node ratio (LNR), modified lymph node ratio (mLNR), and log odds of positive lymph nodes (LODDS) against the standard American Joint Committee on Cancer (AJCC) N-stage for the prognosis of BC patients. MATERIALS AND METHODS: This study was designed retrospectively. The socio-demographic data, clinical features, histopathological factors, treatment modalities, receptor status of BC, and lymph node related parameters (AJCC N, LNR, mLNR, LODDS) were identified. Then, lymph node related parameters were compared for cancer-related mortality (CRM), cancer recurrence, disease-free survival (DFS), and overall survival (OS). RESULTS: Eight hundred seven women who underwent surgery for BC were included in this study according to its eligibility criteria. The mean follow-up period was 113.34±74.85 (range: 6-378) months. The NHLN was 21.24±9.22, the NMLN was 4.85±7.38, the NNLN was 16.39±9.48, the LNR was 0.23±0.29, the mLNR was 5.38±7.38 and the LODDS was -0.74±0.80 on average. During the follow-up period, 42 (5.2%) patients had local recurrence, 188 (23.3%) had distant metastases, and 252 (31.2%) patients died due to BC. NMLN, LNR, mLNR, and LODDS were found to be significantly higher, and NNLN was significantly lower in those patients with cancer recurrence and CRM (p<0.001). AJCC N-stages, and also LNR, mLNR, and LODDS groups according to the calculated cut-off values, were significant for DFS and OS according to survival analysis. In Cox regression analysis, only LODDS was a significant independent risk factor for OS [p=0.014, heart rate (HR)=3.78, 95% confidence interval (CI) for HR: 1.30-10.94)]. CONCLUSION: The results indicated that LODDS was more successful compared to other lymph node staging systems, especially for OS. However, randomized prospective controlled studies with larger samples and homogeneous study groups are needed to create standard classification systems as alternatives to AJCC N.