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    Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer
    (Springer, 2024) Acar, Ceren; Celik, Sibel Kucukyildirim; Ozdemirel, H. Ozgur; Tuncdemir, Beril Erdem; Alan, Saadet; Mergen, Hatice
    The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.
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    Investigation of Fibrillar Aggregates Formed by Pathogenic Pre-pro-vasopressin Mutants that Cause ADNDI
    (Endocrine Soc, 2025) Vaizoglu, Refika Dilara; Erdem, Beril; Gul, Mehmet; Acar, Ceren; Ozdemirel, Huseyin Ozgur; Ozer, Emel Saglar; Mergen, Hatice
    Context: Aggregations of unfolded or misfolded proteins, both inside and outside cells, are implicated in numerous diseases, collectively known as amyloidosis. Particularly, autosomal dominant neurohypophyseal diabetes insipidus (ADNDI) is a rare disease caused by mutations in the AVPNPII gene, leading to the inability to secrete arginine vasopressin. These misfolded proteins accumulate within the endoplasmic reticulum (ER), causing cellular dysfunction. Objective: This study aimed to investigate the formation of amyloid-like aggregates within the cell resulting from misfolded mutant precursor proteins, which induce disulfide-linked oligomers due to the G45C, 207_209delGGC, G88V, C98X, C104F, E108D-1, E108D-2 and R122H mutations identified by our group in the AVP-NPII gene of ADNDI patients. Methods: Deglycosylation studies were performed to analyze the glycosylation patterns of mutant protein precursors. The involvement of these precursors in the ER-related degradation pathway was studied by conducting protease inhibition experiments. Disulfide-linked oligomer analysis determined the oligomerization status of the mutant precursors. Immunofluorescence and electron microscopy studies provided evidence of aggregate structures in the ER lumen. In vitro studies involved bacterial expression and fibril formation in Escherichia coli (E. coli). Results: Our findings demonstrated that the N-glycan structure of mutant precursors remains intact within the ER. Protease inhibition experiments indicated the involvement of these precursors in the ER-related degradation pathway. Disulfide-linked oligomer analysis revealed homo-oligomer structures in mutations. Immunofluorescence and electron microscopy studies confirmed the presence of aggregate structures in the ER lumen. In vitro studies showed that mutant precursors could form fibril structures in E. coli. Conclusion: Our study may support the idea that ADNDI belongs to the group of neurodegenerative diseases due to the formation of fibrillar amyloid aggregates in the cell.
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    Lipoid proteinosis and epilepsy: Molecular analysis
    (2019) Tecellioğlu, Mehmet; Kamışlı, Özden; Acar, Ceren; Mergen, Hatice; Sözen, Mustafa Mert; Karaduman, Tuğçe; Saraç, Gülbahar; Erbay, Mehmet Fatih
    Abstract: Aim: Lipoid proteinosis (LP) is also known as Urbach-Wiethe disease which is a rare autosomal recessive disorder characterized by intracellular accumulation of hyaline material in skin and mucosae. LP has typical neurological, dermatological and radiological findings. The pathogenesis of disease is unknown. In literature several cases have been reported up to date. Mutations in extracellular matrix protein 1 (ECM1) gene have been found to cause the disease. We evaluated the molecular features of a family diagnosed with LP and evaluate the known and novel mutations of LP. Material and Methods: Genomic DNA was extracted from peripheral blood of the patients and family members including clinically normal parents and two siblings of the two affected subjects by using a commercial DNA extraction kit. Polymerase chain reaction was performed for all 10 exons of ECM1 gene by using the primers defined. Results: All of the exons of the ECM1 gene were sequenced and this revealed a 2-bp deletion in exon 7 of the ECM1 gene in both patients and both parents. Patients have the homozygous 2-bp deletions (c735del TG) and the parents and two healthy siblings showed heterozygous 2-bp deletion. Conclusions: Our patients found to be homozygous for the deletion in ECM1 gene. In order to understand the molecular pathology of the disease in detail, further functional analysis of the mutations should be performed.