Evaluation of the role of Nrf2/Keap1 pathway-associated novel mutations and gene expression on antioxidant status in patients with deep vein thrombosis.

Deep vein thrombosis (DVT) is a type of venous thromboembolism and a clinically complex vascular disease. Oxidative stress serves a key role in the pathogenesis of numerous cardiovascular diseases, particularly in endothelial dysfunction-associated syndromes. Nuclear factor erythroid-2-like 2(Nrf2) transcription factor is the primary regulator of antioxidant responses. The levels of reactive oxygen species (ROS) are regulated by Nrf2 and its suppressor protein Kelch-like ECH-associated protein 1 (Keap1). However, to the best of our knowledge, genetic abnormalites in the Nrf2/Keap1 pathway in DVT syndrome have not been thoroughly investigated. The aim of the present study was to investigate the association between the Nrf2/Keap1 pathway and antioxidant responses in DVT. Mutations and expression levels of genes involved in the Nrf2/Keap1 pathway were measured in 27 patients with DVT via DNA sequencing analysis and reverse transcription-quantitative PCR, respectively. The Polymorphism Phenotyping v2 program was used to identify the pathogenic mutations. Total antioxidant activity levels were determined by measuring the effect of serum samples from 27 patients with DVT on oxidation of the 2,2'-azino-bis (3-ethylbenz-thiazoline-6-sulfonic acid) system. A total of 23 mutations, including seven novel mutations, were detected in the Nrf2/Keap1 pathway in 24 (89%) of the 27 patients with DVT. Keap1 mRNA expression levels were significantly higher compared with Nrf2 expression levels in patients with DVT (P=0.02). Analysis of molecular characteristics and gene expression levels demonstrated that Nrf2/Keap1-associated mutations and total antioxidant levels can be used as precursor markers in the diagnosis of DVT.

Identification of novel Nrf2/Keap1 pathway mutations in pediatric acute lymphoblastic leukemia.

Acute lymphoblastic leukemia (ALL) is a malignancy of lymphoid progenitor cells, characterized by a wide range of biological and clinical heterogeneity. Oxidative stress is a common problem observed in carcinogenesis and it is involved in developing treatment resistance. Nuclear Factor Erythroid-2-Like 2 (Nrf2) transcription factor is the main regulator of antioxidant responses. The levels of reactive oxygen species (ROS) are tightly controlled and regulated by Nrf2 and its suppressor protein Kelch-like ECH-associated protein 1 (Keap1). Recently, many studies have shown that most of the genes in the Nrf2/Keap1/nuclear factor kappa-B (NF-κB)/phosphotyrosine-independent ligand for the Lck SH2 domain Of 62 KDa (p62) pathway show abnormally high mutational variations in cancer. However, variations in the Nrf2/Keap1/NF-κB1/p62 pathway in pediatric ALL have not been thoroughly investigated, yet. Thirty children, who were diagnosed with pediatirc ALL were included in the study. The Nrf2/Keap1/NF-κB1/p62 pathway variants were analyzed by DNA sequencing analysis. The PolyPhen-2 program was used for identifying pathogenic mutations. Our study examined the molecular dynamics (MD) perspectives of the effect of A159T and E121K mutations on protein stability for the first time in the literature by using the GROMACS45 software package utilizing the OPSLAA force field. Of the detected 17 nucleotide changes, 6 were novel. The study predicted the potential pathological effect of two mutations p. A159T and p.E121K in the Keap1 gene. The MD perspectives revealed that the E121K mutant's observed structural behavior accounted for the key role of His-129 and E121K, where E121K exhibited much higher drift compared to His-129. For a future perspective, it would be meaningful to study the protein-small molecule interactions of the Keap1 protein to elaborate on the drug effects in patients carrying these mutations.

Determination of genetic variations in the genus Dryomys Thomas, 1906 (Rodentia: Gliridae) distributed in Turkey using NADH dehydrogenase 1 (ND1) gene.

Genetic diversity and phylogeny of Dryomys nitedula and Dryomys laniger from Turkey was described in the present study by using mitochondrial DNA NADH dehydrogenase 1 gene (ND1). Genetic variation in ND1 gene was determined by two model-based phylogenetic analyses and a network analysis revealed 27 haplotypes of D. nitedula constructing four main lineages (Thrace, Anatolia, North-eastern Anatolia and Savsat) that have non-overlapping geographic distributions and no shared haplotypes, but on the other hand, three haplotypes were detected in four samples of D. laniger from Turkey. It was determined that nucleotide diversity was low but haplotype diversity was high in D. laniger, whereas, D. nitedula has both high level of haplotype and nucleotide diversity. Characterization of Thrace lineage of D. nitedula with low nucleotide diversity and determination of the total nucleotide diversity of Anatolian lineages (Anatolia + North-eastern Anatolia+Savsat) to be approximately four times higher than that of Thrace lineage indicated that Anatolia may have served as a refuge for D. nitedula. Divergence times and high level of nucleotide differences between D. nitedula lineages showed that diversification of the lineages may have occurred before and during ice ages in Turkey, thought to be a refuge for post-glacial colonization and biodiversity resource of Europe. Additionally, estimated divergence times and calculated genetic distances yielded compatible results with the previous paleontological and genomic data for the diversification time of two species in the genus.

Genetic variations of Turkish bank vole, Myodes glareolus (Mammalia: Rodentia) inferred from mtDNA.

The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kizilirmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations.