Turkish journal of biology = Turk biyoloji dergisi最新文献

Type 2 diabetes mellitus (T2D) constitutes 90% of the diabetes cases, and it is a complex multifactorial disease. In the last decade, genome-wide association studies (GWASs) for T2D successfully pinpointed the genetic variants (typically single nucleotide polymorphisms, SNPs) that associate with disease risk. In order to diminish the burden of multiple testing in GWAS, researchers attempted to evaluate the collective effects of interesting variants. In this regard, pathway-based analyses of GWAS became popular to discover novel multigenic functional associations. Still, to reveal the unaccounted 85 to 90% of T2D variation, which lies hidden in GWAS datasets, new post-GWAS strategies need to be developed. In this respect, here we reanalyze three metaanalysis data of GWAS in T2D, using the methodology that we have developed to identify disease-associated pathways by combining nominally significant evidence of genetic association with the known biochemical pathways, protein-protein interaction (PPI) networks, and the functional information of selected SNPs. In this research effort, to enlighten the molecular mechanisms underlying T2D development and progress, we integrated different in silico approaches that proceed in top-down manner and bottom-up manner, and presented a comprehensive analysis at protein subnetwork, pathway, and pathway subnetwork levels. Using the mutual information based on the shared genes, the identified protein subnetworks and the affected pathways of each dataset were compared. While most of the identified pathways recapitulate the pathophysiology of T2D, our results show that incorporating SNP functional properties, PPI networks into GWAS can dissect leading molecular pathways, and it could offer improvement over traditional enrichment strategies.

The effects of 5,10-Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism on human bone marrow-derived mesenchymal stem cells (hBM-MSCs) viability, morphology, physiology and differentiation capacity were investigated in this study. For this purpose, primary hBM-MSCs with wild type (WT, C/C), heterozygote (HTZ, C/T) and homozygote (HMZ, T/T) for the MTHFR gene were obtained with ethical committee permission and donor informed. Mutations were detected using RFLP and Sanger sequencing methods from genomic DNA isolated from cells, colonization properties were investigated by CFU-F test and proliferative differences were investigated by MTT test. Adipogenic, osteogenic, and chondrogenic differentiation were induced to study changes in their differentiation potentials, and the results were statistically analyzed using one-way ANOVA with Graphpad Prism. A total of 13 donors were screened and there were no differences in the hBM-MSC markers and in vitro morphologies of the cells. While there were significant differences between WT and HTZ as a result of the CFU-F test, there were no significant differences in the MTT test after 24 and 48 h. As a result of differentiation tests, it was found that adipogenic differentiation was significantly more in HMZ cells than WT cells. Osteogenic and chondrogenic differentiation results did not give statistically significant results. As a result of these experiments, adipogenic differentiation was found to be affected by the MTHFR genotype in hBM-MSCs.

Chitosan has high biocompatibility, supports proliferation of many cells, and can be a good carrier for various growth factors. However, low attachment ratio and spheroid formation of several stem cell types on plain chitosan scaffolds/films is still a problem. In this study, it was aimed to obtain 3D scaffolds using medical grade chitosan (MC) with a high deacetylation degree (DD ≥ 92.6%) to overcome the spheroid formation of rat adipose tissue derived mesenchymal stem cells (rAdMSCs) on control chitosan (C, DD = 75%-85%) scaffolds. Genipin was used as a biological chemical crosslinker, and glycerol phosphate salt was used both as a pH adjusting agent and physical crosslinker. MTT and SEM analyses and live/dead staining indicated the increase in the attachment, cell viability, and proliferation of rAdMSCs on MC scaffolds with or without crosslinking when compared to the cells in spheroid formation on control scaffolds. Moreover, filamentous actin protein organization of rAdMSCs was found to be triggered on the crosslinked MC scaffolds. In conclusion, plain medical grade chitosan scaffolds with or without crosslinking prevented spheroid formation, supported the attachment, proliferation, and organization of rAdMSCs indicating that medical grade type of chitosan scaffolds with high DD can be a very good candidate as 3D carriers in stem cell cultivation.

Majority of 37 human aminoacyl tRNA synthetases have been incriminated in diverse, mostly recessive, genetic diseases. In accordance with this, we uncovered a novel homozygous valyl-tRNA synthetase 1 (VARS1) gene variant, leading to p.T1068M mutation. As in the previously reported VARS1 mutations, the affected individual harboring p.T1068M was experiencing a neurodevelopmental disorder with intractable seizures, psychomotor retardation, and microcephaly. To link this phenotypic outcome with the observed genotype, we structurally modeled human VARS1 and interpreted p.T1068M within the spatial distribution of previously reported VARS1 variants. As a result, we uncovered that p.T1068M is clustered with three other pathogenic mutations in a 15 amino acid long stretch of the VARS1 anticodon-binding domain. While forming a helix-turn-helix motif within the anticodon-binding domain, this stretch harbors one-fourth of the reported VARS1 mutations. Here, we propose that these clustered mutations can destabilize the interactions between the anticodon-binding and the tRNA synthetase domains and thus hindering the optimal enzymatic activity of VARS1. We expect that the depiction of this mutation cluster will pave the way for the development of drugs, capable of alleviating the functional impact of these mutations.

Embryonic stem cells (ESCs), which are derived from the undifferentiated inner cell mass of the embryo, can differentiate every cell type of the body regarding their pluripotency. Therefore, human or mouse ESCs can be used as an unlimited cell source for numerous researches or therapeutical approaches. However, pluripotency maintenance of ESCs during in vitro culture is challenging because of their endless differentiation capacity. In the current study, the effect of USP7 on pluripotency maintenance of mouse ESCs (mESCs) has been investigated with the help of cell viability assay, morphological analysis, alkaline phosphatase (ALP) staining, qPCR analysis, and Western Blotting. 600 nM P5091 application, which showed no significant toxicity in mESCs, increased the total ubiquitinated protein amount as a proof of the accomplishment of proper USP7 inhibition. Morphological analysis and ALP activity evaluation indicated that dual inhibition of GSK3 and MEK together with leukemia inhibitory factor (LIF) treatment protects the pluripotency in presence of active USP7 enzyme. Yet, inactivation of USP7 reduced the ALP activity and altered the cell morphology in each treatment group. This morphological change and decreased ALP activity refer to differentiated mESCs. These findings were supported by gene expression and protein analysis. Gene expressions and protein amounts of pluripotency related Oct4, Nanog, c-Myc, Sox2 and Klf4 transcription factors decreased significantly after USP7 inhibition. Together with this observation, a remarkable reduction in β-Catenin expression was also noticed. It was also observed that USP7 inactivation shortens the half-live of β-Catenin and GSK3β proteins. This study demonstrates that USP7 activation is crucial for proper pluripotency maintenance, which is provided through β-Catenin stabilization.

BEX family genes are expressed in various tissues and play significant roles in neuronal development. A mouse model of Bex3 gene knock-out was generated in this study, using the CRISPR-Cas9 system. Transcriptomic analysis of the brain was performed to identify genes and pathways under Bex3 regulation. Essential biological functions under the control of Bex3 related to brain development were identified. Ninety-five genes were differentially expressed under Bex3^-/- regulation, with 53 down and 42 up. Among down-regulated genes, LOC102633156 is a member of zf-C2H2, Xlr3a is an X-linked lymphocyte regulated gene, LOC101056144 is a hippocampal related gene, 2210418O10Rik and Fam205a3 are cortex related genes. Among the upregulated genes, Zfp967 is a zf protein, Tgtp2 is a T cell-specific regulator, Trpc2 is a neuron-related gene, and Evi2 is related to NF1. A total of 34 KEGG disease terms were identified under the Bex3^-/- regulation. The most prominent is non-syndromic X-linked mental retardation, where Fgd1 is enriched. Similarly, IRF, MBD, SAND, zf-BED, and zf-C2H2 were significantly enriched transcription factors. A further study is required to confirm and explain each aspect that has been identified in this study.

Cervical cancer (CxCa) is preventable and treatable via vaccination and screening. Cervicovaginal fluid (CVF) represents the physiological components of the female genital tract. These components are suitable to be utilized for clinical purposes, therefore, making CVF a suitable material for disease screening approaches. Due to high false-negative result rates and low attendance of current expensive routine CxCa screening methods, it has become more important to develop a point-of-care (POC) screening method that every single woman could reach worldwide. For this purpose, various self-usage apparatus have been developed for screening of the human papilloma virus (HPV) infection. Furthermore, due to the low specificity of HPV tests and the high clearance rate of HPV infections, many patients undergo overtreatment. Since proteins play an important role in cellular process and carcinogenesis, it is appropriate to use proteins in a simple screening test for the detection of carcinogenesis. In this article, POC screening tests and the studies of discovery of CVF protein biomarkers will be overviewed to consider the development of a method that can be used for the rapid and conceivable screening method of CxCa.

Acute lung injury (ALI) is an inflammation of the lungs with high incidence rate and mortality. Ferroptosis is a new cell death, which has influence in body organs. Transient receptor potential vanillin-4 (TRPV4) channel is a key mediator of Ca²⁺, its activation induces ferroptosis. The purpose of the study is to investigate the function of TRPV4 on ferroptosis in ALI mice induced by lipopolysaccharide (LPS). In vitro, the regulation of TRPV4 on Ca²⁺ and ferroptosis was detected by CCK-8, fluorescent probe, and western blot in BEAS-2B cells. In vivo, the role of TRPV4 antagonists on ALI mice was analyzed by determination of pulmonary inflammation, pulmonary edema, and ferroptosis. In vitro, ferroptosis was induced in ALI. TRPV4 expression and intracellular Ca²⁺ concentration were up-regulated in ALI, and TRPV4 antagonist suppressed LPS-induced ferroptosis in BEAS-2B cells, including decreased MDA and ROS levels, increased GPX4 protein level and cell viability. In vivo, ALI mice showed activated ferroptosis compared with the control group, and administration of TRPV4 inhibition had protective effects on ALI mice, including improving lung pathological characteristics, and reducing the degree of pulmonary edema, inflammation, and ferroptosis. The results manifested that ferroptosis mediated lung injury in LPS-induced ALI, and TRPV4 antagonists might moderate LPS-induced damage by suppressing ferroptosis.

Stimulator of interferon genes (STING) plays a significant role in a cell's intracellular defense against pathogens or self-DNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the C-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally. STING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a closed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1 (TBK1). TBK1 then phosphorylates STING aiding its entry to the cell's nucleus. In this study, we focused on the loop modeling of the CTT domain in both the active and inactive STING conformations. After the modeling step, the active and inactive STING structures were docked to one of the cGAS-cGAMP-STING pathway members, TBK1, to observe the differences of binding modes. CTT loop stayed higher in the active structure, while all the best-scored models, active or inactive, ended up around the same position with respect to TBK1. However, when the STING poses are compared with the cryo-EM image of the complex structure, the models in the active structure chain B displayed closer results to the complex structure.

Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.