Hub genes, key miRNAs and interaction analyses in type 2 diabetes mellitus: an integrative in silico approach.

Diabetes is a rising global metabolic disorder and leads to long-term consequences. As a multifactorial disease, the gene-associated mechanisms are important to know. This study applied a bioinformatics approach to explore the molecular underpinning of type 2 diabetes mellitus through differential gene expression analysis. We used microarray datasets GSE16415 and GSE29226 to identify differentially expressed genes between type 2 diabetes and normal samples using R software. Following that, using the STRING database, the protein-protein interaction network was constructed and further analyzed by Cytoscape software. The EnrichR database was used for Gene Ontology and pathway enrichment analysis to explore key pathways and functional annotations of hub genes. We also used miRTarBase and TargetScan databases to predict miRNAs targeting hub genes. We identified 21 hub genes in type 2 diabetes, some showing more significant changes in the PPI network. Our results revealed that GLUL, SLC32A1, PC, MAPK10, MAPT, and POSTN genes are more important in the PPI network and can be experimentally investigated as therapeutic targets. Hsa-miR-492 and hsa-miR-16-5p are suggested for diagnosis and prognosis by targeting GLUL, SLC32A1, PC, MAPK10, and MAPT genes involved in the insulin signaling pathway. Insight: Type 2 diabetes, as a rising global and multifactorial disorder, is important to know the gene-associated mechanisms. In an integrative bioinformatics analysis, we integrated different finding datasets to put together and find valuable diagnostic and prognostic hub genes and miRNAs. In contrast, genes, RNAs, and enzymes interact systematically in pathways. Using multiple databases and software, we identified differential expression between hub genes of diabetes and normal samples. We explored different protein-protein interaction networks, gene ontology, key pathway analysis, and predicted miRNAs that target hub genes. This study reported 21 significant hub genes and some miRNAs in the insulin signaling pathway for innovative and potential diagnostic and therapeutic purposes.

In silico engineering and simulation of RNA interferences nanoplatforms for osteoporosis treating and bone healing promoting.

Osteoporosis is a bone condition characterized by reduced bone mineral density (BMD), poor bone microarchitecture/mineralization, and/or diminished bone strength. This asymptomatic disorder typically goes untreated until it presents as a low-trauma fracture of the hip, spine, proximal humerus, pelvis, and/or wrist, requiring surgery. Utilizing RNA interference (RNAi) may be accomplished in a number of ways, one of which is by the use of very tiny RNA molecules called microRNAs (miRNAs) and small interfering RNAs (siRNAs). Several kinds of antagomirs and siRNAs are now being developed to prevent the detrimental effects of miRNAs. The goal of this study is to find new antagonists for miRNAs and siRNAs that target multiple genes in order to reduce osteoporosis and promote bone repair. Also, choosing the optimum nanocarriers to deliver these RNAis appropriately to the body could lighten up the research road. In this context, we employed gene ontology analysis to search across multiple datasets. Following data analysis, a systems biology approach was used to process it. A molecular dynamics (MD) simulation was used to explore the possibility of incorporating the suggested siRNAs and miRNA antagonists into polymeric bioresponsive nanocarriers for delivery purposes. Among the three nanocarriers tested [polyethylene glycol (PEG), polyethylenimine (PEI), and PEG-PEI copolymer], MD simulations show that the integration of PEG-PEI with has-mIR-146a-5p is the most stable (total energy = -372.84 kJ/mol, Gyration radius = 2.1084 nm), whereas PEI is an appropriate delivery carrier for has-mIR-7155. The findings of the systems biology and MD simulations indicate that the proposed RNAis might be given through bioresponsive nanocarriers to accelerate bone repair and osteoporosis treatment.

Fabrication of Chitosan Silk-based Tracheal Scaffold Using Freeze-Casting Method

Background: Since the treatments of long tracheal lesions are associated with some limitations, tissue engineered trachea is considered as an alternative option. This study aimed at preparing a composite scaffold, based on natural and synthetic materials for tracheal tissue engineering. Methods: Nine chitosan silk-based scaffolds were fabricated using three freezing rates (0.5, 1, and 2°C/min) and glutaraldehyde (GA) concentrations (0, 0.4, and 0.8 wt%). Samples were characterized, and scaffolds having mechanical properties compatible with those of human trachea and proper biodegradability were selected for chondrocyte cell seeding and subsequent biological assessments. Results: The pore sizes were highly influenced by the freezing rate and varied from 135.3×372.1 to 37.8×83.4 µm. Swelling and biodegradability behaviors were more affected by GA rather than freezing rate. Tensile strength raised from 120 kPa to 350 kPa by an increment of freezing rate and GA concentration. In addition, marked stiffening was demonstrated by increasing elastic modulus from 1.5 MPa to 12.2 MPa. Samples having 1 and 2°C/min of freezing rate and 0.8 wt% GA concentration made a non-toxic, porous structure with tensile strength and elastic modulus in the range of human trachea, facilitating the chondrocyte proliferation. The results of 21-day cell culture indicated that glycosaminoglycans content was significantly higher for the rate of 2°C/min (12.04 µg/min) rather than the other (9.6 µg/min). Conclusion: A homogenous porous structure was created by freeze drying. This allows the fabrication of a chitosan silk scaffold cross-linked by GA for cartilage tissue regeneration with application in tracheal regeneration.

The association between single nucleotide polymorphism in interleukin-27 gene and recurrent pregnancy loss in Iranian women.

BACKGROUND: Recurrent pregnancy loss (RPL) has been defined as two or more miscarriages before 20(th) week of gestation. It seems that IL-27 may reduce inflammatory responses and affect the survival of the embryo during human pregnancy. IL-27 polymorphisms may influence RPL by altering the levels or the activity of gene product. OBJECTIVE: We studied for the first time the association of IL-27 -964 A>G single nucleotide polymorphism (SNP) with RPL in Iranian women. MATERIALS AND METHODS: A case-controlled study was performed on two groups consisting of 150 healthy women with at least one delivery (control group) and 150 women with two or more primary RPLs history (RPL group). The -964 A>G SNP in IL-27 gene was determined by PCR-RFLP technique. Genotype and allele frequencies were compared using (2) tests between two groups. RESULTS: There was no difference between the two groups regarding age of women (29±4.4 [control] vs. 30.84±5.2 years [case]). In the RPL group, the genotype frequencies of -964 A>G polymorphism were AG (49.3%), AA (40%), and GG (10.7%), and in the control group, they were AG (43.3%), AA (48.7%), and GG (8%). There was no significant difference between the genotypes of AA, AG, and GG in two groups (p=0.23). As the frequency of allele A was 64.7% in the RPL group and 70.3% in the control group, the difference in frequency of allele A in -964 A>G between two groups was not significant (p=0.19). CONCLUSION: Our findings indicate that SNP of -964 A>G in IL-27 gene is not a risk factor for RPL in Iranian women.