Introduction: IQ motif-containing GTPase-activating protein3 (IQGAP3) contributes to the progression of bladder urothelial carcinoma (BLCA), but its mechanisms are not systematically specified. Due to the oncogenic potential of IQGAP3, the current in-silico study intended to elucidate IQGAP3's role in BLCA progression. Materials and Methods: Many bioinformatics tools, including UALCAN, Kaplan–Meier plotter, TNMplot, cBioPortal, GeneMania, Enrichr, TIMER2, muTarget, and UCSC Xena, were applied in the current study. Results: The IQGAP3 level was more pronouncedly raised in BLCA tissues than in normal bladder tissues, and its increased expression was related to the advanced stage and higher grade. Enhanced IQGAP3 expression could result from its genetic alteration. Moreover, the mutation in P53 and RB1 genes was robustly associated with increased IQGAP3 expression. Besides, IQGAP3 correlative genes were dominantly involved in the cell cycle. On the other hand, IQGAP3 upregulation influenced immune checkpoint levels in the tumor microenvironment. Conclusion: The in-silico findings suggested that IQGAP3 overexpression could be a crucial biomarker in BLCA.

Background: Various mutations in factor VIII (F8) gene locus are led to an X-linked bleeding disorder in patients with hemophilia A. Oneof the leading causes of inefficient treatment available for hemophiliaAis the lack of specificandsensitive diagnostic procedure for the disease. The discovery of a functional role of microRNAs (miRNAs) in the pathogenesis of a wide range of human diseases makes them the potential, non-invasive, biomarker candidates for hemophilia A. Therefore, advances in computational tools for miRNA discovery leads to numerous recent publications on miRNAs as putative biomarkers. Objectives: The current study aimed at scanning the F8 gene region to predict novel miRNAs as regulators of the F8 gene. Methods: The potential of the FVIII locus to express new miRNAs was studied via reliable bioinformatics databases, such as SSCprofiler, RNAfold, miREval, miR-Find, FOMmiR, UCSC genome browser, and miRBase. Results: Data analysis from previously mentioned databases offered two stem-loop structures predicted to express novel miRNAs. Conclusions: The presented stem-loop structures can be used as powerful non-invasive biomarkers in early diagnosis of the disease and regulation of the factor VIII gene after subsequent experimental verification.

Background: Designing the primer pairs is one of the most important factors in the amplification and quantitative analysis of the nucleic acid sequences of interest. Using in silico methods, the present study intends to design highly specific primers for quantitative analysis of the genes with minimum expression. To achieve this aim, we selected two candidate genes with little expression, namely, G-protein coupled receptor 120 (GPR120) and peroxisome proliferator-activated receptor-γ (PPARγ), in peripheral blood leukocytes of healthy volunteers. Methods: Peripheral blood was collected from 30 healthy volunteers. Primers for GPR120 and PPARγ were designed using online websites (UCSC, OligoCalc, and OligoAnalyzer) and the primer designing tool (NCBI). Total RNA extraction and cDNA synthesis were done using commercially available kits based on manufacturer instructions. Finally, the melting curve analysis of GPR120 and PPARγ was assessed using the quantitative real-time PCR method. Results: The in silico gene expression investigation revealed that GPR120 and PPARγ have minimal leukocyte expression. Besides, the melting curves analysis for both genes in the studied individuals showed only one melting peak, confirming the specific amplification of the desired genes. Conclusion: Altogether, the study findings indicated that we could utilize the peripheral blood sample for assessing the gene expression and amplification of omega-3 fatty acids receptors, i. e. GPR120 and PPARγ as two candidate genes with very low expression in leukocytes.

Objective: Hemophilia-A is a common genetic abnormality resulted from decreased or lack of factor VIII (FVIII) pro-coagulant protein function caused by mutations in the F8 gene. Majority of molecular studies consider screening of mutations and their relevant impacts on the quality and expression levels of FVIII. Interestingly, some of the functions in FVIII suggest a probable involvement of small non-coding RNAs embedded within the sequence of F8 gene. Therefore, microRNAs which are encoded within the F8 gene might have a role in hemophilia development. In this study, miRNAs production in the F8 gene was investigated by bioinformatics prediction and experimental validation. Materials and Methods: In this experimental study, bioinformatics tools have been utilized to seek the novel microRNAs inserted within human F8 gene. The ability to express new microRNAs in F8 locus was studied through reliable bioinformatics databases such as SSCProfiler, RNA fold, miREval, miR-FIND, UCSC genome browser and miRBase. Then, expression and processing of the predicted microRNAs were examined based on bioinformatics methods, in the HEK293 cell lines. Results: We are unable to confirm existence of the considered mature microRNAs in the transfected cells. Conclusion: We hope that through changing experimental conditions, designing new primers or altering cell lines as well as the expression of vectors, exogenous and endogenous expressions of the predicted miRNA will be confirmed.

MicroRNAs are small non-coding RNAs that can regulate gene expression that affects various cellular processes. Krüppel-like factor 4 (KLF4) is a transcription factor that has different regulatory functions, and it plays a role in various cellular processes. This study aims to identify novel microRNAs in KLF4 gene using bioinformatics tools. This study significantly contributes to our understanding of the complex function of KLF4 and reveals additional layers of regulatory complexity that affect gene function and cellular dynamics. Advanced bioinformatics methods, including SSCprofiler website, were used to predict stem-loop structures in KLF4 gene, and MatureBayes website was used to predict the mature sequence of microRNAs, which indicate potential miRNA candidates. Using the RNAfold website, the stem-loop structure of microRNAs was determined. The UCSC database assessed the conservation status of these miRNAs and their precursors. From the results of bioinformatics analysis of KLF4 gene, three microRNAs were predicted. Websites and bioinformatics tools were able to predict the sequence of possible microRNAs along with their mature sequence and then depict their stem-loop structure. The analysis of the obtained sequences showed that they are highly conserved, which indicates their importance in the genome. The results obtained in this study show the power and functionality of bioinformatics tools. While the bioinformatic results increase our understanding of the function of the KLF4 gene, experimental studies are needed to confirm these results, which can give us more information about the function of this gene in the future.

Kidney stones, caused by mineral deposits, lead to severe pain and infections. Genetic factors, including the UMOD gene, influence stone formation, while medicinal plants like Silybum marianum and Zingiber officinale may offer protective effects. This study investigates how plant extracts modulate UMOD gene expression to prevent kidney stones and infections, exploring their therapeutic potential in renal health. For this purpose, 100 microliters of extracts of the medicinal plants Zingiber officinale, Silybum marianum, Alhagi, Urtica, and Brassica napus were used as samples, and the expression level of the UMOD gene was examined using the real-time PCR technique. Real-time PCR analysis revealed a significant increase in UMOD expression compared to the control, suggesting a protective role against kidney damage. Bioinformatics analysis used NCBI, ProtScale, UCSC, MBC, and OMIM databases. Bioinformatics analysis identified 23 miRNAs targeting UMOD, potentially influencing kidney disease progression. Additionally, 3D protein modeling confirmed UMOD's structural stability (GMQE = 0.83, 92.79% stability via Ramachandran plot). Network analysis highlighted UMOD's interaction with kidney stone-related genes, while domain analysis revealed functional ZP and EGF domains involved in infection resistance. Tissue-specific expression was highest in kidneys and liver, supporting its renal protective role. The results of this study provide a promising perspective, indicating that the medicinal plants examined possess antioxidant and anti-inflammatory properties. These properties help alleviate symptoms, prevent the reformation of kidney stones, and assist in expelling existing stones.