transcription factors

Developing miRNA-mediated cell engineering introduces a novel technology for cell reprogramming and generating patient-specific tissues for therapeutic use, facilitating basic research on human adult stem cells. Furthermore, optimizing a reprogramming method without transduction minimizes the risk of tumorigenesis, especially for reprogrammed cells. This study aimed to explore the use of liposomes as vehicles for delivering miRNAs to cells, focusing on their role in regulating gene networks and facilitating nuclear reprogramming.

This study utilized cationic liposomal nanoparticles preserved under different conditions to introduce miRNAs into hMSCs. Using qPCR, the effective induction of pluripotency factors (OCT4, SOX2, and NANOG) was examined.

Results indicated that miR-302a and miR-34a regulate pluripotency by interacting with key transcription factors, including OCT4, SOX2, and NANOG. Notably, the expression pattern of OCT4 showed that lipoplexes containing miR-302a increased the expression of this gene, while in the case of miR-34a, it decreased. Additionally, the study found that pluripotency precursors can be induced by delivering liposomal microRNA (LP-miRs).

LP-miRs, as small-molecule therapeutics, can influence reprogramming/engineering and the conversion of cells into other lineages. These findings have significant implications for our understanding of the mechanisms underlying the regulation of pluripotency and may have potential applications in regenerative medicine.

T helper 1 (TH1) and TH2 lymphocytes are the most important components of the immune system affected by blood transfusion. This study aimed`` to evaluate the effect of blood transfusion on gene expression of transcription factors related to the development of TH1, TH2, TH17 and regulatory T cells (Tregs). In this cross-sectional study, 20 patients diagnosed with abdominal aortic aneurysms requiring surgical repair were studied from January 2018 to August 2020. We utilized real-time PCR to evaluate the expression of transcription factor genes associated with TH1, TH2, TH17, and Treg, namely T-box-expressed-in-T-cells (T-bet), GATA-binding protein 3 (GATA-3), retinoid-related orphan receptor (RORγt), and fork head box protein 3 (Foxp3), respectively. The sampling occurred before anesthesia, 24- and 72 hours post-transfusion, and at the time of discharge. The results showed that the T-bet gene expression, compared to the time before transfusion, was significantly decreased 24 hours after blood transfusion and upon discharge while GATA3 genes exhibited a significant reduction both 24 and 72 hours after the transfusion, as compared to the pre-transfusion levels and the time of patient discharge. The Foxp3 gene demonstrated an increase at all study stages, with a notable surge, particularly 72 hours after red blood cell (RBC) transfusion. Conversely, the expression of RORγt gene, consistently decreased throughout all stages of the study. RBC transfusion in abdominal aortic aneurysm patients altered the balance of transcription gene expression of TH1, TH2, TH17, and Treg cells.

Acquired aplastic anemia is an autoimmune disease in which auto-aggressive T cells destroy hematopoietic progenitors. T-cell differentiation is controlled by transcription factors that interact with NOTCH-1, which influences the respective T-cell lineages. Notch signaling also regulates the BM microenvironment. The present study aimed to assess the gene expressions of NOTCH-1 and T helper cell transcription factors in the acquired aplastic anemia patients.  

Using quantitative real-time PCR, we studied the mRNA expression level for NOTCH-1, its ligands (DLL-1 and JAG-1), and T helper cell transcription factors (T-BET, GATA-3, and ROR-γt) in both PB and BM of aAA patients and healthy controls. Further, patients of aplastic anemia were stratified by their disease severity as per the standard criteria.

The mRNA expression level of NOTCH-1, T-BET, GATA-3, and ROR-γT genes increased in aAA patients compared to healthy controls. There was no significant difference in the mRNA expression of Notch ligands between patients and controls. The mRNA expression level of the above-mentioned genes was found to be higher in SAA and VSAA than NSAA patients. In addition, NOTCH-1 and T helper cell-specific transcription factors enhanced in aAA. We also observed a significant correlation between the genes and hematological parameters in patients.

 The interaction between NOTCH-1, T-BET, GATA-3, and ROR-γT might lead to the activation, proliferation, and polarization of T helper cells and subsequent BM destruction. The mRNA expression levels of genes varied with disease severity, which may contribute to pathogenesis of aAA.

Sox2 (SRY box2) is an essential transcription factor that plays a vital role in spermatogenesis and regulates the genes in this process. Sox2 is important for pluripotency, self-renewal, and even spermatogonial stem cell differentiation. This gene is found in pluripotent and specialized cells, and it is involved in their biological activities.

Protein-protein interaction (PPI) network analysis was performed during spermatogenesis using NCBI, STRING, and Cytoscape databases. Then, after isolating spermatogonial stem cells from 6 C57BL/6 mice, mouse embryonic stem cells and ES-like cells were prepared. In the following, Sox2 expression was examined in differentiated and undifferentiated spermatogonia by immunohistochemistry (IMH), immunocytochemistry (ICC), and Fluidigm PCR (polymerase chain reaction). Finally, the results were compared using the Kruskal-Wallis and Dunn tests at the significance level of p<0.05.

The results of this experiment showed that contrary to expectations, Sox2 has cytoplasmic expression in undifferentiated cells and nuclear expression in differentiated cells in in vitro conditions. In addition, the expression of Sox2 increased during differentiation. Fluidigm PCR showed a significantly higher expression of Sox2 (p<0.05) in differentiated compared to undifferentiated spermatogonia. Sox2 has an interaction with other genes during spermatogenesis such as Oct4, Nanog, Klf4, Stra8, Smad1, Tcf3, and Osm.

Sox2, which is known as a pluripotency marker, has a vital role in spermatogenesis and could be a differential marker. Sox2 has strong connections with other genes such as Oct4, Nanog, Klf4, Tcf3, Osm, Stra8, Lim2, Smad1, Gdnf, and Kit.

Liver cancer accounts for more than 700,000 deaths each year making it the third leading cause of cancer-related deaths worldwide. Late diagnosis of the disease is the reason behind most deaths. Driver mutations are genetic alterations in tumor cells, which are responsible for the development of liver cancer; therefore, the identification of genetic biomarkers is necessary for the prediction and early diagnosis of liver cancer.

The main objective of this study is to identify pathogenic alleles that may act as potential biomarkers for the prediction of liver cancer. It also identifies the role of novel genes in liver cancer that are not known to cause the disease.

The mutation data of non-coding variants were downloaded from the catalogue of somatic mutations in cancer (COSMIC) databases. Different bioinformatics tools were, then, used to retrieve mutations in liver cancer. The genetic alterations in hepatocellular carcinoma (HCC) were analyzed.

The present study successfully identified pathogenic alleles (consistent mutations) along with a set of novel genes that might be involved in the development of liver cancer. It identified non-coding mutations near human genes and transcription factor binding sites of HepG2 cells. This study also identified mutations near the genes that are involved in the Ras/MAFK signaling pathway of the Hepatitis B virus.

The pathogenic alleles identified in this study may provide targeted therapy for the treatment of liver cancer. The identification of novel genes may help to understand the progression of liver cancer at the molecular level. The identified driver mutations may act as potential biomarkers and therapeutic targets for early prediction and treatment of liver cancer.

Primordial germ cell (PGCs) lines are a source of a highly specialized type of cells, characteristically oocytes,during female germline development in vivo. The oocyte growth begins in the transition from the primary follicle. It isassociated with dynamic changes in gene expression, but the gene-regulating signals and transcription factors that control oocyte growth remain unknown. We aim to investigate the differentiation potential of mouse bone marrow mesenchymal stem cells (mMSCs) into female germ-like cells by testing several signals and transcription factors. In this experimental study, mMSCs were extracted from mice femur bone using the flushingtechnique. The cluster-differentiation (CD) of superficial mesenchymal markers was determined with flow cytometric analysis. We applied a set of transcription factors including retinoic acid (RA), titanium nanotubes (TNTs), and fibrin such as TNT-coated fibrin (F+TNT) formation and (RA+F+TNT) induction, and investigated the changes in gene, MVH/ DDX4, expression and functional screening using an in vitro mouse oocyte development condition. Germ cell markers expression, (MVH / DDX4), was analyzed with Immunocytochemistry staining, quantitative transcription-polymerase chain reaction (RT-qPCR) analysis, and Western blots. The expression of CD was confirmed by flow cytometry. The phase determination of the TNTs and F+TNT were confirmed using x-ray diffraction (XRD) and scanning electron microscope (SEM), respectively. Remarkably, applying these transcription factors quickly induced pluripotent stem cells into oocyte-like cells that were sufficient to generate female germlike cells, growth, and maturation from mMSCs differentiation. These transcription factors formed oocyte-like cells specification of stem cells, epigenetic reprogramming, or meiosis and indicate that oocyte meiosis initiation and oocyte growth are not separable from the previous epigenetic reprogramming in stem cells in vitro. Results suggested several transcription factors may apply for arranging oocyte-like cell growth and supplies an alternative source of in vitro maturation (IVM).

Osteoarthritis (OA) is known to be the most prevalent form of joint disease. We conducted this clinical trial to investigate the effects of KrocinaTM, a natural product containing crocin, on the gene expression of unique transcription factors of various T cell subsets in patients with OA. We collected 40 peripheral blood samples of OA patients receiving Krocina™ and equal number of those who took a placebo (IRCT2015021910507N2, NCT03375814). RNA extraction was performed from the cultured peripheral blood mononuclear cells of the OA patients who received Krocina™ and placebo and SYBR Green Real-time PCR technique was applied to assess the relative gene expression of T-bet, GATA3, ROR-γt, and FOXP3 as the unique transcription factors of various T cell subsets. The relative gene expression of T-bet and ROR-γt insignificantly decreased in the Krocina™ receiving group as compared to the placebo group. In addition, the relative gene expressions of GATA-3 and FOXP3 after the treatment with KrocinaTM showed a significant and insignificant increase, respectively. Moreover, an insignificant decrease was observed in the gene expression of GATA-3 and FOXP3 in the placebo group. A significant and insignificant decrease in the gene expression of T-bet and ROR- γt was detected in the OA patients who received a placebo. GATA-3 is known as a unique transcription factor for the differentiation of T-cells to the Th2 subset. The significant increase in the gene expression of GATA-3 in the patients with OA treated with crocin may suggest the beneficial effect of crocin on shifting towards the Th2 subset and enhancing an anti-inflammatory condition.

Stem cells are unique biological cells that can differentiate into specialized adipocytes. In mammals, there are two broad types of stem cells: embryonic stem cells that break away from the blastocyst cell proliferation, and adult stem cells that are found in different tissues. Mesenchymal Stem Cells (MSCs) are multipotent cells that are one of the most important adult stem cells. Due to their high proliferative capacity and the proper self-renewal ability, they have provided a powerful and promising source to use in the field of repair plaque. Also, MSCs can differentiate into several cell types, such as: osteoblasts (adipocytes), chondrocytes (chondrocytes), adipocytes (adipocytes) and myocytes (muscle cells). Because of the importance of MSCs as a source of autologous transplantation in the field of regenerative medicine, in depth studies of involved cell and molecular signaling cycles are needed. These cycles are the reason in which these cells are able to differentiate into other cell types. Also, the molecular changes that occur during these cells differentiation are needed to be closely examined. The role of cytokines, chemokines, and transcription factors on the process of differentiation of these cells is considered significant. The differentiation of MSCs into other cell lines is manipulated and stimulated by specific transcription factors associated with specific cell lines, thus, the important role of non-coding small mRNAs (miRNAs) is increased as a result. In the following study, the process of differentiation of MSCs into the chondrogenic lineage and the effect of several miRNAs on the regulation of the process of differentiation into adipose-derived stem cell cartilage have been scrutinized.

Context:

 Metastasis is a main cause of death in patients with cancer, whereby tumor cells withdraw from the primary site of the tumor mass and produce secondary tumor mass in new sites. Primary tumor cells depart collectively and individually to invade closed and distant sites.

Evidence Acquisition: 

This review considers TME-derived factors that actuate signaling pathways to induce epithelial-mesenchymal transition (EMT). National Center for Biotechnology Information (NCBI) was the main resource. Google Scholar and Scopus were other databases for finding articles. Keywords that were inserted into the search box of databases to identify related articles were ‘metastasis’, ‘invasion’, ‘epithelial-mesenchymal transition’, ‘EMT’, ‘tumor microenvironment’, ‘TME’, ‘TME cells’, and ‘signaling pathway in EMT’. Titles and abstracts of the articles were studied to choose the right articles. Finally, 107 articles were selected to study in detail and use as references.

 EMT is a type of metastasis that deprives epithelial single-cells of their characteristic features and acquires mesenchymal features facilitating the departure from the primary tumor mass. During EMT, cell-adhesion and apical-basal polarity rapture and cells obtain movement capability. The tumor microenvironment (TME) leads EMT through secretion factors and signaling pathways. As a result of activating these pathways, transcription factors that abolish epithelial gene expressions and augment mesenchymal gene expression are induced.

 In this review, recent research published in TME and EMT fields were highlighted and critically appraised. Effect of factors-derived TME cells on EMT were manifested that propose favorite targets for a therapeutic goal to inhibit metastasis. However, data about the effect of the combination of TME cells on metastasis have a small part in the literature.

The application of non-viral systems for delivering genes to cells is becoming a very interesting issue, especially in the treatment of neoplasms such as Breast Cancer (BC). Polymer-based non-viral systems are safe and feasible gene carriers to be used in targeted cancer therapy. SALL4 gene encodes a transcription factor and is overexpressed in some cancers.

In this study, carboxyalkylated-PEI25 (25 kDa) was used to deliver plasmids expressing SALL4-siRNA into MCF-7 cells. DLS and AFM were applied to determine the size of nanoparticles. The MTT method was used to assess cytotoxicity, and the efficiency of transfection was confirmed both qualitatively and quantitatively. Finally, the effect of silencing SALL4 was investigated on the migration of MCF7 cells using the scratch test.

The results showed that transferring the SALL4-siRNA using PEI25G10C50 reduced the expression of the corresponding transcription factor by 14 folds which attenuated the migration of MCF-7 cells by 58%.

In conclusion, PEI25G10C50 can serve as an effective gene delivery system for treating BC by targeting SALL-4.

MicroRNAs play acritical role in EMT regulation through tightly regulating the transcription factors. EMT (Epithelial-Mesenchymal Transition) in the colorectal cancer cell (CRC) is a highly controlled mechanism, contributing to the development of progressive cancer. Throughout this research, miR-200a/205 was focused as a component implicated throughout regulating the EMT process in colorectal cancer cells. In this sense, the induction of the EMT process was made using colorectal cancer cell lines.

The mRNA levels of E-cadherin, Vimentin, β-catenin, Zeb1, and Snail were determined using real time-PCR for characterization of the EMT process. True real time-PCR was conducted for evaluating the alteration amount of microRNAs.

The findings of this study verified the in-vitro EMT model being developed. The in vitro analysis revealed a negative correlation between the Zeb1 and Snail miR-200a and miR205 (P=0.001) (P=0.0001). The results of miR-200a and miR205 are regulated down in vitro.

miR-200a and miR205 may be used as candidates in further research to prevent colorectal cancer's invasive properties via the EMT process

GyrA and gyrB genes encode DNA gyrase subunits. This enzyme regulates DNA supercoiling. Inhibitors of this enzyme, such as ciprofloxacin, may change the level of supercoiling and the expression level of genes, including gyrA and gyrB.

The aims of this research were first to select some transcription factors, which regulate the expression of gyrA and gyrB. Secondly, the effect of these transcription factors was investigated on the expression of these genes in Escherichia coli mutants with different levels of resistance to ciprofloxacin in the presence and absence of these transcription factors.

For this purpose, the online software called Promoter Analyzer in Virtual Footprint version 3 was used to find and select some transcription factors. The relative expression of genes was determined by quantitative real-time polymerase chain reaction (qRT-PCR).

Theoretical results showed that CspA, FhlA, and SoxS transcription factors (with a score of match higher than 6), could be selected for further analysis. The expression of gyrA and gyrB genes remained unchanged in the presence and absence of CspA and FhlA transcription factors following exposure to the low amount of ciprofloxacin. However, SoxS transcription activator might have indirect effects on the expression of these genes, as soxS gene was overexpressed following treatment with a higher amount of ciprofloxacin.

It is concluded that overexpression of gyrA and gyrB genes is not dependent on CspA and FhlA transcription factors, but may be dependent indirectly on regulatory proteins involved in oxidative stress following exposure to ciprofloxacin.

Any irregularities in self-renewal/differentiation balance in endometriotic MSCs can change their fate and function, resulting in endometriosis development. This study aimed to evaluate the expression of OCT4 transcripts (OCT4A, OCT4B, and OCT4B1), SOX2, and NANOG in endometriotic MSCs to show their aberrant expression and to support self-renewal/differentiation imbalance in these cells.

MSCs were isolated from three endometriotic and three normal endometrium samples and characterized and analyzed for the expressions of OCT4A, OCT4B, OCT4B1, SOX2, and NANOG using the qRT-PCR.

The expressions of OCT4 transcripts and NANOG increased significantly in endometriotic MSCs, whereas SOX2 expression did not show any significant difference.

Our findings provide further evidence for confirming the self-renewal/ differentiation imbalance in endometriotic MSCs, as the main underlying cause of endometriosis development. This study also paves the way for further research on endometriosis treatment by focusing on endometriotic
stem cells.

The clinical relevance of epithelial‑to‑mesenchymal transition (EMT) in colorectal cancer (CRC) progression has been highlighted over the last decade. Several EMT‑inducing transcription factors (EMT‑TFs) have been implicated in the regulation of EMT, including Twist, Snail1, Slug, ZEB1, and ZEB2. Here, this meta‑analysis aimed to predict the risk of distance metastasis and overall survival in CRC patients with high expression of EMT‑TFs.

All eligible studies were searched in PubMed, Scopus, and Web of Science databases. The search was carried out to include literatures published as late as September 1, 2018. In overall, 16 studies that investigated the relationship between EMT‑TFs with distance metastasis and survival in CRC patients were included. In meta‑analysis, a pooled hazard ratio (HR) and odds ratio (OR) were estimated for associations.

The results of this review indicated that expressions of all EMT‑TFs are significantly correlated with poor overall survival in CRC. Moreover, there are a significant association between Twist (OR, 1.46; 95% confidence interval [CI], 1.03–2.09), Slug (OR, 3.43; 95% CI, 1.98–5.93), and ZEB2 (OR, 2.42; 95% CI, 1.09–5.40) expression with distance metastatic in CRC patients.

These findings suggest that the overexpression of EMT‑TFs plays a key role in increasing the risk of distance metastasis as well as decreasing overall survival in CRC patients.

Epiretinal membrane (ERM) is a pathologic tissue that develops at the vitreoretinal interface. ERM is responsible for pathological changes of vision with varying degrees of clinical significance. It is either idiopathic or secondary to a wide variety of diseases such as proliferative diabetic retinopathy (PDR) and proliferative vitreoretinopathy (PVR). A great variation in the prevalence of idiopathic ERM among different ethnic groups proposed that genetic and lifestyle factors may play a role in ERM occurrence. Histopathological studies demonstrate that various cell types including retinal pigment epithelium (RPE) cells, fibrocytes, fibrous astrocytes, myofibroblast-like cells, glial cells, endothelial cells (ECs) and macrophages, as well as trophic and transcription factors, including transforming growth factor (TGF), vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF) etc., are directly or indirectly involved in the pathogenesis of  idiopathic or secondary ERMs. These processes are driven (on the last count) by more than 50 genes, such as Tumor Necrosis Factor (TNF), CCL2 ((chemokine (C-C motif) ligand 2)), MALAT1, transforming growth factor (TGF)-β1, TGF-β2, Interleukin-6 (IL-6), IL-10, VEGF and glial fibrillary acidic protein (GFAP), some of which have been studied more intensely than others. The present paper tried to summarize, highlight and cross-correlate the major findings made in the last decade on the function of these genes and their association with different types of cells, genes and gene expression products in the ERM formation.

Uterine leiomyomas are steroid hormone dependent myometrial neoplasms of female genital tract which appear after menarche and regress at menopause. The present study evaluated the role of ER-β gene polymorphisms (rs3020449 C/T, rs3020450 G/A, rs1271572 G/T, rs1256049 G/Aand rs4986938 G/A) in the etiology of disease. A total of 150 clinically, ultrasonographically evaluated uterine leiomyoma patients and an equal number of individuals as controls were considered for the present study. Genotype analysis was carried out by TETRA Primer Amplification Refractory Mutation System–PCR for promoter polymorphisms and PCR- RFLP method was done for exonic polymorphisms followed by agarose gel electrophoresis. The strength of the association of ER-β gene polymorphisms between controls and patients were measured by appropriate statistical methods. An increased frequency of T/T genotype and T allele of rs3020449, AA genotype and A allele of rs3020450, T/T genotype and T allele of rs1271572, AA genotype and A allele of rs1256049 and A/A genotype and A allele of rs4986938 was observed in cases when compared with controls. The study indicates that the ER-β gene polymorphisms may act as a major genetic regulator in the etiology of uterine leiomyomas.

Diabetic nephropathy (DN) is a serious complication of diabetes mellitus involving damage to the capillaries in the glomerulus. This study aimed to explore key genes and signaling pathways participate in the progression of DN. Two gene expression profile datasets GSE1009 and GSE30528 downloaded from Gene Expression Omnibus (GEO) were used to analyze the differentially expressed genes (DEGs) between DN samples and controls. Coupled two-way clustering (CTWC) and correspondence analysis were performed to explore the potential functions of DEGs. Then, Gene Ontology (GO) terms and pathways associated with DEGs were identified, followed by constructing of the co-expressed gene network and module. Ultimately, the regulatory network based on the DEGs, miRNAs and transcription factors (TFs) was established. Total 283 common DEGs were identified from the two datasets, including 219 down-regulated ones (bone morphogenetic protein 7 (BMP7), decay accelerating factor (CD55) and coagulation Factor V (F5) etc.) and 64 up-regulated ones (inhibin beta c subunit (INHBC) and colony stimulating factor 1 receptor (CSF1R) etc.). The miRNA-TF regulatory network was established with three miRNAs, 8 TFs and 58 DEGs. Besides, three significant pathways including cytokine-cytokine receptor interaction, complement and coagulation cascades and TGF-beta signaling pathways were identified. BMP7, CD55, CSF1R, INHBC and F5 are likely to take crucial roles in the pathogenesis of DN.