Molecular Biology Research Communications最新文献

Teratozoospermia is an abnormal sperm morphology that is a common cause of male infertility. Epigenetic factors have been implicated in the regulation of gene expression in teratozoospermia, but the specific mechanisms are not fully understood. This study aimed to identify differentially expressed genes (DEGs) between teratozoospermia and normozoospermia samples, and to investigate the role of epigenetic regulatory factors in the observed gene expression changes. The study integrated data from three publicly available datasets in the GSE6969 superseries. The DEGs were compared to a list of known human epigenetic-related genes obtained from the EpiFactors database. The protein-protein interaction (PPI) network and hub gene identifications for Epi-DEGs and the RNA-protein interaction (RPI) network to obtained the RBPs interacting with Epi-DEGs were constructed. siRNA design for the candidate mRNA was performed using various bioinformatics tools. As a result, the obtained 1,292 DEGs were compared to a list of 796 known human epigenetic factors, revealing 63 Epi-DEGs. The PPI network of Epi-DEGs identified top 10 hub genes including RBBP7, HDAC2, EZH2, SMARCA5, SUV39H1, CTCF, DNMT1, MORF4L1, ARID4B and KDM5B. The RPI network analysis revealed IGF2BP2, SFPQ and A1CF as key RNA-binding protein regulators epigenetic modifiers. Based on these findings, the study designed the sequence GCAACAAGAGAAGAA GCAATT as an optimal siRNA candidate targeting the master regulator IGF2BP2, which exhibited the most significant change in expression among the RNA-binding proteins (RBPs). This integrative analysis sheds light on the epigenetic mechanisms underlying teratozoospermia and highlights the potential of RBPs as diagnostic biomarkers and therapeutic targets for further investigation.

SPIN.DOC was discovered as a transcriptional co-repressor of wingless related integration site (WNT) pathway. However, it has been found to be upregulated in various types of cancer, including hepatocellular carcinoma, colorectal cancer, renal papillary cell carcinoma. Whether SPIN.DOC functions as an oncogene or tumour suppressor gene remains uncertain. Here, we report that ectopic expression of SPIN.DOC in normal NIH3T3 fibroblast cells promotes cell proliferation, colony formation, migration and invasion. Moreover, SPIN.DOC expressing NIH3T3 cells show increased spheroid formation, suggesting enhanced stemness and transformation potential. Immunofluorescence analysis using anti-β-Tubulin suggests that SPIN.DOC may induce, formation of tubulin-based microtentacles (McTNs), indicating epithelial-to-mesenchymal (EMT) transition. In conclusion, our study helps in establishing that SPIN.DOC can function as an oncogene.

Long non-coding RNAs (lncRNAs) have recently emerged as critical regulators of oncogenic or tumor-suppressive pathways in human cancers. LINC01133 is a lncRNA that has exhibited dichotomous roles in various malignancies but to the best of our knowledge, the role of LINC01133 in laryngeal squamous cell carcinoma (LSCC) has not been previously investigated. This study aimed to investigate the expression, clinical significance, and potential functions of the LINC01133 in LSCC. Integrative bioinformatics analysis of sequencing data obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed LINC01133 as a differentially expressed lncRNA in head and neck/laryngeal cancers. Experimental validation via quantitative real-time PCR in 41 pairs of stage III and IV LSCC tissues and normal tissues adjacent to the tumor (NAT) demonstrated significant downregulation of LINC01133 in tumors (p<0.0001). Decreased LINC01133 expression associated with advanced tumor stage (p=0.0206) and lymph node metastasis (p=0.0203). The receiver operating characteristic analysis indicated potential diagnostic utility (AUC=0.7115, p=0.001). Bioinformatic predictions and literature mining suggested two potential competing endogenous RNA (ceRNA) mechanisms whereby LINC01133 may act as a tumor suppressor by sponging miR-205-5p to derepress the leucine-rich repeat kinase 2 (LRRK2) and androgen receptor, leading to dysregulation of cancer-related signaling cascades. This study provides initial evidence that loss of lncRNA LINC01133 expression may promote LSCC tumorigenesis, possibly by dysregulating microRNA interactions. Further verification of its regulatory mechanisms and diagnostic value is warranted.

The recent pernicious COVID-19 pandemic is caused by SARS-CoV-2. While most therapeutic strategies have focused on the viral spike protein, Open Reading Frame 8 (ORF8) plays a critical role in causing the severity of the disease. Nonetheless, there still needs to be more information on the ORF8 binding epitopes and their appropriate safe inhibitors. Herein, the protein binding sites were detected through comprehensive structural analyses. The validation of the binding sites was investigated through protein conservation analysis and blind docking. The potential natural product (NP) inhibitors were selected based on a structure-function approach. The solo and combined inhibition functions of these NPs were examined through molecular docking studies. Two binding epitopes were identified, one between the ORF8 monomers (DGBM) and the other on the surface (Gal1-Like). E92 was predicted to be pivotal for DGBM, and R101 for Gal1-like, which was then confirmed through molecular dockings. The inhibitory effects of selected phytochemical (Artemisinin), bacterial (Ivermectin), and native-liken (DEG-168) NPs were compared with the Remdesivir. Selected NPs showed solo- and co-functionality against Remdesivir to inhibit functional regions of the ORF8 structure. The DGBM is highly engaged in capturing the NPs. Additionally, the co-functionality study of NPs showed that the Ivermectin-DEG168 combination has the strongest mechanism for inhibiting all the predicted binding sites. Ivermectin can interfere with ORF8-MHC-I interaction through inhibition of A51 and F120. Two new binding sites on this non-infusion protein structure were introduced using a combination of approaches. Additionally, three safe and effective were found to inhibit these binding sites.

During Ramadan, Muslims fast to spiritually prepare their bodies and spirits. The autophagy pathway restores cellular homeostasis and is being studied as a therapy for a variety of disorders. According to previous studies, fasting or calorie restriction has a role in the up-regulation of autophagy especially through the initiation step. The effects of Ramadan fasting on the autophagy pathways and metabolic health outcome in healthy adults were investigated in this study. In this controlled cohort study, 50 healthy subjects (20-78 years old) 24-fasting and 26 non-fasting were included. At the end of Ramadan, a blood was drawn to assess biochemical, hematological, and inflammatory variables. Serum IL-6 and hs-CRP levels were measured. The serum proteins (Beclin-1 and LC3β) and mRNAs gene expressions' (Beclin-1, p62, and LC3β) of the autophagy marker were evaluated by ELISA and real-time PCR, respectively. During Ramadan, there were no significant differences for biochemical parameters (except for BUN-level), inflammatory markers (IL-6 and hs-CRP), and hematological indices during Ramadan. Beclin-1 gene expression was significantly upregulated in the fasting-group as the main marker of initiation of autophagy; yet, the LC3β and the p62 levels were decreased in the fasting-group in peripheral blood mononuclear cells. However, fasting women alone displayed a significantly high serum Beclin-1 level. Ramadan fasting does not have any adverse effects on biochemical, hematological, and inflammatory parameters. According to our results, people observing Ramadan may benefit from the autophagy pathway to compensate reduction in energy and vital metabolites in the face of food restriction.

Human Epidermal Neural Crest Stem Cells (hEPI-NCSCs), as a transient population of multipotent migratory stem cells can differentiate into multiple types of neural and non-neural cells and tissues in the body. Here, we tried to determine the role of chemo agents in mediating the stress induced pathways like autophagy and unfolded protein responses (UPR), as well as the migratory potential of NCSCs. hEPI-NCSCs were treated with chemo agents including Dithiothreitol [(DTT) 10µM)], Salinomycin (9mM), Ebselen (10mM), 5-Fluorouracil [(5-FU) 8µM] and Cisplatin (6mM) for 72 hours. The reverse transcription-quantitative polymerase chain reaction (RT- qPCR) and scratch wound healing assays were used to assess the effect of chemo agents on NCSCs function. After treatment with DTT, hEPI-NCSCs upregulated the expression of genes related to autophagy and UPR pathways including LC3, P62 and CHOP. These genes were also overexpressed when NCSCs were treated with Salinomycin. Reverse results were verified by 5-FU, Ebselen and Cisplatin treatment. Salinomycin and Cisplatin upregulated the expression of XBP-1, which down regulated with DTT, 5-FU and Ebselen. Inhibition in migratory capacity of NCSCs was detected following treatment by Salinomycin, 5-FU, Ebselen and Cisplatin. DTT and 5-FU promoted the expression of BDNF, while Salinomycin, Cisplatin and Ebselen treatment reduced its expression. During exposition to DTT, the autophagy pathway was activated, implying that autophagy functions as a survival mechanism for deactivating the inhibitory effects of DTT on the migratory capacity of NCSCs. Chemotherapeutic agents like 5-FU and cisplatin exert cytotoxic effects on NCSCs by suppressing autophagy, UPR pathways, and the migratory potential of NCSCs.

Chromosome aberrations certainly aneuploidie are the cause of the majority of spontaneous abortions in humans. BUB1 (budding uninhibited by benzimidazole 1) and BUBR1 (BUB1 mitotic checkpoint serine/threonine kinase B) are two key proteins mediating spindle-checkpoint activation that play a role in the inhibition of the anaphase-promoting complex/ cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. This study aimed to evaluate the probable roles of BUB1 and BUBR1 pathogenic variants in abortion of the fetuses with aneuploidy. Fifty aborted fetuses with approved aneuploidy using array comparative genomic hybridization (aCGH) were included. BUB1 and BUBR1 genes were studied using the Sanger sequencing for the single nucleotide variant (SNV) detection, certainly rs121909055 and rs28989185 as the pathogenic target variants. The sequencing results were analyzed by finch TV software.Neither homozygous nor heterozygous variant of the targeted SNVs was observed in the samples. No other SNV was detectable in the analyzed parts of the BUB1 and BUBR1 genes in all samples. Since the allele frequencies of the variants of interest were zero in 50 studied samples, these SNVs would not be prioritized for screening in the parents with a history of miscarriage due to aneuploidy.

Ovarian cancer (OC) is one of the most common malignancies of the genitourinary system in women that has a high mortality rate worldwide. Drug resistance and tumor relapse are the main causes of high mortality rate in OC patients. Therefore, investigation of the molecular mechanisms involved in OC progression can be valuable to introduce effective therapeutic targets for these patients. Epithelial-mesenchymal transition (EMT) as a key regulator of tumor relapse and drug resistance can be regulated by different signaling pathways such as WNT and NOTCH. VOPP1 is an activator of NF-κB pathway during tumor progression. Considering the importance of cross talks between different signaling pathways during tumor progression, we assessed the role of VOPP1 in OC progression through the modulation of WNT and NOTCH pathways. The expression levels of components of WNT and NOTCH signaling pathways, as well as the EMT process, were evaluated in VOPP1-induced A2780 cells compared to control cells. Role of VOPP1 in OC invasiveness was also assessed through migration and drug resistance assays. VOPP1 inhibited EMT process and NOTCH and WNT pathways in A2780 cells. VOPP1 also significantly reduced cell migration (p=0.04) and paclitaxel (PTX) resistance in A2780 cells (p<0.0001). VOPP1 reduced ovarian tumor cell migration and PTX resistance via regulation of NOTCH and WNT mediated EMT process. Therefore, it can be suggested as a novel therapeutic target in OC patients following further animal studies and clinical trials.

Heterocephalus glaber, known as the Naked mole-rat, has an extraordinary immunity to Alzheimer's disease. The pathological hallmark of Alzheimer's disease is cerebral accumulations of plaques, consisting of self-aggregated amyloid beta peptides. Homo sapiens and H. glaber amyloid beta peptides are different in only one amino acid. Herein, computational structural analyses were carried out to determine whether plaque development in H. glaber is prevented by the replacement of His13 with Arg13 in the amyloid beta peptide. AlphaFold2 was used to predict the structure of the H. glaber amyloid beta peptide. HADDOCK and Hex were used to self-dock the peptides and dock ions on peptides, respectively. Illustrations were made by PyMol and ChimeraX. Using VMD, we calculated the radius of gyration. The phylogenetic analysis was conducted by Mega. The results showed an accurate structure with two alpha helices separated by a short coil for H. glaber. Self-docking of the two amyloid beta peptides demonstrated a globular conformation in the H. glaber dimer, implying the unlikeliness of amyloid beta peptides' self-aggregation to form fibrillar structures. This conformational state resulted in lower electrostatic energy compared to H. sapiens, contributing to H. glaber's lower tendency for fibril and, ultimately, plaque formation. Phylogenetic analysis confirmed that amyloid precursor protein is highly conserved in each taxon of rodentia and primata. This study provides insight into the connection between the structure of H. glaber amyloid beta and its plaque formation properties, showing that the Arg13 in H. glaber leads to fibril instability, and might prevent senile plaque accumulation.

Sphingosine 1 phosphate (S1P) is involved in the pathogenesis of asthma by stimulation of the alpha-smooth muscle actin (SMA) expression and remodeling of fibroblasts. This study was designed to determine the effects of selected micro RNAs in regulation of S1P and related metabolic pathways in a human lung fibroblast cell line. The fibroblast cell line (CIRC-HLF, C580) was cultured and transfected with individual viral vectors carrying miR124, mi125b, mi133b or mi130a. After 48 hours, expression level of miRNAs and their target genes, sphingosine kinase 1(SPHK1), sphingosine 1-phosphate lyase 1 (SGPL1), sphingosine 1- phosphate receptor 1 (S1PR1) and sphingosine 1- phosphate receptor 2 (S1PR2) were determined. Expression of miRNA and mRNA determined by reverse transcriptionquantitative polymerase chain reaction (qPCR) showed that the expression level of the miRNAs was significantly higher in human lung fibroblasts following transfection compared to controls (vector backbone without miRNA). The expressions of miRNAs-targeted genes were significantly downregulated in transfected fibroblasts compared to control cells (p<0.05). Data show that miR 124, miR 125b, miR 133b and miR130a by targeting regulatory genes in S1P-pathway can down-regulate key factors such as SPHK1, SGPL1, S1PR1 and S1PR2 genes in lung fibroblasts. The results showed that S1P pathway and key factors are suppressed in lung fibroblasts expressing miR124, miR125b, miR130a or miR133b. It appears that suppression of any of the intermediate factors in S1P by miRNA can affect the regulation of the entire S1P pathway.