Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach.

PURPOSE: Identifying the molecular mechanisms behind SARS-CoV-2 disparities and similarities will help find new treatments. The present study determines networks' shared and non-shared (specific) crucial elements in response to HCoV-229E and SARS-CoV-2 viruses to recommend candidate medications. METHODS: We retrieved the omics data on respiratory cells infected with HCoV-229E and SARS-CoV-2, constructed PPIN and GRN, and detected clusters and motifs. Using a drug-gene interaction network, we determined the similarities and disparities of mechanisms behind their host response and drug-repurposed. RESULTS: CXCL1, KLHL21, SMAD3, HIF1A, and STAT1 were the shared DEGs between both viruses' protein-protein interaction network (PPIN) and gene regulatory network (GRN). The NPM1 was a specific critical node for HCoV-229E and was a Hub-Bottleneck shared between PPI and GRN in HCoV-229E. The HLA-F, ADCY5, TRIM14, RPF1, and FGA were the seed proteins in subnetworks of the SARS-CoV-2 PPI network, and HSPA1A and RPL26 proteins were the seed in subnetworks of the PPI network of HCOV-229E. TRIM14, STAT2, and HLA-F played the same role for SARS-CoV-2. Top enriched KEGG pathways included cell cycle and proteasome in HCoV-229E and RIG-I-like receptor, Chemokine, Cytokine-cytokine, NOD-like receptor, and TNF signaling pathways in SARS-CoV-2. We suggest some candidate medications for COVID-19 patient lungs, including Noscapine, Isoetharine mesylate, Cycloserine, Ethamsylate, Cetylpyridinium, Tretinoin, Ixazomib, Vorinostat, Venetoclax, Vorinostat, Ixazomib, Venetoclax, and epoetin alfa for further in-vitro and in-vivo investigations. CONCLUSION: We suggested CXCL1, KLHL21, SMAD3, HIF1A, and STAT1, ADCY5, TRIM14, RPF1, and FGA, STAT2, and HLA-F as critical genes and Cetylpyridinium, Cycloserine, Noscapine, Ethamsylate, Epoetin alfa, Isoetharine mesylate, Ribavirin, and Tretinoin drugs to study further their importance in treating COVID-19 lung complications.

Exosomes as modulators of embryo implantation.

Exosomes, known as extracellular vehicles (EVs), are found in biological fluids. They have the capability to carry and transfer signaling molecules, such as nucleic acids and proteins, facilitating intercellular communication and regulating the gene expression profile in target cells. EVs have the potential to be used as biomarkers in diagnosis, prognosis and also as feasible therapeutic targets. The available evidence suggests that exosomes play critical roles in the reproductive system, particularly during implantation, which is widely recognized as a crucial step in early pregnancy. A proper molecular dialogue between a high-quality embryo and a receptive endometrium is essential for the establishment of a normal pregnancy. This review focuses on the key role of exosomes originated from various sources, including the embryo, seminal fluid, and uterus fluid, based on the available evidence. It explores their potential applications as a novel approach in assisted reproductive technologies (ART).

Comparison of two methods of sperm- and testis-mediated gene transfer in production of transgenic animals: A systematic review.

Transgenic (Tg) animal technology is one of the growing areas in biology. Various Tg technologies, each with its own advantages and disadvantages, are available for generating Tg animals. These include zygote microinjection, electroporation, viral infection, embryonic stem cell or spermatogonial stem cell-mediated production of Tg animals, sperm-mediated gene transfer (SMGT), and testis-mediated gene transfer (TMGT). However, there are currently no comprehensive studies comparing SMGT and TMGT methods, selecting appropriate gene delivery carriers (such as nanoparticles and liposomes), and determining the optimal route for gene delivery (SMGT and TMGT) for producing Tg animal. Here we aim to provide a comprehensive assessment comparing SMGT and TMGT methods, and to introduce the best carriers and gene transfer methods to sperm and testis to generate Tg animals in different species. From 2010 to 2022, 47 studies on SMGT and 25 studies on TMGT have been conducted. Mice and rats were the most commonly used species in SMGT and TMGT. Regarding the SMGT approach, nanoparticles, streptolysin-O, and virus packaging were found to be the best gene transfer methods for generating Tg mice. In the TMGT method, the best gene transfer methods for generating Tg mice and rats were virus packaging, dimethyl sulfoxide, electroporation, and liposome. Our study has shown that the efficiency of producing Tg animals varies depending on the species, gene carrier, and method of gene transfer.

Deciphering molecular mechanisms of SARS-CoV-2 pathogenesis and drug repurposing through GRN motifs: a comprehensive systems biology study.

The world has recently been plagued by a new coronavirus infection called SARS-CoV-2. This virus may lead to severe acute respiratory syndrome followed by multiple organ failure. SARS-CoV-2 has approximately 80-90% genetic similarity to SARS-CoV. Given the limited omics data available for host response to the viruses (more limited data for SARS-CoV-2), we attempted to unveil the crucial molecular mechanisms underlying the SARS-CoV-2 pathogenesis by comparing its regulatory network motifs with SARS-CoV. We also attempted to identify the non-shared crucial molecules and their functions to predict the specific mechanisms for each infection and the processes responsible for their different manifestations. Deciphering the crucial shared and non-shared mechanisms at the molecular level and signaling pathways underlying both diseases may help shed light on their pathogenesis and pave the way for other new drug repurposing against COVID-19. We constructed the GRNs for host response to SARS-CoV and SARS-CoV-2 pathogens (in vitro) and identified the significant 3-node regulatory motifs by analyzing them topologically and functionally. We attempted to identify the shared and non-shared regulatory elements and signaling pathways between their host responses. Interestingly, our findings indicated that NFKB1, JUN, STAT1, FOS, KLF4, and EGR1 were the critical shared TFs between motif-related subnetworks in both SARS and COVID-1, which are considered genes with specific functions in the immune response. Enrichment analysis revealed that the NOD-like receptor signaling, TNF signaling, and influenza A pathway were among the first significant pathways shared between SARS and COVID-19 up-regulated DEGs networks, and the term "metabolic pathways" (hsa01100) among the down-regulated DEGs networks. WEE1, PMAIP1, and TSC22D2 were identified as the top three hubs specific to SARS. However, MYPN, SPRY4, and APOL6 were the tops specific to COVID-19 in vitro. The term "Complement and coagulation cascades" pathway was identified as the first top non-shared pathway for COVID-19 and the MAPK signaling pathway for SARS. We used the identified crucial DEGs to construct a drug-gene interaction network to propose some drug candidates. Zinc chloride, Fostamatinib, Copper, Tirofiban, Tretinoin, and Levocarnitine were the six drugs with higher scores in our drug-gene network analysis. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03518-x.

Identification of Critical Molecular Factors and Side Effects Underlying the Response to Thalicthuberine in Prostate Cancer: A Systems Biology Approach.

Background: Uncontrolled mitosis of cancer cells and resistance cells to chemotherapy drugs are the challenges of prostate cancer. Thalicthuberine causes a mitotic arrest and a reduction of the effects of drug resistance, resulting in cell death. In this study, we applied bioinformatics and computational biology methods to identify functional pathways and side effects in response to Thalicthuberine in prostate cancer patients. Methods: Microarray data were retrieved from Gene Expression Omnibus (GEO), and protein-protein interactions and gene regulatory networks were constructed, using the Cytoscape software. The critical genes and molecular mechanisms in response to Thalicthuberine and its side effects were identified, using the Cytoscape software and WebGestalt server, respectively. Finally, GEPIA2 was used to predict the relationship between critical genes and prostate cancer. Results: The POLQ, EGR1, CDKN1A, FOS, MDM2, CDC20, CCNB1, and CCNB2 were identified as critical genes in response to this drug. The functional mechanisms of Thalicthuberine include a response to oxygen levels, toxic substances and immobilization stress, cell cycle regulation, regeneration, the p53 signaling pathway, the action of the parathyroid hormone, and the FoxO signaling pathway. Besides, the drug has side effects including muscle cramping, abdominal pains, paresthesia, and metabolic diseases. Conclusion: Our model suggested newly predicted crucial genes, molecular mechanisms, and possible side effects of this drug. However, further studies are required.

Identification of Renal Transplantation Rejection Biomarkers in Blood Using the Systems Biology Approach.

Background: Renal transplantation plays an essential role in the quality of life of patients with end-stage renal disease. At least 12% of the renal patients receiving transplantations show graft rejection. One of the methods used to diagnose renal transplantation rejection is renal allograft biopsy. This procedure is associated with some risks such as bleeding and arteriovenous fistula formation. In this study, we applied a bioinformatics approach to identify serum markers for graft rejection in patients receiving a renal transplantation. Methods: Transcriptomic data were first retrieved from the blood of renal transplantation rejection patients using the GEO database. The data were then used to construct the protein-protein interaction and gene regulatory networks using Cytoscape software. Next, network analysis was performed to identify hub-bottlenecks, and key blood markers involved in renal graft rejection. Lastly, the gene ontology and functional pathways related to hub-bottlenecks were detected using PANTHER and DAVID servers. Results: In PPIN and GRN, SYNCRIP, SQSTM1, GRAMD1A, FAM104A, ND2, TPGS2, ZNF652, RORA, and MALAT1 were the identified critical genes. In GRN, miR-155, miR17, miR146b, miR-200 family, and GATA2 were the factors that regulated critical genes. The MAPK, neurotrophin, and TNF signaling pathways, IL-17, and human cytomegalovirus infection, human papillomavirus infection, and shigellosis were identified as significant pathways involved in graft rejection. Concusion: The above-mentioned genes can be used as diagnostic and therapeutic serum markers of transplantation rejection in renal patients. The newly predicted biomarkers and pathways require further studies.

Effects of human chorionic gonadotropin-producing peripheral blood mononuclear cells on the endometrial receptivity and implantation sites of the mouse uterus.

OBJECTIVE: This research investigated the effects of human chorionic gonadotropin (HCG)-producing peripheral blood mononuclear cells (PBMCs) on the implantation rate and embryo attachment in mice. METHODS: In this experimental study, a DNA fragment of the HCG gene was cloned into an expression vector, which was transfected into PBMCs. The concentration of the produced HCG was measured using enzyme-linked immunosorbent assay. Embryo attachment was investigated on the co-cultured endometrial cells and PBMCs in vitro. As an in vivo experiment, intrauterine administration of PBMCs was done in plaque-positive female mice. Studied mice were distributed into five groups: control, embryo implantation dysfunction (EID), EID with produced HCG, EID with PBMCs, and EID with HCG-producing PBMCs. Uterine horns were excised to characterize the number of implantation sites and pregnancy rate on day 7.5 post-coitum. During an implantation window, the mRNA expression of genes was evaluated using real-time polymerase chain reaction. RESULTS: DNA fragments were cloned between the BamHI and EcoRI sites in the vector. About 465 pg/mL of HCG was produced in the transfected PBMCs. The attachment rate, pregnancy rate, and the number of implantation sites were substantially higher in the HCG-producing PBMCs group than in the other groups. Significantly elevated expression of the target genes was observed in the EID with HCG-producing PBMCs group. CONCLUSION: Alterations in gene expression following the intrauterine injection of HCG-producing PBMCs, could be considered a possible cause of increased embryo attachment rate, pregnancy rate, and the number of implantation sites.

A Motif-Based Network Analysis of Regulatory Patterns in Doxorubicin Effects on Treating Breast Cancer, a Systems Biology Study.

Background: Breast cancer is the most common malignancy worldwide. Doxorubicin is an anthracycline used to treat breast cancer as the first treatment choice. Nevertheless, the molecular mechanisms underlying the response to Doxorubicin and its side effects are not comprehensively understood so far. We used systems biology and bioinformatics methods to identify essential genes and molecular mechanisms behind the body response to Doxorubicin and its side effects in breast cancer patients. Methods: Omics data were extracted and analyzed to construct the protein-protein interaction and gene regulatory networks. Network analysis was performed to identify hubs, bottlenecks, clusters, and regulatory motifs to evaluate crucial genes and molecular mechanisms behind the body response to Doxorubicin and its side effects. Results: Analyzing the constructed PPI and gene-TF-miRNA regulatory network showed that MCM3, MCM10, and TP53 are key hub-bottlenecks and seed proteins. Enrichment analysis also revealed cell cycle, TP53 signaling, Forkhead box O (FoxO) signaling, and viral carcinogenesis as essential pathways in response to this drug. Besides, SNARE interactions in vesicular transport and neurotrophin signaling were identified as pathways related to the side effects of Doxorubicin. The apoptosis induction, DNA repair, invasion inhibition, metastasis, and DNA replication are suggested as critical molecular mechanisms underlying Doxorubicin anti-cancer effect. SNARE interactions in vesicular transport and neurotrophin signaling and FoxO signaling pathways in glucose metabolism are probably the mechanisms responsible for side effects of Doxorubicin. Conclusion: Following our model validation using the existing experimental data, we recommend our other newly predicted biomarkers and pathways as possible molecular mechanisms and side effects underlying the response to Doxorubicin in breast cancer requiring further investigations.

Repurposing new drug candidates and identifying crucial molecules underlying PCOS Pathogenesis Based On Bioinformatics Analysis.

BACKGROUNDS: Polycystic ovary syndrome affects 7% of women of reproductive ages. Poor-quality oocytes, along with lower cleavage and implantation rates, reduce fertilization. OBJECTIVE: This study aimed to determine crucial molecular mechanisms behind PCOS pathogenesis and repurpose new drug candidates interacting with them. To predict a more in-depth insight, we applied a novel bioinformatics approach to analyze interactions between the drug-related and PCOS proteins in PCOS patients. METHODS: The newest proteomics data was retrieved from 16 proteomics datasets and was used to construct the PCOS PPI network using Cytoscape. The topological network analysis determined hubs and bottlenecks. The MCODE Plugin was used to identify highly connected regions, and the associations between PCOS clusters and drug-related proteins were evaluated using the Chi-squared/Fisher's exact test. The crucial PPI hub-bottlenecks and the shared molecules (between the PCOS clusters and drug-related proteins) were then investigated for their drug-protein interactions with previously US FDA-approved drugs to predict new drug candidates. RESULTS: The PI3K/AKT pathway was significantly related to one PCOS subnetwork and most drugs (metformin, letrozole, pioglitazone, and spironolactone); moreover, VEGF, EGF, TGFB1, AGT, AMBP, and RBP4 were identified as the shared proteins between the PCOS subnetwork and the drugs. The shared top biochemical pathways between another PCOS subnetwork and rosiglitazone included metabolic pathways, carbon metabolism, and citrate cycle, while the shared proteins included HSPB1, HSPD1, ACO2, TALDO1, VDAC1, and MDH2. We proposed some new candidate medicines for further PCOS treatment investigations, such as copper and zinc compounds, reteplase, alteplase, gliclazide, Etc. CONCLUSION: Some of the crucial molecules suggested by our model have already been experimentally reported as critical molecules in PCOS pathogenesis. Moreover, some repurposed medications have already shown beneficial effects on infertility treatment. These previous experimental reports confirm our suggestion for investigating our other repurposed drugs (in vitro and in vivo).

MicroRNA-21 is involved in oocyte maturation, blastocyst formation, and pre-implantation embryo development.

Follicular fluid is one source of microRNAs (miRNAs). These miRNAs originate from oocytes and their neighboring cells. The changes in the miRNAs profile in the follicular fluid could alter folliculogenesis and oocyte maturation, and lead to infertility. Polycystic ovary syndrome (PCOS) patients have increased miR-21 levels in their sera, granulosa cells, and follicular fluid, and this mi-RNA plays a role in the pathophysiology and follicular dysfunction of PCOS patients. In the current study, we intend to examine whether expression levels of miR-21 influence oocyte maturation and embryo development. We examined miR-21 over-expression and down-regulation of miR-21 by miR-off 21 during in vitro maturation (IVM) to assess its influence on oocyte maturation and embryo development in mice. Over-expression of miR-21 in cumulus cells decreased expansion, meiotic progression, Glutathione-S-transferase GSH levels, and decreased expressions of Bmpr2 and Ptx3 genes. Subsequently, we noted that in vitro fertilization, and the cleavage rate and blastocyst formation significantly increased in cumulus oocyte complexes (COCs) that over-expressed miR-21. Inhibition of miR-21 by miR-off 21 led to increased cumulus expansion and GSH levels, along with decreased cleavage rate and blastocyst formation by alterations in Cdk2ap1 and Oct4 gene expressions. However, oocyte progression from the germinal vesicle (GV) to the metaphase II (MII) stage was not significant. miR-21 altered the gene expression levels in cumulus cells and influenced cytoplasmic oocyte maturation, cumulus expansion, and subsequent embryonic development in mice.

MiRNA-155 regulates cumulus cells function, oocyte maturation, and blastocyst formation.

Numerous oocytes are retrieved during in vitro fertilization from patients with polycystic ovary syndrome (PCOS). The poor quality of these oocytes leads to lower fertilization and decreases in cleavage and implantation. MiR-155 is one of the microRNA (miRNA) that is increased in serum and granulosa cells of PCOS patients. In this study, we investigate the effects of miR-155 expression and its target genes on oocyte maturation and embryo development. We used the calcium phosphate protocol to transfect vectors that contained miR-155 or miR-off 155 and alone eGFP into cumulus oophorus complex (COCs) of B6D2F1 female mice for in vitro maturation. Cumulus expansion, nuclear, and cytoplasmic maturation, as well as cleavage rates were determined in groups transfected and compared with the control groups. Quantitative real-time polymerase chain reaction was performed to analyze expression levels of miR-155 and the target genes in the cumulus cells, oocytes, and blastocysts. MiR-155 overexpression in COCs suppressed cumulus expansion, oocyte maturation, and inhibition of endogenous miR-155 by miR-off 155 improved cumulus expansion and oocyte maturation by downregulation and expression increase of the Smad2 and Bcl2 genes. On the other hand, overexpression and downregulation of miR-155 in the COCs led to increase and decrease in cleavage rates by changes in expressions of the Mecp2, Jarid2, and Notch1 genes, respectively (P < 0.05). These results suggested that miR-155 overexpression in granulosa cells of PCOS patients can negatively affect nuclear and cytoplasmic maturation, but this miRNA expression has a positive impact on embryo development.

Expression, Purification and Docking Studies on IMe-AGAP, the First Antitumor-analgesic Like Peptide from Iranian Scorpion Mesobuthus eupeus.

Scorpion venom contains different toxins with multiple biological functions. IMe-AGAP is the first Analgesic-Antitumor like Peptide (AGAP) isolated from Iranian scorpion Mesobuthus eupeus. This peptide is similar to AGAP toxin with high analgesic activity, extracted from Chinese scorpion and inhibits NaV1.8 and NaV1.9 voltage-gated sodium channels involved in the pain pathway. In this study, IMe-AGAP was cloned in a prokaryotic expression vector; expression of toxin in Escherichia coli (E. coli) was assayed and then purified. In in-silico studies, peptide sequence was compared with other scorpion analgesic toxins. The structures of IMe-AGAP and sodium channels were modeled using homology modeling. Structural evaluation and stereo-chemical analysis of modeled structures were performed using RAMPAGE web server Ramachandran plots. Hex Server was used to investigate the interactions between IMe-AGAP and S3-S4 and also S5-S6 segments of NaV1.8 and NaV1.9. Binding energies calculation was used for evaluation of protein docking. Soluble expression of IMe-AGAP in bacteria was investigated by SDS-PAGE analysis. Pure recombinant protein was obtained by Ni-NTA affinity chromatography. The results of three-dimensional structure prediction showed ßαßß topology for the toxin that is similar to the conserved structure of α-toxins. Comparison analysis between IMe-AGAP and AGAP toxins exhibited high similarity in homology modeling. Docking analysis demonstrated that IMe-AGAP can interact with NaV1.8 and NaV1.9 domains involved in pain. According to the results of homology studies and docking, IMe-AGAP might be a novel potential drug for pain treatment.