Iranian Journal of Biotechnology最新文献

Background: Glioblastoma (GBM) is one of the most aggressive and common tumors of the central nervous system (CNS), distinguished by its significant intratumoral heterogeneity and poor prognosis, with a median overall survival of approximately 15 months. Recent advances in single-cell RNA sequencing (scRNA-seq) have provided deeper insights into the molecular subtypes and heterogeneity of GBM, which include the proneural (PN), classical (CL), and mesenchymal (MES) subtypes.

Objectives: This study hypothesizes that constructing gene regulatory networks (GRNs) using single-cell RNA sequencing (scRNA-seq) data can elucidate the complex regulatory mechanisms underlying glioblastoma (GBM) heterogeneity. The primary aim is to identify key regulators and subtype-specific markers in GBM through the integration of scRNA-seq and GRNs, with the ultimate goal of discovering novel prognostic biomarkers that can improve patient stratification and treatment outcomes.

Materials and methods: Malignant cells were identified based on inferred copy number variations (CNVs) from scRNA-seq data. Consensus clustering of expression profiles was used to assign GBM subtypes. Analyses of differential gene expression, ligand-receptor interactions, pathway activities, and responses to immune checkpoint inhibitors were conducted. GRNs were constructed by retaining co-expressed transcription factor (TF)-gene pairs with enriched transcription-binding motifs. Bulk RNA-seq data were then used to validate marker expression and assess prognostic value.

Results: Distinct functional roles and molecular characteristics were observed across GBM subtypes. Subtype-specific GRNs revealed both unique and shared regulatory features. GATA binding protein 3 (GATA3) emerged as a potential prognostic marker, showing correlation with homologous recombination deficiency (HRD) and patient outcomes.

Conclusions: Subtype-resolved GRN analysis of GBM provides valuable insights into intratumoral heterogeneity and regulatory mechanisms. GATA3 may serve as a novel biomarker for prognosis and therapeutic stratification in GBM patients.

Background: Human papillomavirus type 16 (HPV16) E6 oncoprotein is a key factor in the progression of cervical and other HPV-related cancers. Targeting E6 with small molecule inhibitors represents a promising strategy for the development of novel antiviral therapies.

Objectives: This study aimed to discover and characterize small-molecule compounds that exhibit high affinity for HPV16 E6, possess favorable drug-like properties, and inhibit HPV16 E6, using advanced computational approaches.

Materials and methods: We integrated molecular dynamics simulations to capture the conformational flexibility of HPV16 E6 and employed structure-based virtual screening to identify potential inhibitors from a large chemical library. The binding stability and interaction patterns of selected compounds were evaluated through molecular docking, binding free energy calculations, and extended molecular dynamics simulations. In silico ADMET profiling was performed to assess the pharmacokinetic and toxicity properties of the top candidates.

Results: Nine lead compounds demonstrated stable binding to a key functional residue (CYS51) of HPV16 E6, with strong theoretical binding affinities confirmed by MM-GBSA calculations and molecular dynamics analysis. ADMET predictions indicated that most candidates possessed favorable pharmacokinetic profiles, although two compounds showed potential toxicity concerns.

Conclusion: Our findings provide a robust computational framework for the identification of drug-like small molecules targeting HPV16 E6, offering promising candidates for further development as antiviral agents against HPV-associated diseases. Experimental validation is warranted to confirm the inhibitory activity and therapeutic potential of these compounds.

Background: Multiple myeloma (MM) is a B-cell malignancy characterized by clonal plasma cell proliferation in the bone marrow. Although significant advances have been achieved in treatment, it remains largely incurable, and fundamental insights at the molecular level remain to be obtained.

Objecteves: This study aimed to identify key genes and microRNA (miRNA) involved in multiple myeloma by re-analyzing transcriptomic datasets. We sought to determine differentially expressed genes and miRNAs, perform pathway and network analyses, and highlight their roles in disease progression, prognosis, and therapeutic resistance.

Materials and methods: We identified and characterized the hub genes and miRNAs associated with MM by re-analyzing three microarray datasets, GSE16558, GSE141260, and GSE146649, using high-throughput sequencing. We re-identified DEGs using a strict filtering criterion: |logFC| ≥ 1 and p-value < 0.05. The application of the Venn diagram analysis highlighted 13 common DEGs among the datasets. A total of 3211 differentially expressed genes (DEGs) and 25 differentially expressed microRNAs (DEMs) were screened out, Thereafter, GO and pathway enrichment of the DEGs were analyzed using FunRich software, involving biological processes, cellular components, and molecular functions. The PPI network was constructed using the Cytoscape software to determine the interactions among these DEGs.

Results: Our analyses underlined several key biological processes, including the migration of immune cells, lymphocyte activation, and TGF-β signaling pathways, which play crucial roles in the progression of MM. The PPI network identified a number of hub genes; among these, CCND1, ITGB1, and CREB1 were significantly associated with patient survival outcomes. In addition, the interaction predictions indicated an important function of miR-34c-5p and miR-155-5p in governing apoptosis, thereby promoting drug resistance in MM cells. We identified 13 common DEGs across datasets, with key enrichments in immune cell migration, lymphocyte activation, and TGF-β signaling. PPI analysis revealed CCND1, ITGB1, and CREB1 as top hub genes, significantly linked to survival outcomes. MiRNA interactions, particularly miR-34c-5p and miR-155-5p, were implicated in apoptosis and drug resistance.

Conclusion: These data highlight the complex interplay between genetic alterations and the immune microenvironment in MM, opening new prospects for biomarkers and therapeutic targets that may hopefully improve patient management, treatment strategies, prognosis, and therapeutic resistance.

Background: Lung cancer (LC) remains the leading cause of cancer-related mortality. Circular RNAs (circRNAs) are emerging as important regulators in cancer biology.

Objectives: This study investigated the functional role and therapeutic potential of circFNIP1 (hsa_circ_0073858) in LC.

Materials and methods: The expression of circFNIP1 in multiple lung cancer cell lines was quantified using quantitative real-time PCR, and its subcellular localization was determined by fluorescence in situ hybridization. To investigate function, circFNIP1 was silenced in PC-9 and SPC-A1 cells using siRNA-mediated knockdown. Cellular proliferation was measured by CCK-8 and colony formation assays, while apoptosis was evaluated via flow cytometry. Cell migration and invasion capacities were assessed using wound healing and transwell assays. In vivo tumorigenic potential was examined by establishing subcutaneous xenografts in nude mice, followed by intratumoral administration of antisense oligonucleotides targeting circFNIP1. Bioinformatics analyses, including interrogation of circRNA and miRNA databases and protein-protein interaction networks, were performed to predict circFNIP1-associated miRNAs and downstream targets. All experiments were conducted in triplicate, and statistical analyses were performed to determine significance.

Results: CircFNIP1 was highly expressed in LC cells and localized to both the nucleus and cytoplasm. Knockdown of circFNIP1 significantly reduced proliferation, colony formation, migration, and invasion in vitro, and suppressed tumor growth in a mouse xenograft model. Bioinformatics predicted miR-1231 and miR-657 as key targets, with ICAM1 identified as a downstream effector of miR-657.

Conclusions: CircFNIP1 functions as an oncogenic circRNA in LC and represents a promising target for RNA-based therapeutic strategies. These findings provide a basis for the development of circFNIP1-targeted interventions in LC management.

Background: Esophageal cancer is a highly aggressive malignancy with poor global survival rates and limited efficacy from conventional therapies. Immunotherapy has shown promise, yet its effectiveness remains limited as a standalone approach. The identification of tumor-specific antigens offers a targeted strategy for therapeutic vaccine development.

Objectives: This study aimed to design a cytotoxic T lymphocyte (CTL)-based multi-epitope vaccine targeting immunodominant tumor-specific antigens associated with esophageal cancer using computational immunoinformatics and structural bioinformatics techniques.

Materials and methods: Fourteen validated CTL epitopes were selected based on immunogenicity, antigenicity (VaxiJen), IFN-γ inducibility, and structural stability. These epitopes were linked using AAY linkers to enhance processing by MHC class I molecules. The vaccine construct was evaluated for physicochemical properties, allergenicity, and toxicity. Structural modeling was performed using Robetta, and the model was validated by ProSA, ERRAT, and Ramachandran plot analysis. Molecular docking with TLR4 and MHC-I alleles, molecular dynamics simulation (iMODS), and MM/GBSA free energy calculations were used to assess binding affinity and structural stability. Immune simulations and population coverage analyses were also performed.

Results: The designed vaccine showed strong antigenicity (0.6199), was non-toxic and non-allergenic, and exhibited excellent stability and solubility. Molecular docking revealed strong binding with TLR4 (-1125.3 kcal. moL^-1), and MM/GBSA analysis confirmed favorable binding free energy (-93.41 kcal. moL^-1). Immune simulations indicated robust T-cell responses. Population coverage was highest in Oceania (64.14%) and East Asia (60.66%). Codon optimization and in silico cloning confirmed high expression potential in E. coli.

Conclusion: The vaccine demonstrates strong potential as a safe, stable, and broadly applicable immunotherapeutic candidate against esophageal cancer, pending experimental validation.

Objectives: The objective of this study was to develop a predictive modeling framework for optimizing MgCl₂ concentration and melting temperature (Tm) in PCR conditions.

Materials and methods: The study developed predictive models using multivariate Taylor series expansion and thermodynamic functions integrated with 120 PCR primers across various species. Ridge, Lasso, and Elastic Net multiple regression analyses were applied to fine-tune these models.

Results: The models demonstrated excellent predictive capabilities, achieving an R² =0.9942 for MgCl₂ concentration and 0.9600 for Tm. These findings underscore the efficacy of the proposed optimization strategy.

Conclusion: The research provides a tight framework for optimizing PCR conditions and enhancing specificity and sensitivity in DNA amplification. More importantly, it is based on an approach that combines theoretical modeling with empirical validation, thus offering valuable insight into the advancement of PCR-based methodologies.

Background: Colorectal cancer (CRC) is one of the most common types of cancer worldwide. Current treatments for CRC, in addition to side effects, face limitations such as drug resistance and selective ineffectiveness, which can reduce treatment efficacy. Researchers are seeking new cancer treatment methods to improve patients' quality of life by reducing side effects and increasing effectiveness.

Objective: The aim of this research was to evaluate the efficacy of a novel therapeutic method that combines heat-killed Lactobacillus casei (L.C) and Bacillus coagulans (B.C) with alpha-galactosyl ceramide in a mouse model of CRC.

Materials and methods: CT26 cells were injected subcutaneously into the right flanks of female BALB/c mice aged 6 to 8 weeks (n=60). After the tumors became palpable, the mice were divided into six equal groups to begin therapy. The control group received phosphate-buffered saline (PBS), while the experimental groups were treated with heat-killed L.C and B.C, α-GalCer, a combination of these treatments, and 5-FU. The treatments were administered to the tumor-bearing mice twice, with a one-week interval between each dose. The survival probability and tumor size were recorded during the study. Then, the mice were euthanized, and sampling was performed for laboratory investigations.

Results: Evaluations showed that all treatment groups led to increased survival probability and reduced tumor size compared to the control group (P<0.05). Also, cytokines assays revealed that all trearments caused increased IFN-γ secretion (P<0.05), and decreased IL-4 (P<0.05) and TGF-β (P<0.05) (except for B.C, α-GalCer and 5-FU groups P>0.05). Additionally, all treatment enhanced nitric oxide (NO) and lactate dehydrogenase (LDH) production of spelonocytes compared to the control group (P<0.05). All the mentioned changes related to the evaluation indicators in the combined treatment group were greater than in the other treatment groups (P<0.05) (except for tumor size).

Conclusion: It appears that the combination of natural products in treatment of CRC may serve as an effective complementary therapy alongside chemotherapy, yielding positive outcomes in the mouse model of CRC.

Background: Hepatocellular carcinoma (HCC) is a heterogeneous liver cancer with poor prognosis and diverse etiologies, yet molecular mechanisms across different causes remain unclear.

Objective: To identify key gene expression patterns and pathways associated with HCC progression from diverse pathological backgrounds using integrated bioinformatics analysis.

Materials and methods: Seven HCC-related GEO datasets totaling 1219 samples were analyzed. Differentially expressed genes (DEGs) were identified, followed by pathway enrichment, survival analysis, and immunohisto-chemistry validation.

Results: We identified DEGs such as CBS, ELF3, SPP2, and RPL8 correlated with patient survival. Enrichment analysis highlighted the PI3K-Akt signaling pathway as a central route in liver cirrhosis and tumor progression. A 47-gene set was proposed as a potential regulatory 'brake' during benign-to-malignant transformation. These findings were consistent with recent studies emphasizing PI3K-Akt and metabolic dysregulation in HCC pathogenesis.

Conclusions: Our integrative analysis reveals critical genes and pathways involved in HCC development, providing potential prognostic biomarkers and therapeutic targets. The study underscores the importance of cirrhosis in HCC progression and highlights the PI3K-Akt pathway's pivotal role. Further functional validation and larger cohort studies are warranted.

Background: Functional dyspepsia (FD) is a common gastrointestinal disorder with multifactorial etiology involving impaired motility, mucosal barrier disruption, and inflammation. Non-pharmacological biotechnological interventions, such as external biomechanical modulation, have demonstrated therapeutic benefits; however, the underlying molecular mechanisms remain largely unexplored.

Objectives: To investigate the transcriptomic and molecular changes induced by external biomechanical modulation in a rat model of FD and explore its potential as a physical biotechnological intervention for gastrointestinal dysfunction.

Materials and methods: Thirty-six male Wistar rats were randomly assigned to control, FD model, and biomechanical modulation intervention groups. FD was induced using a multifactorial approach (tail clamping stimulation + irregular diet + ice-cold saline gavage), and external biomechanical modulation was administered daily for one week. Gastrointestinal motility was assessed by measuring gastric emptying and intestinal propulsion rates. Duodenal tissues were analyzed using transcriptome sequencing, differential gene expression profiling, Gene Ontology (GO) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Serum levels of TNF-α, IFN-γ, and IL-1β, as well as expression of tight junction proteins Occludin and ZO-1, were assessed via ELISA, immunofluorescence, and Western blotting.

Results: FD rats exhibited reduced motility and villus atrophy, with elevated inflammatory cytokines and downregulated tight junction proteins. Transcriptomic profiling revealed significant gene expression changes in pathways related to digestion, nutrient absorption, immune modulation, and epithelial barrier integrity. KEGG analysis highlighted the involvement of PI3K-Akt signaling, neuroactive ligand-receptor interaction, and absorption-related pathways. PI3K-Akt pathway is an important pathway to regulate cell growth, proliferation and metabolism, and plays an important regulatory role in gastrointestinal motility disorders. External biomechanical modulation reversed these alterations, improving motility, reducing inflammation, and restoring mucosal integrity. Compared with the model group, the gastric emptying rate was significantly improved, and the small intestinal propulsion rate was increased by 9%.

Conclusion: This study demonstrates that external biomechanical modulation exerts relevant effects on gastrointestinal function in FD through transcriptomic regulation of immune and barrier-related pathways. Further research should explore clinical applications and detailed mechanistic insights.