Molecular Biology Research Communications最新文献

TRPV1 (Transient Receptor Potential Vanilloid 1) is a non-selective ion channel that responds to various thermal, chemical, mechanical, and ligand stimuli. It is expressed in various tissues, mainly in nociceptive neurons, adipocytes, and other cell types. This channel is involved in pain and temperature transition processes, although it has recently been implicated in adipocyte browning processes. That is why the study of this receptor has increased in recent years to understand the process of activation and inactivation by various stimuli. In this work, we focus on modeling a complete channel of human TRPV1 (hTRPV1), the structural changes, and especially the behavior of the pore when this protein is subjected to high temperatures (400 K). We report that when molecular dynamics simulate hTRPV1 at 400 K, it suffers an increase in the diameter of the two gates reported elsewhere in the pore, suggesting the opening of the channel. In this work, we describe the structural changes in the entire protein, concomitant to those in the pore, favoring this process, which might be associated with its biological activity.

Adjuvant chemotherapy with TMZ (Temozolomide) does not improve the survival of patients suffering from GBM (Glioblastoma). Given the importance of autophagy and UPR (Unfolding Protein Response) in chemotherapy resistance, as well as the role of Beclin-1, LC3IIβ, and P62 in the regulation of autophagy, we evaluated the effect of TMZ along with CPUK02 on U87 cells as a model of Glioblastoma cancer in this study. To achieve this goal, we treated the U87 cells with different doses of TMZ (50, 100, 200, 400, and 800 μM) and CPUK02 (1, 0.5, 0.25, 0.125, 0.06, 0.03, 0.01, and 0.007 μM); then, cell viability was assessed by MTT assay. The gene expression of Beclin1, P62, LC3IIβ, and XBP-1s was analyzed using quantitative real-time polymerase chain reaction. The comparison of the control group with the groups treated with the TMZ drug showed that, in 48 and 72 hours, doses of TMZ more than IC₅₀ (100 μM) (p<0.001) significantly led to cell death. CPUK02 doses more than 0.125 (p<0.0001) significantly led to cell death. TMZ and CPUK02 combination therapy (100 and 0.03 μM, respectively) increased the expression of Beclin-1, LC3IIβ, and P62 and activated the IRE-1 arm of UPR by increasing the expression of XBP-1s. TMZ and CPUK02 treatment inhibits the autophagic flux (p62, LC3IIβ). Increased XBP-1s expression might contribute to the enhanced TMZ sensitivity. This combination therapy is promising for TMZ-resistant cancers, but it needs further investigation.

Colorectal cancer (CRC) remains a major global health concern, especially given its increasing incidence among younger individuals. While genome-wide association studies (GWAS) have identified numerous CRC-associated polymorphisms, their spatial distribution and functional implications are not fully understood. This study examined the locations of 1,346 CRC-linked polymorphisms across chromosomal bands. The results revealed significant nonrandom clustering across thirteen chromosomal bands: 1q41, 6p21, 8q24, 9q34, 10p14, 10q25, 11q12, 12p13, 15q13, 18q21, 19q13, 20p12, and 20q13. Functional enrichment analysis of genes within these bands revealed several Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Reciprocal chromosomal enrichment confirmed that many of these terms and pathways were not randomly localized within the same bands, highlighting their potential biological significance. Survival analysis using TCGA data identified three KEGG pathways and 33 GO terms mapped to nine of the thirteen bands that were significantly associated with poor prognosis. Notably, the 8q24 and 20q13 regions were enriched for differentially expressed genes and survival-associated terms yet showed no significant enrichment for genes with high somatic mutation rates. These results imply that 8q24 and 20q13 act as regulatory hotspots rather than mutation-driven regions. Overall, this integrative approach identified functionally and clinically relevant genomic regions that may contribute to inherited CRC risk and progression, providing valuable targets for the development of diagnostic and prognostic biomarkers.

Prior studies have shown that conditioned media derived from Wharton's jelly mesenchymal stem cells (WJ-CM) have anti-cancer properties. This research investigated the impact of WJ-CM on HT-29 colorectal adenocarcinoma cells by examining autophagy biomarkers and the AMPK/mTOR pathway. The HT-29 cells were subjected to WJ-CM and an AMPK activator (AICAR). Autophagy and levels of AMPK and mTOR proteins were investigated. WJ-CM increased the expression of phosphorylated AMPK while reducing the level of phosphorylated mTOR in HT-29 cells. WJ-CM treatment elevated the LC3B/LC3A ratio and ATG7, ATG5, and Beclin-1 expression. However, there was a parallel drop in p62 expression, which indicates autophagy induction. AICAR increased the influence of WJ-CM on viability, as well as the levels of biomarkers associated with autophagy, phosphorylated  AMPK, and phosphorylated  mTOR in the HT-29 cells. WJ-CM inhibits colorectal cancer cell growth via activating AMPK/mTOR-mediated autophagy.

Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor essential for regulating genes involved in lipid metabolism, including fatty acid synthase (Fasn). Although NF-Y activity is known to be dynamically regulated during adipocyte differentiation, the amino acid residues responsible for its transcriptional function remain unclear. In this study, we examined the contribution of nuclear factor Ya (NF-Ya) to DNA-binding activity and transcriptional regulation in 3T3-L1 adipocytes. Using deletion constructs and adenoviral expression systems, we identified a region spanning amino acid residues 184-347 of NF-Ya as critical for acquiring DNA-binding ability during differentiation. Electrophoretic mobility shift assays revealed that NF-Ya undergoes modification within this region, conferring stage-specific DNA-binding activity to the Fasn promoter. These findings suggest that post-translational modification of NF-Ya is a key mechanism regulating NF-Y function in adipogenesis. Our work provides novel insights into transcriptional control of lipogenic genes and their relevance to metabolic regulation.

Formaldehyde (FA) is a known human carcinogen for the upper respiratory tract. However, its hematotoxicity remains unclear. This study was performed to assess probable effects of FA on blood parameters and to determine the common polymorphisms in the detoxification enzymes GSTM1 and GSTT1 as biomarkers of susceptibility. Sixty-four workers with high occupational FA exposure and 57 non-exposed controls were studied. Complete blood count was performed. Also, GSTM1/GSTT1 genotypes were determined. After adjusting for potential confounding variables, FA exposure was only associated with the levels of hemoglobin, mean corpuscular hemoglobin concentration, and reticulocytes. Notably, workers with homozygous deletions of GSTM1 or GSTT1 had hematological parameters similar to those with active genes. In conclusion, very high FA exposure resulted in only slight alterations in MCHC and no overt hematotoxicity was observed. These findings suggest that even at high exposure levels, FA may not reach the bone marrow in sufficient amounts to cause hematotoxicity. Also, it seems that GSTM1/GSTT1 polymorphisms do not influence the workers' susceptibility to FA-related blood effects.

Abnormal expression levels of microRNAs are associated with numerous diseases in the female reproductive tract. A small subset of human endogenous retroviruses (HERVs) genes have retained open reading frames (ORFs) that serve beneficial functions for the host. Syncytin-1 (HERV-W) and Syncytin-2 (HERV-FRD) play crucial roles in mammalian development and are expressed in placental trophoblasts. The miRNAs associated with HERV-W and HERV-FRD in spontaneous abortion and endometriosis have not been elucidated. The present study aimed to identify potential miRNAs that affect the regulation of Syncytin-1 and Syncytin-2 in endometriosis and miscarriage using bioinformatics tools. Complete CDS of Syncytin-1 (ERVW-1) and Syncytin-2 (ERVFRD-1) genes were collected from the gene bank database. Several target prediction algorithms were utilized, such as TargetScan, DIANA, miRDB, and miRWalk. Complete CDS of Syncytin-1 (ERVW-1) and Syncytin-2 (ERVFRD-1) genes were collected from the gene bank database. By integrating data from these diverse bioinformatics databases, miR-509-3p and miR-625-5p were consistent across multiple platforms, ensuring robust selection criteria. These tools facilitate the identification of differentially expressed miRNAs, understanding their roles in cellular processes, and potentially utilizing them as biomarkers for disease diagnosis and prognosis. Validation of the identified miRNAs in experimental models or clinical samples is needed to confirm their roles in endometriosis and miscarriage.

Farnesyltransferase plays a critical role in the post-translational modification of mammalian proteins, including the Ras oncogene, which is strongly associated with cancer development. Essential oils from Syzygium cumini have demonstrated promising therapeutic effects, particularly in cancer treatment, potentially through the inhibition of farnesyltransferase activity. This study employed integrative computational approaches to investigate the anticancer potential of essential oils derived from S. cumini. Various compounds were screened for toxicity, biological activities, membrane permeability, gene expression profiles, and survival correlations were conducted to investigate cancer-associated properties. Molecular docking and molecular dynamics (MD) simulations were performed to evaluate the binding interactions and stability of ligand-protein complexes involving farnesyltransferase. α-Humulene epoxide II exhibited antineoplastic activity, functioned as an apoptosis agonist, and inhibited cancer-related targets such as HIF1A and MMP9. Bornyl acetate showed potential as a JAK2 inhibitor. Both compounds demonstrated favorable membrane permeability, indicating high bioavailability and effective cellular uptake. Analysis of the farnesyltransferase (FNTB) gene revealed significantly higher expression in cancerous tissues and a positive correlation with pro-tumor immune cell infiltration. Molecular docking identified Tipifarnib as the strongest binder, serving as a positive control, while α-humulene epoxide II and bornyl acetate showed moderate to weaker binding affinities. However, MD simulations confirmed that both essential oil compounds exhibit binding stability comparable to that of Tipifarnib. Finally, α-humulene epoxide II and bornyl acetate from S. cumini exhibit favorable drug-like properties, high predicted safety margins, and a lack of organ-specific toxicity, underscoring their suitability for further drug development.

Dedifferentiated Liposarcoma (DDLPS) is one of the common subtypes of liposarcoma that is considered a highly malignant category. This study aims to investigate DDLPS through a system biology approach. The gene expression profiles and clinical traits of the DDLPS were acquired from The Cancer Genome Atlas (TCGA). The identification of co-expressed modules was conducted using the weighted gene co-expression network analysis. The immune cell-related gene function was studied by a web-based tool, TIMER, and, the survival analysis was performed at both the module and single-gene levels through Cox Regression analysis. Gene enrichment analysis was also conducted using the DAVID tool. One of the nine co-expressed DDLPS modules was significantly correlated with leukocyte fraction, hyper/hypo methylation, tumor purity, and chromosome instability (CIN). Based on the biological processes used to classify genes, the hub genes in a particular module play important roles in DNA repair, microtubule organizing clusters, mitotic checkpoint dysregulation, and cell proliferation signaling pathways. After screening the genes based on intra-module connectivity, module membership, and gene significance RAD54L was selected as one of the important hub genes. RAD54L showed poor prognosis to the overall survival (OS) analysis (HR=1.6, 95% CI=1.1-2.4, p=0.02). No co-expressed modules had relationship with OS. Through DDLPS traits, CIN and hyper/hypo methylation had significant negative relationship with OS. Our achievement confirmed the inverse association between tumor purity for DDLPS gene profiles and leukocyte fraction and negative leukocyte fraction (LF) gene significance in some genes was justified according to the sub-population analyses of immune cells in TIMER.