Critical Reviews in Eukaryotic Gene Expression最新文献

Fibromyalgia (FM) is a chronic condition marked by widespread pain, fatigue, and other debilitating symptoms, affecting 2-4% of the population, predominantly women. Diagnosing FM is challenging due to its complex symptoms and lack of specific biomarkers. To characterize the gene expression profile in FM and identify target genes and potential biomarkers for FM. The RNA-sequencing data (RNA-seq) from FM patients and healthy controls were downloaded from the GEO database and analyzed in R to detect differentially expressed genes (DEGs). A weighted gene co-expression network analysis (WGCNA) was conducted on all genes to identify FM-associated modules. The intersection of DEGs with key module genes was used to build four machine learning models, with the top features from the support vector machine model tested for drug sensitivity to identify therapeutic targets. Expression of the top five genes was validated using real-time quantitative polymerase chain reaction and Western blotting. We identified 1599 DEGs between FM and healthy control. WGCNA revealed that 267 genes in the pink module were correlated with FM. The overlapped 76 key DEGs allow us to build machine-learning models that predict FM with high accuracy (area under the curve = 0.877). The top five genes that are contributing to the model were tested for potential drug targets. Drug sensitivity analysis showed a strong correlation between HAVCR1 and 10 tyrosine kinase inhibitors among the top gene-drug relationships. This study identified key FM-associated gene targets, demonstrating that their expression profiles can be used to predict FM risk. Our findings provide insights into the molecular mechanisms of FM and highlight potential therapeutic targets for improved FM treatment.

Diabetic peripheral neuropathy (DPN) is a diabetic complication, featured by impaired vascular functions. This study investigates the roles of arachidonate 15-lipoxygenase (ALOX15) in DPN. High glucose (HG) is used to establish in vitro DPN model. mRNA levels are detected using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Protein expression is detected using Western blot. The release of MDA, GSH, and iron is detected using ELISA assays. Mitochondrial functions are detected using immunofluorescence. Cell viability is detected using CCK-8 assay. Cell proliferation is detected using colony formation. Vascular angiogenesis is detected using tube formation assay. The death of human umbilical vein endothelial cells (HUVECs) is detected using TUNEL staining. The results show that HG treatment increases the release of ox-mtDNA. Ox-mtDNA stress promotes the lipid peroxidation and the accumulation of iron in an ALOX15-depedent manner, resulting in the ferroptosis of HUVECs. Moreover, HG treatment suppresses the expression of proliferation and angiogenesis of HUVECs. However, ALOX15 deficiency promotes the proliferation and angiogenesis of HUVECs, as well as suppresses the ox-mtDNA synthesis and ferroptosis. In conclusion, inhibition of ALOX15 suppresses ox-mtDNA synthesis and the ferroptosis of endothelial cells in DPN. Therefore, targeting ALOX15 may be a promising strategy for DPN.

This study aimed to investigate the polymorphisms and protein expression of PD-1/PD-L1 molecules concerning non-small-cell lung cancer (NSCLC) susceptibility and their potential relationship with clinical parameters. PD-1 (rs2227981) and PD-L1 (rs2890658) gene variants were genotyped using PCR and RFLP in 80 NSCLC patients and 79 healthy controls. Serum soluble PD-1 levels were measured by ELISA, and PD-L1 protein expression was analyzed via Western blot. Clinical parameter differences between NSCLC cases and controls were evaluated. The PD-L1 A/C AA genotype frequency was significantly higher in patients than in controls (P = 0.043). In PD-1 C/T variants, the CC genotype was more prevalent in cases with lymphovascular invasion than those without (P = 0.028), while the CT genotype was more frequent in patients without lymphovascular invasion (P = 0.047). Additionally, the CC genotype was associated with perineural invasion (P = 0.026). Serum PD-1 levels were significantly elevated in patients with the CC genotype for PD-1 C/T compared with controls (P = 0.008). Combined genotype analysis revealed that the CTAC genotype was more common in the control group than in NSCLC patients (P = 0.016). Moreover, PD-L1 protein expression was significantly higher in tumor tissues than controls (P < 0.0001). These findings suggest that PD-1 and PD-L1 polymorphisms and their expression levels may play crucial roles in NSCLC susceptibility and progression. Understanding these molecular mechanisms could contribute to developing novel therapeutic strategies for NSCLC patients.

Methyltransferase 3 (METTL3) is dysregulated in various brain disorders. This study aimed to investigate the roles of METTL3 in cerebral ischemia and reperfusion (I/R) injury. Oxygen-glucose deprivation/reoxygenation (OGD/R) was used to establish an in vitro cerebral I/R injury model. mRNA levels were detected by reverse transcription-quantitative PCR. Protein expression was detected by Western blot. Mitochondrial function was detected by immunofluorescence, mitochondrial superoxide (Mitosox) staining, and JC-1 staining. Mitochondrial morphology was detected by transmission electron microscopy. N6-methyladenosine (m6A) levels were detected by m6A assay. The m6A site was verified by luciferase assay. Cellular functions were detected using Cell Counting Kit 8 and propidium iodide staining assays. We found that METTL3 was upregulated in in vitro cerebral I/R injury model. However, inhibition of METTL3 inhibited OGD/R-induced mitochondrial dysfunction and neuronal ferroptosis. Moreover, METTL3 interacted with YTH N6-methyladenosine RNA binding protein C1 (YTHDC1) to promote m6A modification of solute carrier family 7 member 11 (SLC7A11), inhibiting its mRNA and protein stability. Additionally, SLC7A11 knockdown mediated mitochondrial dysfunction and neuronal ferroptosis. In conclusion, METTL3 mediates the progression of cerebral I/R injury through regulating SLC7A11. Therefore, targeting METTL3/YTHDC1/SLC7A11 axis may provide a novel strategy for cerebral I/R injury.

RNA methylation is involved in the pathogenesis of ankylosing spondylitis (AS). This study aimed to investigate the potentials of METTL17 in AS. mRNA expression was detected using RT-qPCR. RNA methylation was detected using MeRIP assay. Protein expression was detected using western blot. Cell proliferation was detected using EdU assay. Macrophage functions was detected using flow cytometry. METTL17 was upregulated after exposure to LPS. However, METTL17 knockdown promoted inflammatory response. Moreover, METTL17 knockdown promoted M1 macrophage polarization. Mechanically, METTL17 regulate RNA methylation. Mechanically, METTL17 promoted the RNA methylation of STAT1, inhibiting the mRNA and protein stability of STAT1. In summary, METTL17 inhibits inflammatory response and M1 macrophage polarization via mediating the RNA methylation of STAT1. Therefore, targeting METTL17/STAT1 may be a promising strategy for AS.

This study aimed to investigate the potential effects and underlying mechanism of plumbagin (PL) on the proliferation and apoptosis of SU-DHL-4 cells, a type of diffuse large B-cell lymphoma (DLBCL), through in vitro and in vivo experiments. The in vitro experiments were performed by subjecting SU-DHL-4 cells to different concentrations of PL. The proliferation rate of the cells was evaluated using the CCK8 assay. Flow cytometry, quantitative real-time polymerase chain reaction (qRT-PCR), and a commercial ROS detection kit were employed to quantify the apoptosis rate, the antioxidant enzyme activity, and the levels of reactive oxygen species (ROS), respectively. The protein expression of Bax, BCL2, caspase-3, cleaved caspase-3, PI3K, p-PI3K, Akt, p-Akt, mTOR, and p-mTOR were determined by western blotting. The cell-derived tumor xenograft tumor model was constructed by subcutaneously injecting SU-DHL-4 cells into NOD-SCID mice. The therapeutic effect of PL was then evaluated by morphological staining. Results from the in vitro experiments demonstrated that PL could effectively inhibit cell proliferation, increase the production of reactive oxygen species (ROS), and induce apoptosis in SU-DHL-4 cells in both a time- and a dosage-dependent manner. Furthermore, PL treatment upregulated the protein expression of Bax and cleaved caspase-3 (P < 0.05). In parallel, PL treatment concurrently DOWNREGULATED the protein expression of Bcl-2, p-PI3K, p-Akt, and p-mTOR (P < 0.05). More important, it inhibits the growth of mouse xenograft tumors. PL promotes apoptosis of DLBCL cells, potentially by upregulating ROS and suppressing the PI3K/Akt/mTOR signaling pathway. These findings might be a useful reference for future drug discovery.

Epigenetic control synergizes with DNA encoded regulatory information to provide a blueprint for gene expression that supports biological processes including phenotype, proliferation, growth control, metabolic regulation, cell survival, and immune function. Epigenetic regulation, non-DNA encoded regulatory information, mediates the selective expression and suppression of transcription in a phenotypically responsive manner. Parameters of epigenetic control are post-translational histone modifications, DNA methylation, mitotic gene bookmarking, nucleosome structure, and higher order chromatin organization. Epigenetically compromised gene expression is functionally linked to the onset and progression of diseases that include cancer. Epigenetic targeting strategies have the potential for cancer therapy with enhanced specificity and reduced off-target consequences.

Uterine corpus endometrial carcinoma (UCEC) is one of the most common gynecological malignancies, and understanding the molecular mechanisms underlying its development is essential for improving diagnosis and treatment. However, the role of DNA methylation, a key epigenetic modification, in UCEC prognosis prediction and clinical treatment strategies has rarely been studied. This study utilized publicly available datasets from The Cancer Genome Atlas (TCGA) and online bioinformatics tools to analyze the differential methylation and expression of six selected genes: TP53, PTEN, PTX3, TNK1, PPP2R1A, and KLRG2. These genes were chosen based on their known roles in cancer-related pathways, previous associations with oncogenic processes, and preliminary data showing significant changes in methylation and expression in UCEC compared with normal tissues. We integrated mRNA expression and DNA methylation data with the MethylMix method to identify genes with methylation-driven expression changes. Our analysis revealed that these genes exhibit distinct differential expression and methylation patterns in UCEC, suggesting potential regulatory mechanisms. The expression patterns across the six genes were observed, and TP53, TNK1, PPP2R1A, and KLRG2 were upregulated in tumors, and PTX3 was downregulated in tumors. At the same time, there was no significant change in the expression of PTEN gene. The differential expression correlates with changes in methylation, providing insights into the gene regulation occurring in UCEC. Additionally, Kaplan-Meier survival analysis revealed that the expression levels of specific genes, particularly PTX3, TNK1, and KLRG1, are significantly associated with overall survival in UCEC patients. Higher expression of these genes correlated with poorer survival outcomes, suggesting their potential as prognostic markers. In contrast, the expression of TP53, PTEN, and PPP2R1A did not show a significant impact on patient survival. The functional importance of these genes was investigated utilizing pathway enrichment and protein-protein interaction networks. Additionally, pathway enrichment analysis indicated these genes are involved in critical cancer pathways. The findings highlight the importance of integrating epigenetic and transcriptomic data to understand UCEC pathogenesis and suggest that the identified genes could serve as potential biomarkers for early diagnosis and treatment strategies.

Subretinal hemorrhage-induced neurotoxicity is a key cause of vision loss in age-related macular degeneration (AMD). The purpose of this study is to investigate the effects of Propofol on neurotoxicity. Oxygen glucose deprivation (OGD) was used to establish in vitro subretinal hemorrhage model. Gene expression was determined using reverse transcription-quantitative polymerase chain reaction and western blot. Cytokine release was determined using enzyme-linked immunosorbent assay. The interaction between sirtuin 6 (SIRT6) and NLR family pyrin domain containing 3 (NLRP3) was detected using co-immunoprecipitation assay. Cellular function was determined using cell counting kit-8 assay, lactate dehydrogenase assay, and terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Propofol suppressed the inflammatory response induced by OGD. Moreover, Propofol inhibited the neurotoxicity and pyroptosis of photoreceptors. Propofol mediated the overexpression of SIRT6, which was downregulated in AMD. Inhibition of SIRT6 alleviated its deacetylation of NLRP3. Additionally, SIRT6 deficiency antagonized the effects of Propofol and promoted the neurotoxicity and pyroptosis of photoreceptors. Taken together, Propofol protects against subretinal hemorrhage-induced neurotoxicity and pyroptosis of photoreceptors via promoting SIRT6-mediated deacetylation of NLRP3.

N6-methyladenosine (m6A) plays a role in tumorigenesis of lung cancer (NSCLC); FTO functions as an oncogene in various cancers. However, the molecular mechanism underlying FTO-promoted lung cancer progression is still unclear. Gene expression was detected using RT-qPCR, western blot, and immunohistochemistry. The behaviors of lung cancer cells were detected using CCK-8, colony formation assay, and transwell assays. MeRIP and luciferase assays were conducted to FTO-mediated RNA hypomethylation. In vivo assays were performed to verify the roles of FTO in NSCLC. High levels of FTO in NSCLC patients predicted poor outcomes. However, FTO knockdown suppressed the proliferation and migration of A549 cells. Mechanically, FTO downregulated KCTD11 expression through promoting the RNA hypomethylation of KCTD11, the expression of which was decreased in NSCLC. KCTD11 knockdown attenuated the effects of FTO and promoted the malignancy of lung cancer. In summary, FTO functions as an oncogene in NSCLC via downregulating KCTD11. Therefore, FTO/KCTD11 can be a novel target for NSCLC.