Differentially Expressed Genes Research Articles

Integrative multi-omics analysis of chilling stress in pumpkin (Cucurbita moschata).

Pumpkin (Cucurbita moschata) is an important vegetable crop that often suffers from low-temperature stress during growth. However, the molecular mechanism involved in its response to chilling stress remains unknown. In this study, we comprehensively investigated the effect of chilling stress in pumpkin seedlings by conducting physiological, transcriptomic, and metabolomic analyses. Under chilling stress, there was an overall increase in relative electrical conductivity, along with malondialdehyde, soluble sugar, and soluble protein contents, but decreased superoxide dismutase and peroxidase activities and chlorophyll contents in seedling leaves compared with controls. Overall, 5,780 differentially expressed genes (DEGs) and 178 differentially expressed metabolites (DEMs) were identified under chilling stress. Most DEGs were involved in plant hormone signal transduction and the phenylpropanoid biosynthesis pathway, and ERF, bHLH, WRKY, MYB, and HSF transcription factors were induced. Metabolomic analysis revealed that the contents of salicylic acid (SA), phenylalanine, and tyrosine increased in response to chilling stress. The findings indicated that the SA signaling and phenylpropanoid biosynthesis pathways are key to regulating the responses to chilling stress in pumpkins. Overall, our study provides valuable insights into the comprehensive response of C. moschata to chilling stress, enriching the theoretical basis of this mechanism and facilitating the development of molecular breeding strategies for pumpkin tolerance to chilling stress.

Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: genome-wide polymorphisms, differential gene expression, and drug resistance

BackgroundThe study of rodent malaria parasites has significantly advanced our understanding of malaria parasite biology and host responses to parasite infections. There are four well-characterized rodent malaria parasite species (Plasmodium yoelii, P. chabaudi, P. berghei, and P. vinckei). Each species also has multiple strains that cause different disease phenotypes. P. yoelii nigeriensis N67C and N67, two isogenic parasites, are particularly intriguing as they differ in virulence and incite different immune responses in mice. The genome of the N67 parasite has been assembled recently, but not that of N67C. This study used PacBio HiFi sequencing data to assemble the N67C genome, compared the two genomes, and performed RNA sequencing to identify polymorphisms and differentially expressed genes (DEGs).ResultsThe assembled N67C parasite genome consisted of 16 scaffolds and three contigs of approximately 22.5 Mb with 100% and 96.6% completeness based on well-characterized single-copy orthologs specific to the Apicomplexa phylum and the Plasmodium genus, respectively. A comparison between the annotated N67C and N67 genomes revealed 133 single nucleotide polymorphisms (SNPs) and 75 indels. Among the polymorphic sites, an S (N67) to N (N67C) amino acid substitution at position 114 (S114N) in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) confers resistance to pyrimethamine in mice. Additionally, 60 differentially expressed single-copy genes (DEGs) were detected after comparing mRNA levels between the two parasites. Starting with the predicted and annotated 5,681 N67C and 5,749 N67 genes, we identified 4,641 orthogroups that included at least one gene from the four P. yoelii parasites (N67, N67C, 17X, and YM), whereas 758 orthogroups showed subspecies or strain-specific patterns.ConclusionThe identification of polymorphic sites between the N67 and N67C genomes, along with the detection of the DEGs, may provide crucial insights into the variations in parasite drug responses and disease severity between these two isogenic parasites. The functional characterization of these genetic differences and candidate genes will deepen our understanding of disease mechanisms and pave the way for developing more effective control measures against malaria.

MaPom1, a Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase, Positively Regulates Thermal and UV-B Tolerance in Metarhizium acridum

Fungi play irreplaceable roles in the functioning of natural ecosystems, but global warming poses a significant threat to them. However, the mechanisms underlying fungal tolerance to thermal and UV-B stresses remain largely unknown. Dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) Pom1 is crucial for fungal growth, conidiation, and virulence. However, its role in stress tolerance within kingdom fungi has not been explored. In this study, we analyzed the function of MaPom1 (a Pom1 homologous gene) in the entomopathogenic fungus Metarhizium acridum and its regulatory roles in stress tolerance. Conidial thermal and UV-B tolerance significantly decreased in the MaPom1 disruption strain (ΔMaPom1), whereas conidial yield and virulence were unaffected. RNA-Seq analysis indicated that the differentially expressed genes (DEGs) were primarily related to amino sugar, nucleotide sugar metabolism, cell wall components, growth and development, and stress response pathways. Under heat shock treatment, the expression levels of heat shock protein genes decreased significantly, leading to reduced thermotolerance. Moreover, under UV-B treatment, MaPom1 expression and the enzyme activity significantly changed, indicating its involvement in regulating UV-B tolerance. The percentage of nuclear damage in ΔMaPom1 under UV-B treatment was higher than that in the wild-type strain (WT) and the complementary strain (CP). Additionally, the transcription levels of DNA damage-related genes significantly decreased, whereas those of several genes involved in the DNA damage repair response increased significantly. Overall, MaPom1 contributed to thermal and UV-B tolerance by regulating the expression of heat shock protein genes and DNA damage repair genes.

An integrative lipidomics and transcriptomics study revealing Bavachin and Icariin synergistically induce idiosyncratic liver injury

Objectives: Reports of traditional Chinese medicine (TCM)-related liver injury have increased over recent years; however, identifying susceptibility-related components and biomarkers remains challenging due to the heterogeneous nature of TCM and idiosyncratic drug-induced liver injury (IDILI). Psoraleae Fructus (PF) and Epimedii Folium (EF), commonly found in TCM prescriptions, have been implicated in IDILI, but their constituents and underlying mechanisms are poorly understood. Methods: In this study, we identified bavachin (Bav) and icariin (Ica) as susceptibility components for IDILI in PF and EF using a TNF-α-mediated mouse model. Lipidomics and transcriptomics were used to investigate their related mechanism. Results: Liver biochemistry and histopathology analyses revealed that co-exposure to Bav, Ica, and a non-toxic dose of TNF-α prestimulation induced significant liver injury, while Bav and Ica alone did not. Lipidomics identified seven differentially abundant metabolites in the Bav/Ica/TNF-α group compared to the Ica/TNF-α or Bav/TNF-α groups, mainly enriched in alpha-linolenic acid (ALA), arachidonic acid (AA), and linoleic acid (LA) metabolic pathways. Additionally, transcriptomics revealed 49 differentially expressed genes (DEGs) in the Bav/TNF-α vs Bav/Ica/TNF-α and Ica/TNF-α vs Bav/Ica/TNF-α groups, primarily associated with the PI3K/AKT/mTOR signaling pathway and sphingolipid metabolism. Integrative lipidomics and transcriptomics analyses identified significant positive correlations between five differential metabolites (DMs) – PC (O-16:0_14:1), PG (22:1_20:3), PI (16:0_14:1), PS (18:0_19:2), and TG (17:0_18:2_22:5) – and ten DEGs – Nr0b2, Btbd19, Btg2, Fam222a, Fam83f, Gtse1, Anln, Gja4, Srrm4, and Zfp13. Conslusions: Collectively, these results suggest that alterations in intracellular metabolism and gene expression levels may contribute to the synergistic induction of IDILI by the incompatible pair Bav and Ica in the presence of TNF-α.

Transcriptional Profiling Analysis Providing Insights into the Harsh Environments Tolerance Mechanisms of Krascheninnikovia arborescens

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. arborescens’ adaptation to desert conditions, focusing on its physiological, biochemical, and transcriptomic responses to drought, salt, and alkali stresses. The results revealed that the three stresses have significant impacts on the photosynthetic, antioxidant, and ion balance systems of the plants, with the alkali stress inducing the most pronounced changes and differential gene expression. The clustering and functional enrichment analyses of differentially expressed genes (DEGs) highlighted the enrichment of the induced genes in pathways related to plant hormone signaling, phenylpropanoid biosynthesis, and transcription factors following stress treatments. In these pathways, the synthesis and signal transduction of abscisic acid (ABA) and ethylene, as well as the flavonoid and lignin synthesis pathways, and transcription factors such as MYB, AP2/ERF, bHLH, NAC, and WRKY responded actively to the stress and played pivotal roles. Through the WGCNA analysis, 10 key modules were identified, with the yellow module demonstrating a high correlation with the ABA and anthocyanin contents, while the turquoise module was enriched in the majority of genes related to hormone and phenylpropanoid pathways. The analysis of hub genes in these modules highlighted the significant roles of the bHLH and MYB transcription factors. These findings could offer new insights into the molecular mechanisms that enable the adaptation of K. arborescens to desert environments, enhancing our understanding of how other desert plants adapt to harsh conditions. These insights are crucial for exploring and utilizing high-quality forage plant germplasm resources and ecological development, with the identified candidate genes serving as valuable targets for further research on stress-resistant genes.

Transcription-Aided Selection (TAS) for Crop Disease Resistance: Strategy and Evidence

A transcription-aided selection (TAS) strategy is proposed in this paper, which utilizes the positive regulatory roles of genes involved in the plant immunity pathways to screen crops with high disease resistance. Increased evidence has demonstrated that upon pathogen attack, the expression of diverse genes involved in salicylic acid (SA)-mediated SAR are differentially expressed and transcriptionally regulated. The paper discusses the molecular mechanisms of the SA signaling pathway, which plays a central role in plant immunity, and identifies differentially expressed genes (DEGs) that could be targeted for transcriptional detection. We have conducted a series of experiments to test the TAS strategy and found that the level of GmSAGT1 expression is highly correlated with soybean downy mildew (SDM) resistance with a correlation coefficient R2 = 0.7981. Using RT-PCR, we screened 2501 soybean germplasms and selected 26 collections with higher levels of both GmSAGT1 and GmPR1 (Pathogenesis-related proteins1) gene expression. Twenty-three out of the twenty-six lines were inoculated with Peronospora manshurica (Pm) in a greenhouse. Eight showed HR (highly resistant), four were R (resistant), five were MR (moderately resistant), three were S (susceptible), and three were HS (highly susceptible). The correlation coefficient R2 between the TAS result and Pm inoculation results was 0.7035, indicating a satisfactory consistency. The authors anticipate that TAS provides an effective strategy for screening crops with broad-spectrum and long-lasting resistance.

Exploring the Molecular Mechanisms underlying SADI-S Improves Glucose Metabolism in Type 2 Diabetic Rats through Liver Transcriptomics and Proteomics Analysis.

Metabolic surgery could improve or even reverse type 2 diabetes mellitus (T2DM). Single-anastomosis duodenal-ileal bypass with sleeve gastrectomy (SADI-S) is one of the most effective metabolic surgeries for T2DM. However, the molecular mechanisms behind the SADI-S-induced T2DM improvement are not fully understood.Here,T2DM rats received SADI-S and were sacrificed after 8 weeks; the controls received sham surgery; Liver tissues were collected for transcriptomics and proteomics analysis to identify differentially expressed genes (DEGs) and proteins (DEPs). Parallel reaction monitoring (PRM) was performed to validate the accuracy of the proteomics results.SADI-S significantly improved glucose metabolism in T2DM rats.A total of 120 genes/proteins(e.g., phosphoenolpyruvate carboxykinase (Pck1) and pyruvate kinase (Pklr)) exhibited consistent expression trends at both mRNA and protein levels. Among the upregulated genes/proteins involved in glucose metabolic pathways, enrichment was observed in pathways such as the pyruvate metabolic pathway, insulin signaling pathway, glycolysis/gluconeogenesis biological processes, glucagon signaling pathway, and AMPK signaling pathway. Downregulated genes/proteins were enriched in the pyruvate metabolic pathway. The above-mentioned signaling pathways are implicated in glucose metabolism, suggesting a potential mechanism for SADI-S-mediated alleviation of T2DM. The PRM validation results indicated that all selected proteins showed consistent trends between PRM and proteomics data. This consistency suggests the reliability of the proteomics results.

Research on the Therapeutic Effect of Qizhu Anti Cancer Recipe on Colorectal Cancer Based on RNA Sequencing Analysis.

Colorectal cancer is one of the common malignant tumors in clinical practice, and traditional Chinese medicine, as an important adjuvant treatment method, plays important roles in the treatment of malignant tumors. This study aims to explore the mechanism of action of the Qizhu anti-cancer recipe on colorectal cancer through transcriptome sequencing. The control group and Qizhu anti-cancer recipe group were established separately, and sequencing of the cells of the two groups was performed using the Illumina sequencing platform. Two sets of Differentially Expressed Genes (DEGs) were screened using the DESeq2 algorithm, and Principal Component Analysis (PCA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, Disease Ontology (DO), and Protein-Protein Interaction (PPI) were used to comprehensively analyze the molecular functions and signaling pathways enriched by DEGs. A total of 122 DEGs were identified through differential analysis, including 24 upregulated genes and 98 downregulated genes. GO analysis showed that DEGs were mainly enriched in functions such as alkaline phase activity, ion transport, cell differentiation, etc.; KEGG analysis showed that DEGs were mainly enriched in pathways such as Thiamine metabolism, apoptosis, signaling pathways regulating pluripotency of stem cells, cellular senescence and so on. Reactom analysis showed that DEGs were mainly enriched in response pathways such as EGR1,2,3 bind to the NAB2 promoter, EGR binds ARC gene, EGR-dependent NAB2 gene expression, etc.; DO analysis showed that differentially expressed genes were mainly enriched in diseases such as disease of cellular proliferation, disease of anatomical entity, organ system cancer, etc.; PPI analysis identified key differentially expressed genes, including DDIT3, CHAC1, TRIB3, and ASNS. Based on transcriptome sequencing and bioinformatics analysis, it was found that the Qizhu anti-cancer recipe may involve DEGs and signaling pathways in the treatment of colorectal cancer. Our study may provide potential drug targets for developing new treatment strategies for colorectal cancer.

Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD Cohort.

Localized diseases can be affected by and affect the systemic environment via blood circulation. In this study, we explored the differences in circulating serum mRNAs between patients with wet AMD (wAMD) and controls. Blood samples were obtained from 60 Finnish patients with wAMD and 64 controls. After serum preparation and RNA sequencing, the count data was examined for differentially expressed genes (DEGs) and further checked for enriched molecular pathways and ontology terms as well as links to clinical data. We found many DEGs and some enriched pathways, including the inflammation and cell survival-associated pathway tumour necrosis factor alpha (TNF-α) signaling via nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). The related DEGs were oxidized low-density lipoprotein receptor 1 (OLR1), salt inducible kinase 1 (SIK1), and coagulation factor III (F3). DEGs from degradative macular and retinal processes were also examined, many of which were also related to cardiovascular disease and maintenance. Additionally, DEG counts were inspected in relation to clinical and anti-VEGF treatment parameters, and glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A) levels were found to be significantly lower in patients with wAMD treated with anti-VEGF. Differentially expressed systemic mRNAs that are linked to mitochondrial function, oxidative stress, and inflammation may have a role in the pathology of wAMD. Our observations provide new data for the understanding of the progression of wAMD.

Transcriptomic Analysis of Cell Stress Response in Wickerhamomyces anomalus H4 Under Octanoic Acid Stress

The purified yeast strain H4, identified as W. anomalus through morphological, genetic, and phylogenetic analyses, was characterized and compared to a commercial Saccharomyces cerevisiae strain X16. W. anomalus H4 exhibited distinct morphological features. It demonstrated notable tolerance to 11% ethanol, 220 g/L glucose, and 200 mg/L octanoic acid, similar to X16, except for having a lower tolerance to SO2. Survival analysis under various stress conditions revealed that ethanol and octanoic acid had the most detrimental effects, with 56% cell mortality at 13% ethanol and 400 mg/L octanoic acid. Transcriptomic analysis under octanoic acid stress showed that at 200 mg/L, 3369 differentially expressed genes (DEGs) were induced, with 1609 being upregulated and 1760 downregulated, indicating broad transcriptional reprogramming. At 400 mg/L, only 130 DEGs were detected, suggesting a more limited response. KEGG pathway analysis indicated that most DEGs at 200 mg/L were associated with the “ribosome” and “proteasome” pathways, reflecting disruptions in protein synthesis and turnover. At 400 mg/L, the DEGs were primarily related to “DNA replication” and “pyruvate metabolism”. These findings highlight the adaptive mechanisms of W. anomalus H4 to environmental stresses, particularly octanoic acid, and its potential for use in brewing and fermentation processes.

Multiple Machine Learning Identifies Key Gene PHLDA1 Suppressing NAFLD Progression.

Non-alcoholic fatty liver disease (NAFLD) poses a serious global health threat, with its progression mechanisms not yet fully understood. While several molecular markers for NAFLD have been developed in recent years, a lack of robust evidence hampers their clinical application. Therefore, identifying novel and potent biomarkers would directly aid in the prediction, prevention, and personalized treatment of NAFLD. We downloaded NAFLD-related datasets from the Gene Expression Omnibus (GEO). Differential expression analysis and functional analysis were initially conducted. Subsequently, Weighted Gene Co-expression Network Analysis (WGCNA) and multiple machine learning strategies were employed to screen and identify key genes, and the diagnostic value was assessed using Receiver Operating Characteristic (ROC) analysis. We then explored the relationship between genes and immune cells using transcriptome data and single-cell RNA sequencing (scRNA-seq) data. Finally, we validated our findings in cell and mouse NAFLD models. We obtained 23 overlapping differentially expressed genes (DEGs) across three NAFLD datasets. Enrichment analysis revealed that DEGs were associated with Apoptosis, Parathyroid hormone synthesis, secretion and action, Colorectal cancer, p53 signaling pathway, and Biosynthesis of unsaturated fatty acids. After employing machine learning strategies, we identified one gene, pleckstrin homology like domain family A member 1 (PHLDA1), downregulated in NAFLD and showing high diagnostic accuracy. CIBERSORT analysis revealed significant associations of PHLDA1 with various immune cells. Single-cell data analysis demonstrated downregulation of PHLDA1 in NAFLD, with PHLDA1 exhibiting a significant negative correlation with macrophages. Furthermore, we found PHLDA1 to be downregulated in an in vitro hepatic steatosis cell model, and overexpression of PHLDA1 significantly reduced lipid accumulation, as well as the expression of key molecules involved in hepatic lipogenesis and fatty acid uptake, such as FASN, SCD-1, and CD36. Additionally, gene set enrichment analysis (GSEA) pathway enrichment analysis suggested that PHLDA1 may influence NAFLD progression through pathways such as Cytokine Cytokine Receptor Interaction, Ecm Receptor Interaction, Parkinson's Disease, and Ribosome pathways. Our conclusions were further validated in a mouse model of NAFLD. Our study reveals that PHLDA1 inhibits the progression of NAFLD, as overexpression of PHLDA1 significantly reduces lipid accumulation in cells and markedly decreases the expression of key molecules involved in liver lipogenesis and fatty acid uptake. Therefore, PHLDA1 may emerge as a novel potential target for future prediction, diagnosis, and targeted prevention of NAFLD.

Common molecular basis for MASH and hepatitis C revealed via systems biology approach

BackgroundMetabolic dysfunction-associated steatohepatitis (MASH) is characterized by liver inflammation and damage caused by a buildup of fat in the liver. Hepatitis C, caused by hepatitis C virus (HCV), is a disease that can lead to liver cirrhosis, liver cancer, and liver failure. MASH and hepatitis C are the common causes of liver cirrhosis and hepatocellular carcinoma. Several studies have shown that hepatic steatosis is also a common histological feature of liver in HCV infected patients. However, the common molecular basis for MASH and hepatitis C remains poorly understood.MethodsFirstly, differentially expressed genes (DEGs) for MASH and hepatitis C were extracted from the GSE89632, GSE164760 and GSE14323 datasets. Subsequently, the common DEGs shared among these datasets were determined using the Venn diagram. Next, a protein-protein interaction (PPI) network was constructed based on the common DEGs and the hub genes were extracted. Then, gene ontology (GO) and pathway analysis of the common DEGs were performed. Furthermore, transcription factors (TFs) and miRNAs regulatory networks were constructed, and drug candidates were identified. After the MASH and hepatitis C cell model was treated with predicted drug, the expression levels of the signature genes were measured by qRT-PCR and ELISA.Results866 common DEGs were identified in MASH and hepatitis C. The GO analysis showed that the most significantly enriched biological process of the DEGs was the positive regulation of cytokine production. 10 hub genes, including STAT1, CCL2, ITGAM, PTPRC, CXCL9, IL15, SELL, VCAM1, TLR4 and CCL5, were selected from the PPI network. By constructing the TF-gene and miRNA-gene network, most prominent TFs and miRNAs were screened out. Potential drugs screening shows that Budesonide and Dinoprostone may benefit patients, and cellular experiments showed that Budesonide effectively inhibited the expression of genes related to glycolipid metabolism, fibrosis, and inflammatory factors.ConclusionWe extracted 10 hub genes between MASH and hepatitis C, and performed a series of analyses on the genes. Molecular docking and in vitro studies have revealed that Budesonide can effectively suppress the progression of MASH and hepatitis C. This study can provide novel insights into the potential drug targets and biomarkers for MASH and hepatitis C.

Transcriptomic Profile of the Male Rat Hypothalamus and Nucleus Accumbens After Paroxetine Treatment and Withdrawal: Possible Causes of Sexual Dysfunction.

Paroxetine, a selective serotonin reuptake inhibitor (SSRI), may induce sexual dysfunction during treatment and upon discontinuation. The mechanisms involved have been poorly explored so far. We have analyzed, by RNA sequencing, the whole transcriptomic profile in the hypothalamus and nucleus accumbens (NAc) (two brain regions involved in sexual behavior) of male rats daily treated for 2weeks with paroxetine (T0) and at 1month of withdrawal (T1). Data here reported show seven differentially expressed genes (DEGs) at T0 and 1 at T1 in the hypothalamus and 245 at T0 and 6 at T1 in the NAc. In addition, Gene-Set Enrichment, Gene Ontology, and Reactome analyses confirm that inflammatory signature and immune system activation were present at T0 in both brain areas. Considering that inflammation is generally associated with depression and that no paradigms inducing the pathology were here applied, these SSRI pro-depressive effects should be considered in patients without a clear indication of depression. Moreover, DEGs related to neurotransmitters with a role in sexual behavior and the reward system, such as dopamine (e.g., sialyltransferase 8B-ST8SIA3), glutamate (e.g., glutamate receptor ionotropic delta-2-GRID2) and GABA (e.g., glutamate decarboxylase type 2-GAD2) or associated with neurexin and neuroligin pathways and brain-derived neurotrophic factor (BDNF) signaling, were reported to be dysregulated in the NAc, further confirming dysfunction in this brain area. Interestingly, the analysis of DEGs altered at T1 in the NAc confirms the persistence of some of these side effects providing further information for post-SSRI sexual dysfunction (PSSD) etiopathogenesis.

Molecular mechanisms of acquired idiopathic generalized anhidrosis: differential gene expression and potential therapeutic targets

Eccrine sweat glands are essential for thermoregulation. Acquired idiopathic generalized anhidrosis (AIGA) is a rare disorder characterized by the absence of sweating, leading to severe complications like heatstroke and skin dryness. The underlying etiology remains unknown, complicating diagnosis and treatment. This study aimed to elucidate the genetic mechanisms of AIGA by analysing the gene expression in eccrine sweat glands using the GSE193125 dataset from the NCBI Gene Expression Omnibus (GEO). This study identified differentially expressed genes (DEGs) (genes that show statistically significant differences in expression levels in AIGA), with JUN and CCN1 significantly downregulated in anhidrotic lesions of AIGA patients. Receiver operating characteristic (ROC) curve demonstrated the accuracy of these genes in classification (JUN = 0.88 and CCN1 = 0.77). Gene and protein interaction networks which are defined as networks of physical interactions between genes and proteins, constructed using GeneMANIA and STRING, revealed substantial physical interactions among them. Gene set enrichment analysis highlighted the neuroinflammatory and estrogen receptor signaling pathways are associated with this condition, suggesting hormonal regulation’s role in the anhidrosis mechanism. Key miRNAs, including hsa-let-7b-5p, hsa-miR-10b-5p, and hsa-miR-124-3p, are associated with the DEGs, underscoring the importance of post-transcriptional and transcriptional regulation. Through the Drug Gene Interaction Database (DGIdb), ciprofibrate is identified as a potential therapeutic agent targeting the JUN gene. Molecular docking confirmed a strong binding affinity between ciprofibrate and JUN, suggesting ciprofibrate could modulate JUN activity and regulate AIGA symptoms. ADMET analysis, which refers to the assessment of absorption, distribution, metabolism, excretion, and toxicity of a drug or compound, is crucial for evaluating its pharmacokinetic and safety profile. The analysis indicated that ciprofibrate has favourable pharmacokinetic properties and a relatively safe toxicity profile. This comprehensive bioinformatics approach, integrating gene expression analysis, miRNA identification, and drug interaction, provides valuable insights into anhidrosis molecular pathology and highlights ciprofibrate’s potential as a targeted therapeutic strategy. Despite limitations, including a small sample size and reliance on computational predictions, this study paves the way for further research and potential therapeutic interventions for AIGA.

Luteolin alleviates cerebral ischemia/reperfusion injury by regulating cell pyroptosis.

This study aimed to clarify the roles and underlying mechanisms of luteolin in the progression of cerebral ischemia/reperfusion injury (CIRI). A mouse model of CIRI was established using the middle cerebral artery occlusion (MCAO) method, after which luteolin was administered. Subsequently, neuronal apoptosis and pyroptosis were measured and the brain tissues of each group were subjected to RNA sequencing. Luteolin alleviated MCAO-induced brain infarction, apoptosis, and pyroptosis. RNA sequencing identified 3,379, 2,777, and 3,933 differentially expressed genes (DEGs) in the MCAO vs sham, MCAO vs MCAO + luteolin, and MCAO + luteolin vs sham groups, respectively. The identified DEGs showed enrichment in multiple processes, including pattern specification, forebrain development, anion transport, leukocyte migration, regulation of cell-cell adhesion, and positive regulation of the response to external stimuli, as well as the calcium, PI3K-AKT, JAK-STAT, NF-kappa B, IL-17, cAMP, cGMP-PKG, and Wnt signaling pathways. In addition, Ccl2 and Angpt2 interacted more with the other top 30 DEGs with high interaction weights. Finally, RT-qPCR results showed that MCAO induction significantly up-regulated the expression of Stoml3, Eomes, and Ms4a15 and down-regulated Nms, Ttr, and Avpr1a; however, luteolin could partially reverse the expression caused by MCAO. Luteolin can alleviate brain infarction, apoptosis, and pyroptosis in CIRI, and may improve MCAO-induced CIRI by targeting the identified DEGs and their enriched pathways.

GZMK Facilitates Experimental Rheumatoid Arthritis Progression by Interacting with CCL5 and Activating the ERK Signaling.

Synovial over-proliferation is a key event in the progression of rheumatoid arthritis (RA) disease. Ferroptosis may be essential for maintaining the balance between synovial proliferation and death. This study aimed to investigate the molecular mechanisms mediating the activation and ferroptosis of collagen-induced arthritis(CIA)-synovial fibroblasts (SFs). Differentially expressed genes (DEGs) in the synovial tissues of CIA rats and normal rats were screened through sequencing. The GSE115662 dataset from the GEO database was analyzed and screened for DEGs. The viability, proliferation, migration, invasion, cell cycle, and apoptosis of CIA-SFs were analyzed by cell counting kit-8, 5-ethynyl-2'-deoxyuridine, flow cytometry, transwell migration, and invasion assays. The ferroptosis of CIA-SFs was assessed using matching reagent kits to detect indicators like reactive oxygen species, ferrous iron, malondialdehyde, glutathione, and superoxide dismutase. The interaction between Granzyme K (GZMK) and C-C motif chemokine 5 (CCL5) was determined by coimmunoprecipitation assay. We found abnormal GZMK expression in the GSE115662 database and mRNA sequencing data. GZMK was overexpressed in CIA-SFs, and GZMK promoted cell proliferation, migration, invasion, inflammation, and decreased cell apoptosis and ferroptosis in CIA-SFs. GZMK could interact with CCL5 to activate the ERK signaling. GZMK and CCL5 knockdown improved by reducing arthritis scores, redness and swelling of paws, and pathological changes in joint synovium of CIA rats. CCL5 overexpression reversed the effects of GZMK silencing on CIA-SFs cell proliferation, migration, invasion, apoptosis, and ferroptosis. We confirmed that GZMK accelerated experimental rheumatoid arthritis progression by interacting with CCL5 and activating the ERK signaling.

Identification of Sequential Molecular Mechanisms and Key Biomarkers in Early Glaucoma by Integrated Bioinformatics Analysis.

Glaucoma is a neurodegenerative disease characterized by progressive optic nerve degeneration and retinal ganglion cell (RGC) loss. In early glaucoma, before obvious axon loss, highly organized pathological processes in RGCs occur sequentially, involving axons, dendrites and synaptic terminals. The optic nerve head (ONH) is the critical structure of early glaucomatous neurodegeneration. Taking advantage of high-throughput data from the ONH and the weighted gene coexpression network analysis (WGCNA) method, the current study aims to gain insight into the full scope of pathological events in early glaucoma and define their chronological sequence. The expression profiles of GSE26299, GSE110019, and GSE139605, which measure ONH gene expression in different glaucoma models, were downloaded from the Gene Expression Omnibus (GEO) database. In GSE26299, which uses 10.5-month-old DBA/2J mice, WGCNA was utilized to construct a gene coexpression network, and the most significant modules of early (NOE), moderate (MOD) and severe (SEV) glaucoma were identified. The differentially expressed genes (DEGs) of GSE110019 and GSE139605 significantly overlapped with the correlated module of the MOD group, so the 3 gene sets were analyzed together. Pathway enrichment analysis via the GO, KEGG, and Reactome pathways was subsequently performed, followed by protein‒protein interaction (PPI) analysis to screen key genes associated with each stage. Several hub gene expression patterns were identified in a glucocorticoid-induced glaucoma (GIG) model via quantitative PCR and immunostaining. The pink module was positively correlated with the NOE group (r = 0.48, p = 4e-04) and negatively correlated with the glaucoma stage (r = -0.88, p = 3e-17). The genes in the pink module were enriched in the synaptic transmission and axonal transport pathways. The tan module was negatively correlated with the NOE group (r = -0.43, p = 0.002) and positively correlated with the glaucoma stage (r = 0.77, p = 7e-11). The genes in the tan module were associated with pathways such as tight junctions, retinol metabolism, and linoleic acid metabolism. The purple module was positively correlated with the MOD group (r = 0.64, p = 5e-07). The common genes among the purple module and the DEGs of the two other datasets were enriched in pathways related to mitotic cell division, cytokine activity, and the extracellular matrix (ECM). The hub genes identified by PPI included Nrn1, Cplx1, Timp1, and Cdk1. Quantitative PCR and immunostaining confirmed that Limk1 expression was increased in the ONH of GIG mice. In early glaucomatous neuropathy, intrinsic changes in RGCs precede the activation of glial cells and ECM remodeling. These latter events are common pathological changes observed in the ONH in both cats and mice. Our study may provide new targets for the early detection and treatment of glaucoma.

Comparative analysis of acute eccentric contraction-induced changes to the skeletal muscle transcriptome in young and aged mice and humans.

Adaptations to skeletal muscle following resistance exercise are due in part to changes to the skeletal muscle transcriptome. While transcriptional changes in response to resistance exercise occur in young and aged muscle, aging alters this response. Rodent models have served great utility in defining regulatory factors that underscore the influence of mechanical load and aging on changes to skeletal muscle phenotype. Unilateral eccentric contractions in young and aged rodents are widely used to model resistance exercise in humans. However, the extent to which unilateral eccentric contractions in young and aged rodents mimics the transcriptional response in humans remains unknown. We re-analyzed two publicly available RNA sequencing datasets from young and aged mice and humans that were subjected to acute eccentric contractions to define key similarities and differences to the muscle transcriptional response following this exercise modality. The effect of aging on the number of contraction-sensitive genes, the distribution patterns of those genes into unique/common categories, and the cellular pathways associated with the differentially expressed genes (DEGs) were similar in mice and humans. However, there was little overlap between species when comparing specific contraction-sensitive DEGs within the same age group. There were strong intraspecies relationships for the common transcription factors predicted to influence the contraction-sensitive gene sets, whereas interspecies relationships were weak. Overall, these data demonstrate key similarities between mice and humans for the contraction-induced changes to the muscle transcriptome, but we posit species-specific responses exist and should be taken into consideration when attempting to translate rodent eccentric exercise models.

Effects of cold stress on the blood-brain barrier in Plectropomus leopardus

BackgroundThe leopard coral grouper (Plectropomus leopardus) is a commercially valuable tropical marine fish species known to be sensitive to low temperatures. A comprehensive understanding of the molecular mechanisms governing its response to acute cold stress is of great importance. However, there is a relative scarcity of fundamental research on low-temperature tolerance in the leopard coral grouper.MethodsIn this study, a cooling and rewarming experiment was conducted on 6-month-old leopard coral groupers. Within 24 h, we decreased the ambient temperature from 25 °C to 13 °C and subsequently allowed it to naturally return to 25 °C. During this process, a comprehensive investigation of serum hormone levels, enzyme activity, and brain transcriptome analysis was performed.ResultsP. leopardus displayed a noticeable adaptive response to the initial temperature decrease by temporarily reducing its life activities. Our transcriptome analysis revealed that the differentially expressed genes (DEGs) were primarily concentrated in crucial pathways including the blood-brain barrier (BBB), inflammatory response, and coagulation cascade. In situ hybridization of claudin 15a (cldn15a), a key gene for BBB maintaining, further confirmed that exposure to low temperatures led to the disruption of the blood-brain barrier and stimulated a pronounced inflammatory reaction within the brain. Upon rewarming, there was a recovery of BBB integrity accompanied by the persistence of inflammation within the brain tissue.ConclusionsOur study reveals the complex interactions between blood-brain barrier function, inflammation, and recovery in P. leopardus during short-term temperature drops and rewarming. These findings provide valuable insights into the physiological responses of this species under cold stress conditions.

Identification and validation of interferon-stimulated gene 15 as a biomarker for dermatomyositis by integrated bioinformatics analysis and machine learning

BackgroundDermatomyositis (DM) is an autoimmune disease that primarily affects the skin and muscles. It can lead to increased mortality, particularly when patients develop associated malignancies or experience fatal complications such as pulmonary fibrosis. Identifying reliable biomarkers is essential for the early diagnosis and treatment of DM. This study aims to identify and validate pivotal diagnostic biomarker for DM through integrated bioinformatics analysis and clinical sample validation.MethodsGene expression datasets GSE46239 and GSE142807 from the Gene Expression Omnibus (GEO) database were merged for analysis. Differentially expressed genes (DEGs) were identified and subjected to enrichment analysis. Advanced machine learning methods were utilized to further pinpoint hub genes. Weighted gene co‐expression network analysis (WGCNA) was also conducted to discover key gene modules. Subsequently, we derived intersection gene from these methods. The diagnostic performance of the candidate biomarker was evaluated using analysis with dataset GSE128314 and confirmed by immunohistochemistry (IHC) in skin lesion biopsy specimens. The CIBERSORT algorithm was used to analyze immune cell infiltration patterns in DM, then the association between the hub gene and immune cells was investigated. Gene set enrichment analysis (GSEA) was performed to understand the biomarker’s biological functions. Finally, the drug-gene interactions were predicted using the DrugRep server.ResultsInterferon-stimulated gene 15 (ISG15) was identified by intersecting DEGs, advanced machine learning-selected genes and key module genes from WGCNA. ROC analysis showed ISG15 had a high Area under the curve (AUC) of 0.950. IHC findings confirmed uniformly positive expression of ISG15, particularly in perivascular regions and lymphocytes, contrasting with universally negative expression in controls. Further analysis revealed that ISG15 is involved in abnormalities in various immune cells and inflammation-related pathways. We also predicted three drugs targeting ISG15, supported by molecular docking studies.ConclusionOur study identifies ISG15 as a highly specific diagnostic biomarker for DM, ISG15 may be closely related to the pathogenesis of DM, demonstrating promising potential for clinical application.