Enriched Differentially Expressed Genes Research Articles

Analysis of differentially expressed genes related to cell death in porcine kidney-15 cells at 24 and 48 hours post porcine parvovirus infection.

This study aims to identify and characterize differentially expressed genes (DEGs) associated with porcine parvovirus (PPV)-induced cell death in porcine kidney-15 (PK-15) cells. By analyzing the biological processes enriched by these DEGs and exploring their interaction networks, we aim to gain a deeper understanding of the molecular mechanisms underlying PPV-mediated cell death. After infecting cultured PK-15 cells with PPV for 24 and 48 hours, cell viability and cysteine-requiring aspartate protease-3 (caspase-3) activity were assessed using an enzyme marker. Apoptosis was observed using fluorescence microscopy. The genome-wide gene expression levels were analyzed through RNA sequencing. The functional enrichment of DEGs was analyzed using the Kyoto Encyclopedia of Genes and Genomes database, and the protein-protein interaction network was generated using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Porcine parvovirus inhibits cell viability, boosts caspase-3 activity, and enhances cell death at 24 and 48 hours postinfection (HPI). Porcine parvovirus-infected cells showed 547 DEGs at 24 HPI and 1,765 at 48 HPI. Different forms of cell death were enriched in 149 genes that were upregulated at both 24 and 48 HPI. More DEGs associated with cell death were involved at 48 than at 24 HPI. These DEGs are involved in multiple signaling pathways and interact within a complex protein network. Porcine parvovirus infection of PK-15 cells induces multiple cell death-related DEGs and signaling pathways. Our study presents a promising approach to investigating the mechanism of PPV infection, with a particular focus on the induction of cell death.

Transcriptome sequencing analysis of overexpressed SikCDPK1 in tobacco reveals mechanisms of cold stress response

BackgroundCold is a significant limiting factor in productivity, particularly in northwestern and eastern China. Calcium-Dependent Protein Kinases (CDPKs), a primary calcium signaling sensor in plants, play an important role in their response to cold. Snow lotus (Sasussured involucrata Kar L) is a plant that thrives in harsh climates and grows in northwest China. However, there were no reports on the transcriptome of OE-SikCDPK1 transgenic tobacco in response to cold.ResultsWhen exposed to cold stress, OE-SikCDPK1 plants displayed a cold-tolerant phenotype compared to non-transgenic tobacco. Under cold conditions, relative water content reduced, relative conductivity increased, malondialdehyde levels rose, and cold-responsive gene expression increased. The OE-SikCDPK1 gene and non-transgenic tobacco were employed for research purposes. The transcriptome of leaves was sequenced using the HISAT2 sequencing platform, and the data were used to examine gene function annotation and differentially expressed genes (DEGs). 53,022 DEGs in tobacco leaves under cold treatment were obtained. The GO enrichment results revealed that it was enriched for biological-process, defense response and other processes under cold stress. The KEGG pathway enrichment analysis revealed that the metabolic pathways of significant enrichment of DEGs under cold stress mainly involved MAPK signaling pathway transduction. The transcription factor identification results showed that the transcription factors with the largest number of differential expressions under cold treatment were mainly from WRKY, AP2, MYB, bHLH, NAC and other transcription factor families.ConclusionThe cold tolerance mechanism of snow lotus SikCDPK1 was comprehensively analyzed at the transcriptional level for the first time using RNA-seq technology. This study demonstrates that SikCDPK1 can respond to cold by participating in the MAPK signaling pathway and regulating the expression levels of transcription factors, including WRKY, AP2, MYB, bHLH, and NAC. These results offer valuable insights for further exploration of the cold tolerance mechanism associated with SikCDPK1.

Transcriptome Analysis Reveals the Early Development in Subcutaneous Adipose Tissue of Laiwu Piglets.

Adipose tissue plays an important role in pig production efficiency. Studies have shown that postnatal development has a vital impact on adipose tissue; however, the mechanisms behind pig adipose tissue early-life programming remain unknown. In this study, we analyzed the transcriptomes of the subcutaneous adipose tissue (SAT) of 1-day and 21-day old Laiwu piglets. The results showed that the SAT of Laiwu piglets significantly increased from 1-day to 21-day, and transcriptome analysis showed that there were 2352 and 2596 differentially expressed genes (DEGs) between 1-day and 21-day SAT in male and female piglets, respectively. Expression of genes in glycolysis, gluconeogenesis, and glycogen metabolism such as pyruvate kinase M1/2 (PKM), phosphoenolpyruvate carboxy kinase 1 (PCK1) and amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase (AGL) were significantly different between 1-day and 21-day SAT. Genes in lipid uptake, synthesis and lipolysis such as lipase E (LIPE), acetyl-CoA carboxylase alpha (ACACA), Stearoyl-CoA desaturase (SCD), and 3-hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) were also differentially expressed. Functional analysis showed enrichment of DEGs in transcriptional regulation, protein metabolism and cellular signal transduction. The protein-protein interaction (PPI) networks of these DEGs were analyzed and potential hub genes in these pathways were identified, such as transcriptional factors forkhead box O4 (FOXO4), CCAAT enhancer binding protein beta (CEBPB) and CCAAT enhancer binding protein delta (CEBPD), signal kinases BUB1 mitotic checkpoint serine/threonine kinase (BUB1) and cyclin-dependent kinase 1 (CDK1), and proteostasis-related factors ubiquitin conjugating enzyme E2 C (UBE2C) and cathepsin D (CTSD). Moreover, we further analyzed the transcriptomes of SAT between genders and the results showed that there were 54 and 72 DEGs in 1-day and 21-day old SAT, respectively. Genes such as KDM5D and KDM6C showed gender-specific expression in 1-day and 21-day SAT. These results showed the significant changes in SAT between 1-day and 21-day in male and female Laiwu pigs, which would provide information to comprehensively understand the programming of adipose tissue early development and to regulate adipose tissue function.

Effects of Selenium, Iron, and Zinc Enrichment on Cultured Sea Cucumber (Apostichopus Japonicus).

Selenium, iron, and zinc (Se, Fe, Zn) are essential trace elements crucial for animal growth, development, and immune protection, but they can be detrimental in excess. This study evaluates the impacts of Se, Fe and Zn on Apostichopus japonicus over a period of nine days, utilizing concentrations ranging from low to high: Se (0.20 µmol/L and 0.82 µmol/L), Fe (4.74 µmol/L and 18.96 µmol/L), Zn (1.88 µmol/L and 7.51 µmol/L). Concentrations of these trace elements in sea cucumbers increased with exposure time. Activities of CAT, SOD, and GSH-PX enzymes were enhanced. Transcriptomic analyses of sea cucumber body wall revealed significant gene expression changes, with differentially expressed genes (DEGs) numbering 294 at high and 945 at low Se concentrations, 906 at high and 210 at low Fe concentrations, and 423 at high and 123 at low Zn concentrations. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses highlighted DEGs enrichment in critical metabolic and immune-related pathways, including DNA replication, arachidonic acid metabolism, and oxidative phosphorylation. These results suggest that energy metabolism and immune regulation are pivotal in managing these elements, potentially enhancing sea cucumber immunity. This study enhances our comprehension of the physiological responses of sea cucumbers to trace elements and provides a theoretical basis for their use in aquaculture.

A transcriptome-wide analysis provides novel insights into how Metabacillus indicus promotes coral larvae metamorphosis and settlement

BackgroundCoral reefs experience frequent and severe disturbances that can overwhelm their natural resilience. In such cases, ecological restoration is essential for coral reef recovery. Sexual reproduction has been reported to present the simplest and most cost-effective means for coral reef restoration. However, larval settlement and post-settlement survival represent bottlenecks for coral recruitment in sexual reproduction. While bacteria play a significant role in triggering coral metamorphosis and settlement in many coral species, the underlying molecular mechanisms remain largely unknown. In this study, we employed a transcriptome-level analysis to elucidate the intricate interactions between bacteria and coral larvae that are crucial for the settlement process.ResultsHigh Metabacillus indicus strain cB07 inoculation densities resulted in the successful induction of metamorphosis and settlement of coral Pocillopora damicoris larvae. Compared with controls, inoculated coral larvae exhibited a pronounced increase in the abundance of strain cB07 during metamorphosis and settlement, followed by a significant decrease in total lipid contents during the settled stage. The differentially expressed genes (DEGs) during metamorphosis were significantly enriched in amino acid, protein, fatty acid, and glucose related metabolic pathways. In settled coral larvae induced by strain cB07, there was a significant enrichment of DEGs with essential roles in the establishment of a symbiotic relationship between coral larvae and their symbiotic partners. The photosynthetic efficiency of strain cB07 induced primary polyp holobionts was improved compared to those of the negative controls. In addition, coral primary polyps induced by strain cB07 showed significant improvements in energy storage and survival.ConclusionsOur findings revealed that strain cB07 can promote coral larval settlement and enhance post-settlement survival and fitness. Manipulating coral sexual reproduction with strain cB07 can overcome the current recruitment bottleneck. This innovative approach holds promise for future coral reef restoration efforts.

Transcriptomic and physiological responses of Quercus acutissima and Quercus palustris to drought stress and rewatering.

Establishment of oak seedlings, which is an important factor in forest restoration, is affected by drought that hampers the survival, growth, and development of seedlings. Therefore, it is necessary to understand how seedlings respond to and recover from water-shortage stress. We subjected seedlings of two oak species, Quercus acutissima and Quercus palustris, to drought stress for one month and then rewatered them for six days to observe physiological and genetic expression changes. Phenotypically, the growth of Q. acutissima was reduced and severe wilting and recovery failure were observed in Q. palustris after an increase in plant temperature. The two species differed in several physiological parameters during drought stress and recovery. Although the photosynthesis-related indicators did not change in Q. acutissima, they were decreased in Q. palustris. Moreover, during drought, content of soluble sugars was significantly increased in both species, but it recovered to original levels only in Q. acutissima. Malondialdehyde content increased in both the species during drought, but it did not recover in Q. palustris after rewatering. Among the antioxidant enzymes, only superoxide dismutase activity increased in Q. acutissima during drought, whereas activities of ascorbate peroxidase, catalase, and glutathione reductase increased in Q. palustris. Abscisic acid levels were increased and then maintained in Q. acutissima, but recovered to previous levels after rewatering in Q. palustris. RNA samples from the control, drought, recovery day 1, and recovery day 6 treatment groups were compared using transcriptome analysis. Q. acutissima exhibited 832 and 1076 differentially expressed genes (DEGs) related to drought response and recovery, respectively, whereas Q. palustris exhibited 3947 and 1587 DEGs, respectively under these conditions. Gene ontology enrichment of DEGs revealed "response to water," "apoplast," and "Protein self-association" to be common to both the species. However, in the heatmap analysis of genes related to sucrose and starch synthesis, glycolysis, antioxidants, and hormones, the two species exhibited very different transcriptome responses. Nevertheless, the levels of most DEGs returned to their pre-drought levels after rewatering. These results provide a basic foundation for understanding the physiological and genetic expression responses of oak seedlings to drought stress and recovery.

LcINH1 as an inhibitor of cell wall invertase LcCWIN5 regulates early seed development in Litchi chinensis Sonn

Sugar signal mediated by Cell wall invertase (CWIN) plays a central role in seed development. In higher plants, invertase inhibitors (INHs) suppress CWIN activities at a post-translational level. In Litchi chinensis cultivar ‘Nuomici’, impaired CWIN expression is associated with seed abortion. Here, the expression of LcINH1 was significantly higher in the funicle of seed-aborting cultivar ‘Nuomici’ than big-seeded cultivar ‘Heiye’. Promoter analyses found LcINH1 contained a 404 bp repeat fragment with an endosperm regulatory element of Skn-1_motif. LcINH1 and LcCWIN2/5 were located in plasma membrane. LcINH1 was able to interact with LcCWIN5, but not with LcCWIN2. In vitro enzyme activity assay demonstrated that LcINH1 could inhibit CWIN activity. Silencing LcINH1 in ‘Nuomici’ resulted in normal seed development, paralleled increased CWIN activities and glucose levels. Transcriptome analysis identified 1079 differentially expressed genes (DEGs) in LcINH1-silenced fruits. KEGG analysis showed significant enrichment of DEGs in pathways related to transporters and plant hormone signal transduction. Weighted gene co-expression network analysis indicated that the turquoise module was highly correlated with fructose content, and LcSWEET3b was closely associated with early seed development. These findings suggest that LcINH1 regulate LcCWIN5 activity at the post-translational level to alter sucrose metabolism, thereby affecting early seed development in litchi.

Transcriptional dynamic changes in energy metabolism, protein synthesis and cell cycle regulation reveal the biological adaptation mechanisms of juvenile Acrossocheilus wenchowensis under acute temperature changes

In recent years, frequent acute temperature changes have posed a serious threat to the physiology and survival of fish. This study utilized RNA-Seq technology to analyze the transcriptional dynamics in the muscle tissues of Acrossocheilus wenchowensis under various acute temperature conditions (16◦C, 20◦C, 24◦C, 28◦C and 32◦C). Through comprehensive analysis, we identified 11509 differentially expressed genes (DEGs), a gene set (profiles 19) that was significantly up-regulated with increasing temperature, and two weighted gene co-expression network analysis (WGCNA) modules that were significantly correlated with acute temperature changes. Furthermore, we identified 28 transcription factors that are pivotal in oxidative stress and energy metabolism under acute temperature changes. Our results showed that, compared to the control group (24°C), KEGG functional enrichment analysis revealed significant enrichment of DEGs in the cell cycle, DNA replication, and p53 signaling pathway, with an overall trend of suppressed expression. This indicates that maintaining cell stability and reducing cell damage is an effective adaptive mechanism for A. wenchowensis to cope with acute temperature changes. Through STEM analysis and the black WGCNA module associated with high-temperature stress, we identified significant up-regulation of pathways and hub genes related to energy metabolism including oxidative phosphorylation, TCA cycle, purine metabolism, and glutathione metabolism, as well as the central roles of signal transduction pathways such as MAPK signaling pathway and AMPK signaling pathway, which synergistically regulate energy production. Under acute low-temperature stress, the turquoise WGCNA module highlighted significant up-regulation of hub genes associated with Ribosomal and Spliceosomal pathways related to protein synthesis and processing, as well as activation of calcium signaling pathways, which plays an important role in maintaining cellular function during low-temperature adaptation. These findings provide a critical theoretical and molecular basis for the adaptation of eurythermal fish to rapid temperature changes.

Helicobacter pylori infection exacerbates metabolic dysfunction-associated steatotic liver disease through lipid metabolic pathways: a transcriptomic study

BackgroundThe relationship between Helicobacter pylori (H. pylori) infection and metabolic dysfunction-associated steatotic liver disease (MASLD) has attracted increased clinical attention. However, most of those current studies involve cross-sectional studies and meta-analyses, and experimental mechanistic exploration still needs to be improved. This study aimed to investigate the mechanisms by which H. pylori impacts MASLD.MethodsWe established two H. pylori-infected (Cag A positive and Cag A negative) mouse models with 16 weeks of chow diet (CD) or high-fat diet (HFD) feeding. Body weight, liver triglyceride, blood glucose, serum biochemical parameters, inflammatory factors, and insulin resistance were measured, and histological analysis of liver tissues was performed. Mouse livers were subjected to transcriptome RNA sequencing analysis.ResultsAlthough H. pylori infection could not significantly affect serum inflammatory factor levels and serum biochemical parameters in mice, serum insulin and homeostatic model assessment for insulin resistance levels increased in CD mode. In contrast, H. pylori Cag A + infection significantly aggravated hepatic pathological steatosis induced by HFD and elevated serum inflammatory factors and lipid metabolism parameters. Hepatic transcriptomic analysis in the CD groups revealed 767 differentially expressed genes (DEGs) in the H. pylori Cag A + infected group and 1473 DEGs in the H. pylori Cag A- infected group, and the “nonalcoholic fatty liver disease” pathway was significantly enriched in KEGG analysis. There were 578 DEGs in H. pylori Cag A + infection combined with the HFD feeding group and 820 DEGs in the H. pylori Cag A- infected group. DEGs in the HFD groups were significantly enriched in “fatty acid degradation” and “PPAR pathway.” Exploring the effect of different Cag A statuses on mouse liver revealed that fatty acid binding protein 5 was differentially expressed in Cag A- H. pylori. DEG enrichment pathways were concentrated in the “PPAR pathway” and “fatty acid degradation.”ConclusionsClinicians are expected to comprehend the impact of H. pylori on MASLD and better understand and manage MASLD. H. pylori infection may exacerbate the development of MASLD by regulating hepatic lipid metabolism, and the H. pylori virulence factor Cag A plays a vital role in this regulation.

Effects of stocking density on behavior, physiology, and gene expression of the sea cucumber Apostichopus japonicus

The behavioral and physiological mechanisms induced by high density remain mostly unknown in sea cucumbers, although it has been widely adopted to increase the space usage efficiency in aquaculture. The present study focused on investigating how high density affects fitness-related behaviors, physiology, and gene expression in the sea cucumber Apostichopus japonicus. We found that high density significantly increased crawling behavior of sea cucumbers in short-term (one week), while significantly inhibited feeding behavior in long-term (seven weeks). Foraging behavior was not significantly affected in sea cucumbers at high density. Our study found that short-term high density did not have a significant impact on the cortisol and glucose concentration in A. japonicus. There was no significant difference in serotonin (5-HT) of sea cucumbers between high and low density. Gamma-aminobutyric acid (GABA) significantly increased in sea cucumbers at high density. Thus, GABA probably plays a crucial role in regulating the behavior of A. japonicus at high density. In addition, we conducted a transcriptome analysis on intestinal tract of sea cucumbers at two different stocking densities. There were 117 differentially expressed genes (DEGs) were discovered, including 72 up-regulated DEGs and 45 down-regulated DEGs. Gene Ontology (GO) functional annotation revealed that the DEGs were significantly enriched in the processes of oxidation-reduction, dioxygenase activity, and oxidoreductase activity. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed a significant enrichment of DEGs in glycerolipid metabolism and PPAR signaling pathways. We highlighted LPL encoding lipoprotein esterase, which probably plays an important role in lipid metabolism in A. japonicus under high density. In conclusion, the present study clarified the behavioral and physiological reactions and further revealed the related molecular mechanisms of A. japonicus in a high-density condition. This provides valuable information into the management of the high-density aquaculture of sea cucumbers.

The upregulation of POLR3G correlates with increased malignancy of bladder urothelium

Bladder cancer remains a significant health challenge due to its high recurrence and progression rates. This study aims to evaluate the role of POLR3G in the development and progression of bladder cancer and the potential of POLR3G to serve as a novel therapeutic target. We constructed a bladder cancer model in Wistar rats by administering N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN), which successfully induced a transition from normal mucosa to hyperplasia and ultimately to urothelial carcinoma. We observed a progressive upregulation of POLR3G expression during the bladder cancer development and progression. To investigate the functional role of POLR3G, we performed functional experiments in bladder cancer cell lines. The results demonstrated that knocking down POLR3G significantly inhibited cell proliferation, migration, and invasion. We further conducted RNA sequencing on POLR3G-knockdown bladder cancer cells, and Metascape was employed to perform the functional enrichment analysis of the differentially expressed genes (DEGs). Enrichment analysis revealed the enrichment of DEGs in the RNA polymerase and apoptotic cleavage of cellular proteins pathways, as well as their involvement in the Wnt and MAPK signaling pathways. The downregulation of Wnt pathway-related proteins such as Wnt5a/b, DVL2, LRP-6, and phosphorylated LRP-6 upon POLR3G knockdown was further confirmed by Western blotting, indicating that POLR3G might influence bladder cancer behavior through the Wnt signaling pathway. Our findings suggest that POLR3G plays a crucial role in bladder cancer progression and could serve as a potential therapeutic target. Future studies should focus on the detailed mechanisms by which POLR3G regulates these signaling pathways and its potential as a biomarker for early detection and prognosis of bladder cancer.

Transcriptomics and metabolomics reveal the mechanism of metabolites changes in Cymbidium tortisepalum var. longibracteatum colour mutation cultivars.

Foliage color is considered an important ornamental character of Cymbidium tortisepalum (C. tortisepalum), which significantly improves its horticultural and economic value. However, little is understood on the formation mechanism underlying foliage-color variations. In this study, we applied a multi-omics approach based on transcriptomics and metabolomics, to investigate the biomolecule mechanisms of metabolites changes in C. tortisepalum colour mutation cultivars. A total of 508 genes were identified as differentially expressed genes (DEGs) between wild and foliage colour mutation C. tortisepalum cultivars based on transcriptomic data. KEGG enrichment of DEGs showed that genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis and brassinosteroid biosynthesis were most significantly enriched. A total of 420 metabolites were identified in C. tortisepalum using UPLC-MS/MS-based approach and 115 metabolites differentially produced by the mutation cultivars were identified. KEGG enrichment indicated that the most metabolites differentially produced by the mutation cultivars were involved in glycerophospholipid metabolism, tryptophan metabolism, isoflavonoid biosynthesis, flavone and flavonol biosynthesis. Integrated analysis of the metabolomic and transcriptomic data showed that there were four significant enrichment pathways between the two cultivars, including phenylalanine metabolism, phenylpropanoid biosynthesis, flavone and flavonol biosynthesis and flavonoid biosynthesis. The results of this study revealed the mechanism of metabolites changes in C. tortisepalum foliage colour mutation cultivars, which provides a new reference for breeders to improve the foliage color of C. tortisepalum.

Transcriptome Analysis of Juvenile Black Rockfish Sebastes schlegelii under Air Exposure Stress

The study aimed to uncover the molecular response of juvenile Sebastes schlegelii to air exposure stress by identifying differentially expressed genes (DEGs) that may underlie their anti-stress mechanisms. Juvenile Sebastes schlegelii were subjected to varying durations of air exposure stress. The total RNA was extracted from whole tissues and sequenced using the Illumina NovaSeq 6000 platform. The transcriptome data were analyzed to identify DEGs through pairwise comparisons across a control group and two experimental groups exposed to air for 40 s and 2 min 30 s, respectively. The comparative DEG analysis revealed a significant number of transcripts responding to air exposure stress. Specifically, 5173 DEGs were identified in the 40 s exposure group (BS) compared to the control (BC), 6742 DEGs in the 2 min 30 s exposure group (BD) compared to the control (BC), and 2653 DEGs when comparing the BD to the BS group. Notably, Gene Ontology (GO) analysis showed an enrichment of DEGs associated with peptidase activity and extracellular regions, suggesting a role in the organism’s stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis pointed to the involvement of metabolic pathways, which are crucial for energy management under stress. The upregulation of protein digestion and absorption pathways may indicate a physiological adaptation to nutrient scarcity during stress. Additionally, the identification of antibiotic biosynthesis pathways implies a potential role in combating stress-induced infections or damage. The identified DEGs and enriched pathways provide insights into the complex anti-stress response mechanisms in juvenile Sebastes schlegelii. The enrichment of peptidase activity and extracellular region-related genes may reflect the initiation of tissue repair and immune response following air exposure. The connection between protein digestion and absorption pathways and anti-stress capabilities could be interpreted as a metabolic readjustment to prioritize energy-efficient processes and nutrient assimilation during stress. The role of antibiotic biosynthesis pathways suggests a defensive mechanism against oxidative stress or microbial invasion that might occur with air exposure.

Protective efficacy and immune responses of largemouth bass (Micropterus salmoides) immunized with an inactivated vaccine against the viral hemorrhagic septicemia virus genotype IVa

Viral hemorrhagic septicemia virus (VHSV) poses a significant threat to the aquaculture industry, prompting the need for effective preventive measures. Here, we developed an inactivated VHSV and revealed the molecular mechanisms underlying the host's protective response against VHSV. The vaccine was created by treating VHSV with 0.05 % formalin at 16 °C for 48 h, which was determined to be the most effective inactivation method. Compared with nonvaccinated fish, vaccinated fish exhibited a remarkable increase in survival rate (99 %) and elevated levels of serum neutralizing antibodies, indicating strong immunization. To investigate the gene changes induced by vaccination, RNA sequencing was performed on spleen samples from control and vaccinated fish 14 days after vaccination. The analysis revealed 893 differentially expressed genes (DEGs), with notable up-regulation of immune-related genes such as annexin A1a, coxsackievirus and adenovirus receptor homolog, V-set domain-containing T-cell activation inhibitor 1-like, and heat shock protein 90 alpha class A member 1 tandem duplicate 2, indicating a vigorous innate immune response. Furthermore, KEGG enrichment analysis highlighted significant enrichment of DEGs in processes related to antigen processing and presentation, necroptosis, and viral carcinogenesis. GO enrichment analysis further revealed enrichment of DEGs related to the regulation of type I interferon (IFN) production, type I IFN production, and negative regulation of viral processes. Moreover, protein-protein interaction network analysis identified central hub genes, including IRF3 and HSP90AA1.2, suggesting their crucial roles in coordinating the immune response elicited by the vaccine. These findings not only confirm the effectiveness of our vaccine formulation but also offer valuable insights into the underlying immunological mechanisms, which can be valuable for future vaccine development and disease management in the aquaculture industry.

Combating anoikis resistance: bioactive compounds transforming prostate cancer therapy.

The study aims to discuss the challenges associated with treating prostate cancer (PCa), which is known for its complexity and drug resistance. It attempts to find differentially expressed genes (DEGs), such as those linked to anoikis resistance and circulating tumor cells, in PCa samples. This study involves analyzing the functional roles of these DEGs using gene enrichment analysis, and then screening of 102 bioactive compounds to identify a combination that can control the expression of the identified DEGs. In this study, 53 DEGs were identified from PCa samples including anoikis-resistant PCa cells and circulating tumor cells in PCa. Gene enrichment analysis with regards to functional enrichment of DEGs was performed. An inclusive screening process was carried out among 102 bioactive compounds to identify a combination capable of affecting and regulating the expression of selected DEGs. Eventually, gastrodin, nitidine chloride, chenodeoxycholic acid, and bilobalide were selected, as their combination demonstrated ability to modulate expression of 50 out of the 53 genes targeted. The subsequent analysis focused on investigating the biological pathways and processes influenced by this combination. The findings revealed a multifaceted and multidimensional approach to tumor regression. The combination of bioactive compounds exhibited effects on various genes including those related to production of inflammatory cytokines, cell proliferation, autophagy, apoptosis, angiogenesis, and metastasis. The current study has made a valuable contribution to the development of a combination of bioactive natural compounds that can significantly impede the development of treatment resistance in prostate tumor while countering the tumors' evasion of the immune system. The implications of this study are highly significant as it suggests the creation of an enhanced immunotherapeutic, natural therapeutic concoction with combinatorial potential.

Mechanistic insights into Yifei Sanjie pill's regulation of EMT to enhance gefitinib treatment effect in NSCLC by in silico analysis and experimental validation

Ethnopharmacological relevanceThe Yi-Fei San-Jie pill (YFSJ) is a well-known Chinese medicine that has been used to treat non-small cell lung cancer in China for decades. Aim of the studyPrevious studies have shown that YFSJ combined with gefitinib can effectively inhibit the proliferation of gefitinib-resistant non-small cell lung cancer (NSCLC) cell lines by promoting apoptosis and autophagy, but the molecular biological mechanisms involved and whether YFSJ combined with gefitinib can have synergistic effects still need to be further explored. Thus, the present study aimed to establish an in silico and experimental framework to decipher the underlying mechanism by which YFSJ augments the efficacy of gefitinib in treating NSCLC. Materials and methodsIntegrated approaches, including microarray analysis, network pharmacology, RNA sequencing, bioinformatics algorithm analysis and in vivo and in vitro experiments, were applied to elucidate the underlying mechanism. ResultsAnalysis of microarray datasets indicated that gefitinib may play a role in the regulation of the epithelial–mesenchymal transition (EMT) of PC9 cells. EMT-related Gene Ontology (GO) terms and the MAPK pathway were found to be enriched in the differentially expressed genes (DEGs), and a decreasing trend was observed in the EMT score. Network pharmacology analysis revealed that the potential NSCLC-related targets of YFSJ also showed enrichment in EMT-related GO terms and the MAPK pathway. Experimental findings demonstrated that combined YFSJ-treated serum and gefitinib treatment significantly inhibited PC9 cell migration and invasion. In addition, the combined treatment dramatically reduced the tumour volume in an animal model. The effectiveness of the combination treatment surpassed that of gefitinib alone in both cell and animal experiments. RNA sequencing analysis revealed significant enrichment of DEGs in EMT-related GO terms for the gefitinib treatment group, YFSJ treatment group, and combination treatment group compared to the control group. Notably, the negative regulation of EMT showed significant enrichment in the DEGs of the combination treatment group. The MAPK pathway was significantly enriched among the different groups. Moreover, combined treatment with YFSJ and gefitinib may exert synergistic anti-NSCLC effects by inhibiting the p-p38 MAPK/GSK3β signalling axis, subsequently suppressing downstream EMT processes. ConclusionCombined treatment with YFSJ and gefitinib could enhance the sensitivity of NSCLC cells to gefitinib by suppressing EMT through the EGFR/p-p38 MAPK/GSK3β signalling axis. YFSJ may serve as an important adjunctive medication for NSCLC patients receiving gefitinib treatment in clinical practice.

Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata.

To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.

PM2.5-induced ferroptosis by Nrf2/Hmox1 signaling pathway led to inflammation in microglia

Particulate matter (PM) has been a dominant contributor to air contamination, which will enter the central nervous system (CNS), causing neurotoxicity. However, the biological mechanism is poorly identified. In this study, C57BL/6J mice were applied to evaluate the neurotoxicity of collected fine particulate matter (PM2.5), via oropharyngeal aspiration at two ambient equivalent concentrations. The Y-maze results showed that PM2.5 exposure in mice would lead to the damage in hippocampal-dependent working memory. In addition, cell neuroinflammation, microglial activation were detected in hippocampus of PM2.5-exposure mice. To confirm the underlying mechanism, the microarray assay was conducted to screen the differentially expressed genes (DEGs) in microglia after PM2.5 exposure, and the results indicated the enrichment of DEGs in ferroptosis pathways. Furthermore, Heme oxygenase-1 (Hmox1) was found to be one of the most remarkably upregulated genes after PM2.5 exposure for 24 h. And PM2.5 exposure induced ferroptosis with iron accumulation through heme degradation by Nrf2-mediated Hmox1 upregulation, which could be eliminated by Nrf2-inhibition. Meanwhile, Hmox1 antagonist zinc protoporphyrin IX (ZnPP) could protect BV2 cells from ferroptosis. The results taken together indicated that PM2.5 resulted in the ferroptosis by causing iron overload through Nrf2/Hmox1 signaling pathway, which could account for the inflammation in microglia.

Long-term thermal stress induces hepatic injury and alters the thermotolerance response in Hong Kong catfish (Clarias fuscus)

Global climate change has a significant impact on fish survival and the aquaculture industry. Even highly adaptable organisms like Siluriformes fish are susceptible to these effects. This study investigates the consequences of extreme high temperature on Hong Kong catfish (Clarias fuscus), a species known for its long-term habitation in tropical and subtropical regions. In this study, C. fuscus were cultivated for 90 days at high temperature (HT, 34 °C) and normal temperature (NT, 26 °C), followed by subjecting the two groups to high temperature stress (34 °C) and temperature recovery (26 °C). The hepatic histology, biochemical, and transcriptomic characteristics of the species were examined before acute high temperature stress (NT-C, HT-C), after acute high temperature stress (NT-T, HT-T), and after temperature recovery (NT-R, HT-R). The histological analysis revealed that long-term heat stress damaged the liver tissue of C. fuscus. Furthermore, significant damage was observed in the liver tissues of the NT group under acute high temperature stress, while no further damage was observed in the HT group. The biochemical analysis showed that 90 days of heat stress altered the body's immune and oxidative balance, resulting in an increase in alkaline phosphatase (ALP), alanine aminotransferase (ALT), catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities, and a decrease in malondialdehyde (MDA) content. Upon acute heat stress, the liver function of the NT group was disordered and unable to produce enough total-bilirubin (T-BIL), while the aspartate aminotransferase (AST) activity of the HT group was more susceptible to being affected. Long-term heat stress led to significant changes in gene expression, with the NT group showing three times more differentially expressed genes (DEGs) identified in the liver compared to the HT group under acute heat stress conditions. Analysis of DEG enrichment during the same treatment period in both groups revealed significant differences in amino acid metabolism and lipid metabolism pathways. These results suggest that long-term heat stress caused liver tissue damage in C. fuscus, altering immune and oxidative balance, enzyme activity sensitivity, as well as the body's response to acute heat stress pathways and intensity. This study lays the groundwork for future investigations into fish adaptability to sudden temperature changes and aquaculture strategies to mitigate heat stress in fish facing extreme temperatures.

Subacromial bursa in patients with rotator cuff tear with or without adhesive capsulitis exhibits a differential transcriptome with potential molecular biomarkers

BackgroundAlthough adhesive capsulitis (AC) is a common condition, the pathological mechanisms remain understudied. The purpose of our research was to evaluate variations in gene expression across the entire genome in the subacromial bursa tissue of individuals with rotator cuff tears (RCT), with or without AC, and to explore the factors that may influence the occurrence and progression of AC. MethodsTranscription profiles of subacromial bursa samples from 12 RCT patients, of whom 6 had also AC, were evaluated. Data were generated using RNA-seq. DESeq2 was utilized to identify the differentially expressed genes (DEGs) in both groups. In order to conduct a more in-depth examination of the DEGs, we performed Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A network of interactions between proteins was built, and the central genes were determined using Cytoscape. The hub genes were confirmed through qRT-PCR and immunohistochemistry. Results324 of the 16,251 detected genes were identified as DEGs. Analysis of GO functional enrichment showed that the DEGs were enriched in domains of biological process, molecule function and cellular component. Analysis of KEGG pathways revealed enrichment of DEGs in pathways like IL-17 signaling and ECM-receptor interaction. We verified that the association between AC and the increase in expression of the PPI network hub genes. ConclusionThis study investigated the transcriptome differences of subacromial bursa in RCT patients with or without AC. Using bioinformatics technology, we identified the DEGs and screened out the hub genes. The research enhanced the data on gene expression profiles of DEGs in the subacromial bursa tissue of patients with RCT, offering fresh perspectives on the regulation of gene transcription.