Enriched Signaling Pathways Research Articles

Integration of ATAC-seq and RNA-seq reveals signal regulation during post-molt and inter-molt stages in muscle of Eriocheir sinensis

IntroductionThe molting processes are crucial for the survival and development of crustaceans. Eriocheir sinensis demonstrates representative discontinuous growth during molting, while muscle is the most obvious tissue exhibiting this property. However, the signal regulation mechanisms involved in muscle during molting remain unexplored.MethodsIn this work, a comprehensive analysis of the gene expressions in E. sinensis muscle between post-molt and inter-molt stages were performed by integrating the ATAC-seq and RNA-seq techniques.ResultsThe integration analysis identified 446 up-regulated and 21 down-regulated genes in the two stages. GO enrichment analysis revealed that the up-regulated genes are largely associated with protein phosphorylation and phosphorus metabolism, while the down-regulated genes are mainly involved in DNA metabolism, transcription, cell adhesion, and G protein-coupled receptor (GPCR) signaling pathway. In all the enriched signaling pathways, GPCR signaling pathway includes the most differentially expressed genes (8 genes), which underlines its importance in the signal transduction from the post-molt stage to the inter-molt stage. Further protein structure analysis and RT-qPCR validation confirmed five GPCR genes related to molting process, in which four genes (GRM7, FMRFaR, mth2, gpr161) are active during the post-molt stage and one gene (moody) functions during the inter-molt stage.DiscussionThese findings highlight the key regulatory proteins and pathways involved in E. sinensis muscle during molting and also offer foundational data for studying the mechanisms of molting and discontinuous growth in crustaceans.

Organoid modeling identifies USP3-AS1 as a novel promoter in colorectal cancer liver metastasis through increasing glucose-driven histone lactylation.

Dysregulation of long non-coding RNAs (lncRNAs) is common in colorectal cancer liver metastasis (CRLM). Emerging evidence links lncRNAs to multiple stages of metastasis from initial migration to colonization of distant organs. In this study we investigated the role of lncRNAs in metabolic reprogramming during CRLM using patient-derived organoid (PDO) models. We established five pairs of PDOs from primary tumors and matched liver metastatic lesions, followed by microarray analysis. We found that USP3-AS1 was significantly upregulated in CRLM-derived PDOs compared to primary tumors. High level of USP3-AS1 was positively associated with postoperative liver metastasis and negatively correlated with the prognosis of colorectal cancer (CRC) patients. Overexpression of USP3-AS1 significantly enhanced both sphere formation efficiency and liver metastasis in PDOs. Gene set enrichment analysis revealed that USP3-AS1 upregulation significantly enriched glycolysis and MYC signaling pathways. Metabolomics analysis confirmed that USP3-AS1 promoted glycolysis in PDOs, whereas glycolysis inhibition partially attenuated the effects of USP3-AS1 overexpression on PDO growth and liver metastasis. We revealed that USP3-AS1 stabilized MYC via post-translational deubiquitination, thereby promoting glycolysis. We demonstrated that USP3-AS1 increased the stability of USP3 mRNA, resulting in higher USP3 protein expression. The elevated USP3 protein then interacted with MYC and promoted its stability by deubiquitination. The USP3-AS1-MYC-glycolysis regulatory axis modulated liver metastasis by promoting H3K18 lactylation and CDC27 expression in CRC. In conclusion, USP3-AS1 is a novel promoter of CRLM by inducing histone lactylation.

Transcriptome analysis of regenerated dermis stimulated by mechanical stretch.

Mechanical stretch is utilized in the process of tissue expansion to promote skin regeneration, which is crucial for wound healing and organ reconstruction purposes. Enlarged dermal area is one of the significant histological characteristics of the expanded skin. However, the underlying biological processes and molecular pathways associated with dermal regeneration triggered by mechanical stretch are still not well understood. Twelve male Sprague-Dawley (SD) rats were divided into the expansion group and sham group randomly. Upon creating a rat scalp expansion model, the dermis was isolated from the full-thickness skin in both experimental groups for RNA sequencing. This process led to the identification of differentially expressed genes (DEGs). Subsequently, we conducted Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Enrichment Analysis (GSEA) to identify the essential biological processes associated with dermal regeneration induced by mechanical stretch, leveraging data from the DEGs. A network of protein-protein interactions (PPI) was built to detect the critical modules and central genes. The expression levels of these hub genes were evaluated using quantitative real-time polymerase chain reaction (qPCR). Increased expanded skin area and dermal thinning which represent the typical changes of expanded skin were observed in the expansion group. A total of 782 DEGs were identified in the expansion group relative to the sham group. The DEGs were associated with several biological processes, including the organization of the extracellular matrix, the enhancement of macrophage activation, and the promotion of angiogenesis, among others. Cell components encompassing Toll-like receptor 2-Toll-like receptor 6 protein complex, interstitial matrix, extracellular matrix (ECM), and collagen trimer were discovered. Molecular function categories including integrin binding, insulin-like growth factor binding, and fatty acid elongase activity were involved. The KEGG pathway analysis demonstrated the significant enrichment of pathways including the PI3K-Akt signaling pathway, fatty acid metabolism, and extracellular matrix-receptor interactions. GSEA results displayed that mechanical stretch correlated with the regulation of cell activation processes, cytokine-mediated signaling pathways, and immune system processes. PPI network resulted in the identification of 598 nodes along with a total of 5,304 interaction pairs between proteins. And ten hub genes containing Ccl2, Cxcl10, Fasn, Itgad, Cd163, Mmp9, Cd36, Tlr2, Igf1, and Wnt2 were identified by bioinformatics analysis and validated by qPCR. This in vivo study for the first time revealed the DEGs related to mechanical stretch stimulated dermal regeneration and identified the involved pathways and hub genes correlated with macrophage recruitment and polarization, fibroblast proliferation and ECM production and angiogenesis, which may benefit further studies aimed at developing therapeutic strategies for facilitating expanded skin regeneration.

Identification of Hepatocellular Carcinoma Subtypes Based on Global Gene Expression Profiling to Predict the Prognosis and Potential Therapeutic Drugs.

Background: Hepatocellular carcinoma (HCC) is a highly heterogeneous tumor, and distinguishing its subtypes holds significant value for diagnosis, treatment, and the prognosis. Methods: Unsupervised clustering analysis was conducted to classify HCC subtypes. Subtype signature genes were identified using LASSO, SVM, and logistic regression. Survival-related genes were identified using Cox regression, and their expression and function were validated via qPCR and gene interference. GO, KEGG, GSVA, and GSEA were used to determine enriched signaling pathways. ESTIMATE and CIBERSORT were used to calculate the stromal score, tumor purity, and immune cell infiltration. TIDE was employed to predict the patient response to immunotherapy. Finally, drug sensitivity was analyzed using the oncoPredict algorithm. Results: Two HCC subtypes with different gene expression profiles were identified, where subtype S1 exhibited a significantly shorter survival time. A subtype scoring formula and a nomogram were constructed, both of which showed an excellent predictive performance. COL11A1 and ACTL8 were identified as survival-related genes among the signature genes, and the downregulation of COL11A1 could suppress the invasion and migration of HepG2 cells. Subtype S1 was characterized by the upregulation of pathways related to collagen and the extracellular matrix, as well as downregulation associated with the xenobiotic metabolic process and fatty acid degradation. Subtype S1 showed higher stromal scores, immune scores, and ESTIMATE scores and infiltration of macrophages M0 and plasma cells, as well as lower tumor purity and infiltration of NK cells (resting/activated) and resting mast cells. Subtype S2 was more likely to benefit from immunotherapy. Subtype S1 appeared to be more sensitive to BMS-754807, JQ1, and Axitinib, while subtype S2 was more sensitive to SB505124, Pevonedistat, and Tamoxifen. Conclusions: HCC patients can be classified into two subtypes based on their gene expression profiles, which exhibit distinctions in terms of signaling pathways, the immune microenvironment, and drug sensitivity.

Exploring the Mechanism of Acupuncture in Improving Ovarian Function in Rats with Poor Ovarian Response Using High-Throughput Sequencing.

This study aimed to investigate the possible mechanism through which acupuncture protects ovaries with Poor Ovarian Response (POR) in rats based on microRNA (miRNA). Thirty-six SPF SD female non-pregnant rats aged 8 weeks were randomly divided into the blank group, model group, and acupuncture group, with 12 rats in each group. According to the group, the rats were given gavage of Tripterygium wilfordii polyglycosides suspension for 14 days to establish the model of POR, and then the rats were treated with acupuncture for 2 weeks, once a day, for 20 minutes. Afterward, their hormone levels were measured, and HE staining was performed on the ovaries after the intervention. Three rats from each group were randomly selected for ovarian tissue miRNA sequencing, and differential miRNAs were subjected to Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, and Quantitative Polymerase Chain Reaction (QPCR) verification. By using TargetScan to predict the target genes of differential miRNAs, we validated the results with a dual luciferase reporter gene assay. Compared with the blank group, the estrus cycle of the model group was significantly prolonged (P<0.01). Anti-Müllerian Hormone (AMH) (P<0.01) and Estrogen (E2) were significantly decreased (P<0.05). Follicle-Stimulating Hormone (FSH)(P<0.05) and Luteinizing Hormone (LH) increased sharply (P<0.01). Compared with the model group, the estrus cycle was significantly shortened in the acupuncture group (P<0.01). AMH and E2 were markedly raised (P<0.05). FSH (P<0.05) and LH (P<0.01) were significantly declined. miRNA sequencing showed that there were 23 miRNAs significantly different between the model group and the blank group (P<0.05), and 30 miRNAs significantly different between the acupuncture group and the model group (P<0.05). GO demonstrated that the network was mainly involved in cellular components, cells, cellular metabolic processes, binding, and single biological processes; KEGG signaling pathway enrichment showed that it was mainly related to MAPK, adhesion junction, calcium signaling pathways, etc. Q-PCR results showed that after modeling, the expression rose, and after acupuncture, the expression of the following miRNA decreased: miR-154-5p (P<0.01), miR-300-5p (P < 0.05), miR-376c-5p (P<0.05). The dual luciferase reporter assay showed that the relative luciferase activity of the miR-300-5p mimics+MAP3K1-WT group was significantly lower than that of the NC+MAP3K1-WT group (P<0.01). HE results demonstrated that the number of primordial follicles and primary follicles in the model group was significantly lower than that in the blank group (P<0.05). Moreover, the morphology was poorer, and the granulosa cell layer was thinner. Compared with the model group, the number of primary follicles in the acupuncture group increased (P<0.05); the morphology and granulosa cell structure of the ovary were improved to different degrees, and mature follicles could be seen. Acupuncture may improve the ovarian responsiveness of POR rats by regulating miR-154- 5p,miR-300-5p, and miR-376c-5p. Furthermore, miR-300-5p can specifically bind to the 3'-UTR of MAP3K1, and MAP3K1 may be the target of miR-300-5p.

Smu_1558c-mediated regulation of growth and biofilm formation in Streptococcus mutans

Streptococcus mutans is a key etiological agent in dental caries, owing to its strong ability to form biofilms through carbohydrate fermentation. Protein acetylation, facilitated by GNAT family acetyltransferases, plays a critical regulatory role in bacterial physiology, but its impact on S. mutans remains largely unexplored. In this study, we investigated the role of the GNAT family acetyltransferase encoded by smu_1558c in regulating the growth and biofilm formation of S. mutans. The deletion of smu_1558c resulted in impaired growth, reduced biofilm formation, and diminished synthesis of water-insoluble extracellular polysaccharides (EPS). Proteomic analysis revealed 166 differentially expressed proteins in the deletion mutant, with significant enrichment in pathways related to carbohydrate transport and metabolism, and translation. Notably, glucosyltransferases GtfB and GtfC, key enzymes in biofilm formation, were significantly downregulated in the deletion mutant, while ClpL, a Clp-like ATP-dependent protease involved in protein homeostasis under stress conditions, was highly upregulated. These findings highlight that acetyltransferase smu_1558c plays a crucial role in the growth, biofilm formation, and EPS synthesis of S. mutans through its regulation of carbohydrate transport and metabolism pathways, as well as stress response mechanisms. This study provides novel insights into the molecular mechanisms governing S. mutans pathogenicity and suggests potential therapeutic targets for caries prevention.

Berberine ameliorates coronary artery endothelial cell injury in Kawasaki disease through complement and coagulation cascades

To explore the role of berberine (BBR) in ameliorating coronary endothelial cell injury in Kawasaki disease (KD) by regulating the complement and coagulation cascade. Human coronary artery endothelial cells (HCAEC) were divided into a healthy control group, a KD group, and a BBR treatment group (n=3 for each group). The healthy control group and KD group were supplemented with 15% serum from healthy children and KD patients, respectively, while the BBR treatment group received 15% serum from KD patients followed by the addition of 20 mmol/L BBR. Differential protein expression was analyzed and identified using isobaric tags for relative and absolute quantitation technology and liquid chromatography-tandem mass spectrometry, followed by GO functional enrichment analysis and KEGG signaling pathway enrichment analysis of the differential proteins. Western blot was used to detect differential protein expression. A total of 518 differential proteins were identified between the KD group and the healthy control group (300 upregulated proteins and 218 downregulated proteins). A total of 422 differential proteins were identified between the BBR treatment group and the KD group (221 upregulated proteins and 201 downregulated proteins). Bioinformatics analysis showed that compared to the healthy control group, the differential proteins in the KD group were enriched in the complement and coagulation cascade and ribosome biogenesis in eukaryotes. Compared to the KD group, the differential proteins in the BBR treatment group were also enriched in the complement and coagulation cascade and ribosome biogenesis in eukaryotes. Western blot results indicated that compared to the healthy control group, the expression of complement C1q subcomponent subunit C (C1QC), kininogen-1 (KNG1), complement C1s subcomponent (C1S), and C4b-binding protein alpha chain (C4BPA) was increased in the KD group (P<0.05). Compared to the KD group, the expression of KNG1, C1S, C1QC, and C4BPA was decreased in the BBR treatment group (P<0.05). The complement and coagulation cascade may be involved in the regulation of BBR treatment for coronary injury in KD, and C1QC, KNG1, C1S, and C4BPA may serve as biomarkers for this treatment.

Establishment of liquid-liquid phase separation-related prognostic model in lung adenocarcinoma and systematic analysis of its clinical significance.

To detect the prognostic importance of liquid-liquid phase separation (LLPS) in lung adenocarcinoma. The gene expression files, copy number variation data, and clinical data were downloaded from The Cancer Genome Atlas cohort. LLPS-related genes were acquired from the DrLLPS website. The prognostic model based on LLPS was constructed by the Cox regression and LASSO regression analyses after the identification of LLPS-related differentially expressed genes (DEGs). Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed. The LLPS-related prognostic risk score was validated by GSE31210 and GSE72094. The overall survival of lung adenocarcinoma patients was predicted by plotting a nomogram. The biological features of the high-risk lung adenocarcinoma were evaluated by the CIBERSORT, ESTIMATE, Gene Set Variation Analysis, and Genomics of Drug Sensitivity in Cancer. Reverse transcription-quantitative polymerase chain reaction detected hub gene expression. A total of 91 DEGs were screened out in LLPS, among which 9 genes were discovered as prognostic biomarkers of lung adenocarcinoma. GRIA1, CRTAC1, MAGEA4, and MAPK4 were identified as hub genes by the LASSO Cox regression analysis. High-risk and low-risk groups were divided according to the risk index, with the high-risk group displaying a markedly worse outcome. CRTAC1 expression was significantly decreased, MAGEA4 and MAPK4 expressions were increased, while GRIA1 expression was altered in lung adenocarcinoma cells. Tumor microenvironment, signaling pathway enrichment, and drug sensitivity significantly differed between different risk groups. This work proposed a prognostic tool based on the LLPS-related gene signature to offer prospective and effective biomarkers for lung adenocarcinoma prognosis.

A combined proteomic and metabolomic analysis of the early aborted embryonic tissues with maternal COVID-19 infection.

COVID-19 still spreads worldwide, and repeated infections are hard to avoid. Maternal infection during pregnancy is associated with adverse maternal and neonatal outcomes. Our study used a multi-omics profiling method to explore the proteome and metabolome alteration in early embryonic development after COVID-19 infection. A total of 30 chorionic tissues after artificial abortion (15 infection and 15 no-infection samples) were collected, and the UHPLC-MS/MS and LC-MS/MS were applied in the present study. As a result, 311 significantly differentially expressed proteins were identified. The function annotations revealed that the thermogenesis pathway is the most significantly enriched signaling pathway; PRKAG2, IGF1R, and RPS6KB2 were identified as the hub proteins. There were 359 metabolites significantly altered after infection. The functional annotations revealed that amino acid metabolism was significantly affected, especially beta-alanine metabolism, glutamate metabolism, and histidine metabolism pathways. The metabolites in ovarian steroidogenesis showed a down-regulating trend in the infection group. Finally, we combined the results of proteins and metabolomics analysis. The biosynthesis of the cofactors pathway was identified as significantly enriched in both proteomics and metabolomics datasets. Our findings provide a network of protein regulation and metabolite perturbation during early embryonic development with COVID-19 infection. Our findings can provide valuable insights for further exploration of the complex mechanism of COVID-19-associated pregnancy complications and outcomes. SIGNIFICANCE: COVID-19 has developed into the most prominent and deadliest pandemic respiratory disease in the world, and repeated infections are complicated to avoid. COVID-19 infection during pregnancy increases the risk of adverse maternal and neonatal outcomes, such as preterm birth and stillbirth. However, previous studies mainly focused on its effect on pregnant women, such as the clinical characteristics and gestation outcomes. There is no relevant report about the effects of virus infection on embryos in early pregnancy. The effects of COVID-19 infection changes of the proteins and metabolites during early embryonic development are undefined. Our findings provide an association between protein regulation, metabolite perturbation, and COVID-19 infection, which can provide valuable insights for further exploration of the complex mechanism COVID-19 COVID-19-associated pregnancy complications and adverse pregnancy outcomes.

JOSD2 promotes breast cancer metastasis by deubiquitinating and stabilizing SMAD4.

Breast cancer is one of the most common malignant tumors among women worldwide, and its high degree of metastasis significantly impacts treatment effectiveness leading to poor prognosis. The potential molecular mechanisms underlying breast cancer metastasis remain to be further elucidated. In this study, via database analysis, we revealed that the deubiquitinase josephin domain containing 2 (JOSD2) was abnormally amplified in patients with metastatic breast cancer, and was significantly negatively correlated with patient prognosis. By integrating data from the Gene Expression Omnibus (GEO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis, we found that the transforming growth factor beta (TGF-β) signaling pathway was significantly activated in breast cancer patients with increased JOSD2 expression. Further studies revealed that JOSD2 interacted with and stabilized SMAD family member 4 (SMAD4) by removing polyubiquitin chains. Inhibition of JOSD2 by RNA interference effectively inhibited the metastasis of breast cancer cells both in vitro and in vivo. In conclusion, our study not only reveals the role of JOSD2 in promoting breast cancer metastasis for the first time, but also indicates promising directions for the future development of deubiquitinase inhibitors, which could yield significant therapeutic benefits. Nevertheless extensive research and development are required to fully realize this potential.

Multiscale Cell-Cell Interactive Spatial Transcriptomics Analysis.

Spatial transcriptomics data analysis integrates gene expression profiles with their corresponding spatial locations to identify spatial domains, infer cell-type dynamics, and detect gene expression patterns within tissues. However, the current spatial transcriptomics analysis neglects the multiscale cell-cell interactions that are crucial in biology. To fill this gap, we propose multiscale cell-cell interactive spatial transcriptomics (MCIST) analysis. MCIST combines the advantages of an ensemble of multiscale topological representations of cell-cell interactions in the gene expression space with those of cutting edge spatial deep learning techniques. We validate MCIST by a comparison of 14 cutting edge methods on a huge collection of 37 benchmark spatial transcriptomics datasets. We demonstrate that MCIST yields superior performance in spatial domain detection. It achieves the best clustering score on 23/37 datasets and is among the top three methods on 33/37 datasets, whereas the second best method scored only 6/37 and 17/37 on these measures, respectively. In terms of overall performance with regards to a quantitative metric, MCIST offers over an 11\% improvement to the previous state-of-the-art in spatial domain detection. Additionally, MCIST offers multiscale insights with respect to trajectory inference, differentially expressed gene detection, and signaling pathway enrichment analysis. Our MCIST sheds valuable light on the multiscale perspective in spatial transcriptomics.

Genetic Biomarkers and Circulating White Blood Cells in Osteoarthritis: A Bioinformatics and Mendelian Randomization Analysis.

Background: Osteoarthritis (OA) is a prevalent degenerative joint disease that causes disability and diminishes quality of life. The pathogenesis of OA remains poorly understood, creating an urgent need for biomarkers to aid research, diagnosis, and treatment. Methods: This study integrated transcriptome data from the GEO database with bioinformatics analyses to identify biomarkers associated with OA. The bioinformatics methods utilized include the Limma package, WGCNA, PPI network analysis, and machine learning algorithms. Genetic variants were used as instrumental variables to evaluate the potential causal impact of circulating white blood cell (WBC) counts on OA. Data sources encompassed the largest genome-wide analysis for OA and a comprehensive GWAS summary for circulating WBC counts. Four mendelian randomization (MR) methods were employed to investigate the genetic association, with a primary focus on findings from the inverse variance-weighted (IVW) method. Results: Total of 233 OA-related genes were identified, showing significant enrichment in pathways associated with WBC function. Key biomarkers, including CD4, CSF1R, and TYROBP, were upregulated in OA samples and exhibited strong diagnostic potential. MR analysis findings provided evidence of a genetic association between elevated neutrophil counts and a reduced risk of OA across sites (IVW: OR = 0.97, 95% CI 0.93-1.00, p = 0.047). Additionally, higher circulating WBC counts, particularly neutrophil counts, were associated with a suggestive decrease in hip OA (WBC IVW: OR = 0.94, 95% CI 0.89-0.99, p = 0.015; neutrophil IVW: OR = 0.93, 95% CI 0.88-0.99, p = 0.017). Conversely, reverse MR analysis found no evidence to support a genetic effect of OA on circulating WBC counts. Conclusion: Our findings suggest that elevated neutrophil counts may offer protective effects against OA, underscoring the interplay between the immune functions and OA pathogenesis. CD4, CSF1R, and TYROBP emerge as promising OA biomarkers, meriting further validation in prospective studies.

Glioblastoma Stem Cells: MAP17 as a Novel Predictive Biomarker and Therapeutic Target Associated with Quiescence and Immune Evasion.

Glioblastoma multiforme (GBM) is one of the deadliest and most heterogeneous forms of brain cancer, characterized by its resistance to conventional therapies. Within GBM, a subpopulation of slow-cycling cells, often linked to quiescence and stemness, plays a crucial role in treatment resistance and tumor recurrence. This study aimed to identify novel biomarkers associated with these slow-cycling GBM cells. We utilized The Cancer Genome Atlas (TCGA)-GBM dataset and presented the reproducible bioinformatics analysis for our results. Our analysis highlighted Membrane-Associated Protein 17 (MAP17) as strongly associated with the slow-cycling phenotype. We found that the protein cargo MAP17 expression is related to mesenchymal signatures and stem cell-related pathways. Also, MAP17 was linked to a distinct metabolic profile, characterized by significant enrichment in pathways related to folate, zinc, and fatty acids. Moreover, the immune cell distribution analysis revealed that MAP17 correlates with key molecular immune processes, including interferon-gamma (IFN-γ) signaling and antigen presentation, as well as immunosuppressive cells like myeloid-derived suppressor cells (MDSCs) and macrophages. MAP17-high tumors also showed elevated expression of several immune checkpoint inhibitors, indicating an immunosuppressive microenvironment. These findings provide insight into the role of MAP17 in quiescence, stemness, and immune evasion, positioning it as a promising therapeutic target.

Identification of biomarkers associated with ferroptosis in macrophages infected with Mycobacterium abscessus using bioinformatic tools.

Mycobacterium abscessus is a rapidly growing nontuberculous mycobacterium that causes severe pulmonary infections. Recent studies indicate that ferroptosis may play a critical role in the pathogenesis of M. abscessus pulmonary disease. We obtained gene expression microarray data from the Gene Expression Omnibus database, focusing on THP-1-derived macrophages infected with M. abscessus and uninfected controls. Differentially expressed genes related to ferroptosis were identified through weighted gene co-expression network analysis and the "limma" package, followed by gene set variation analysis and gene set enrichment analysis for enrichment assessment. To explore regulatory network relationships among hub genes, we constructed RBP-mRNA, ceRNA, and TF-mRNA networks. Additionally, a protein-protein interaction network was built, and functional enrichment analyses were conducted for the hub genes. The diagnostic value of these genes was assessed using receiver operating characteristic curves. Six differentially expressed genes associated with ferroptosis were identified in M. abscessus infection. The receiver operating characteristic curves demonstrated that these genes had excellent predictive value for the infection. Functional enrichment analysis showed that these genes were involved in immune responses, inflammation, cellular metabolism, cell death, and apoptosis. Pathway enrichment analysis revealed significant enrichment in pathways related to apoptosis, inflammation, and hypoxia. The RBP-mRNA network highlighted significant interactions between hub genes and key RNA-binding proteins, while the ceRNA network predicted that miRNAs and lncRNAs regulate ferroptosis-related genes NACC2 and ITPKB. Furthermore, interactions between the hub gene HSD3B7 and transcription factors LMNB1 and ASCL1 may promote ferroptosis in macrophages by influencing iron metabolism and reactive oxygen species production, contributing to the M. abscessus infection process. Our findings identified biomarkers linked to ferroptosis in M. abscessus infection, providing new insights into its pathogenic mechanisms and potential therapeutic strategies.

Multi-omics analysis reveals the regulatory mechanism of branching development in Quercus fabri.

The ability of axillary meristems to form axillary buds and subsequently develop into branches is influenced by phytohormones, environmental conditions, and genetic factors. The main trunk of Quercus fabri is prone to branching, which not only impacts the appearance and density of the wood and significantly reduces the yield rate. This study conducted transcriptomic, proteomic, and metabolomic analyses on three stages of axillary bud development in Q. fabri. A total of 12,888 differentially expressed genes (DEGs), 8193 differentially accumulated proteins (DAPs), and 1788 differentially accumulated metabolites (DAMs) were identified through comparisons among the stages and subjected to multi-omics joint analysis. Conduct interaction network analysis on DEGs and DAPs to identify the significant transcription factor family (AP2/ERF) involved in the regulation of axillary bud development. Furthermore, KEGG enrichment analysis of DEGs, DAPs and DAMs indicated significant enrichment in plant hormone signaling pathways. The analysis of endogenous hormone levels and qRT-PCR results for pathway genes demonstrated that the expression levels of IAA and tZ significantly increased during late developmental stages, whereas the expression levels of ABA, ACC and JA significantly decreased. In summary, these findings contribute to a comprehensive understanding of the regulatory networks underlying the branching development of Q. fabri. SIGNIFICANCE: Q. fabri exhibits robust vegetative growth, and its primary trunk is prone to branching, significantly influencing the wood yield rate. Through a joint analysis of transcriptomics, proteomics, and metabolomics, we comprehensively examined the regulatory network governing the axillary bud development of Q. fabri. Our findings revealed the crucial roles of the AP2/ERF transcription factor family and plant hormone signal transduction pathways in branch development. These insights contribute to a deeper understanding of the mechanisms regulating branch development.

Discovery of Active Ingredients Oleanolic Acid, Ursolic Acid, and Arbutin for in Vitro Anti-Melanoma: Network Pharmacology and Experimental Validation

Objective Antitumor effects of the medicinal herb Prinsepia utilis Royle ( P. utilis) have been reported. This study aimed to identify the potential functional components and molecular mechanisms of P. utilis in the treatment of melanoma through network pharmacology and experimental verification. Methods Bioinformatics database and pharmacology analysis platform of the Chinese medicine system were used to obtain the active components of P. utilis, and the potential targets were predicted by the Swiss Target Prediction database. Disease targets associated with melanoma were retrieved from the Genecard database. Network topology analysis and functional enrichment analysis were conducted to screen out the core targets and related signal pathways. The molecular docking method was employed to evaluate the core target binding to bioactive ingredients of P. utilis, and a molecular biology experimental approach was performed to predict and verify the potential molecular mechanism of P. utilis in treating melanoma. Results KEGG pathway analysis revealed the enrichment of multiple cancer-related pathways and signaling pathways. Oleanolic acid (OA), Ursolic acid (UA), Arbutin are the active ingredients of P. utilis. The crude extract of P. utilis was able to inhibit melanin in A375 cells. The active compounds OA and UA in P. utilis can significantly inhibit the growth and migration ability of human melanoma cells A375 while inducing apoptosis and inhibiting tyrosinase activity and melanin synthesis. In contrast, arbutin does not show obvious performance in these biological activities. Conclusion These findings suggest that OA and UA are promising as more effective anti-melanoma active ingredients in P. utilis. In conclusion, these studies suggest that OA and UA can protect against melanoma by regulating tyrosine to inhibit melanogenesis.

Transcriptomics Reveals Crowding Stress Inhibit the Immune Defense of The Head kidney of The Pearl Gentian Grouper Juvenile through NF-κB Signal Pathway

Crowding stress is a significant welfare factor affecting aquatic animals in recirculating aquaculture systems. Little is known regarding the influence of prolonged crowding stress on the immunity of juvenile pearl gentian groupers. However, research exploring the potential mechanisms through which crowding stress affects fish immune function is limited. Therefore, this study aims to investigate the effect of crowding stress on the immune stress of the pearl gentian grouper juvenile (♀Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) under prolonged conditions. We focused on the pearl gentian grouper juvenile and selected low- and high-density groups as the experimental breeding densities. Research shows that crowding stress increases the activities of alkaline acid plum and acid phosphatase, reduces the activities of lysozyme and immunoglobulin M content. RNA sequencing and comparative transcriptomic analyses were employed to explore changes in the gene expression of juvenile pearl gentian groupers subjected to crowding stress. Differential gene expression analyses between the low- and high-density groups identified 5777 unigenes that were differentially expressed following crowding stress, with 3216 and 2561 upregulated and downregulated, respectively. In the GO and KEGG enrichment analyses, many of the enriched signaling pathways related to genes were associated with immunity and oxidative stress. In addition, the combined analyses of enzyme activity and transcriptomics indicated that crowding stress suppressed the immune function of juvenile pearl gentian groupers, reducing their immune ability. Overall, these findings offer new insights into the molecular mechanisms underlying crowding stress tolerance in juvenile pearl gentian grouper, suggesting that the NF-κB pathway plays a crucial role in the immune response of the head kidney of the pearl gentian grouper to long-term crowding stress.

Crosstalk between cancer-associated fibroblasts and non-neuroendocrine tumor cells in small cell lung cancer involves in glycolysis and antigen-presenting features.

Small cell lung cancer (SCLC) is a highly fatal malignancy, the complex tumor microenvironment (TME) is a critical factor affecting SCLC progression. Cancer-associated fibroblasts (CAFs) are crucial components of TME, yet their role in SCLC and the underlying mechanisms during their interaction with SCLC cells remain to be determined. Microenvironmental cell components were estimated using transcriptome data from SCLC tissue available in public databases, analyzed with bioinformatic algorithms. A co-culture system comprising MRC5 fibroblasts and SCLC cell lines was constructed. RNA sequencing (RNA-seq) was performed on co-cultured and separately cultured MRC5 and H196 cells to identify differentially expressed genes (DEGs) and enriched signaling pathways. Glycolysis and STING signaling in SCLC cells were assessed using glucose uptake assays, qRT-PCR, and Western blot analysis. Immunohistochemical staining of SCLC tissue arrays quantified α-SMA, HLA-DRA and CD8 expression. Non-neuroendocrine (non-NE) SCLC-derived CAFs exhibited more abundance and DEGs than NE SCLC-derived CAFs did, which interact with non-NE SCLC cells can induce the enrichment of glycolysis-related genes, increasement of glucose uptake, upregulation of glycolytic signaling proteins in non-NE SCLC cells and accumulation of lactate in the extracellular environment, confirming CAF-mediated glycolysis promotion. Additionally, glycolysis-induced ATP production activated STING signaling in non-NE SCLC cells, which upregulated T cell chemo-attractants. However, CAF abundance did not correlate with CD8 + T cell numbers in SCLC tissues. Additionally, non-NE SCLC cell-educated CAFs exhibited features of antigen-presenting CAFs (apCAFs), as indicated by the expression of major histocompatibility complex (MHC) molecules. Co-localization of HLA-DRA and α-SMA signals in SCLC tissues confirmed apCAF presence. The apCAFs and CD8 + T cells were co-located in the SCLC stroma, and there was a positive correlation between CAFs and regulatory T cell (Treg) abundance. Our findings suggest that crosstalk between CAFs and non-NE SCLC cells promotes glycolysis in non-NE SCLC cells, thereby increase T cell chemo-attractant expression via activating STING signaling. On the other hand, it promotes the presence of apCAFs, which probably contributes to CD8 + T cell trapping and Treg differentiation. This study emphasizes the pro-tumor function of CAFs in SCLC by promoting glycolysis and impairing T cell function, providing direction for the development of novel therapeutic approaches targeting CAF in SCLC.

Unveiling the role of lipopolysaccharide-related genes in diabetic retinopathy: identification of key biomarkers and immune infiltration analysis

BackgroundGrowing evidence suggests a link between systemic lipopolysaccharide (LPS) exposure and worsening diabetic retinopathy (DR). This study aims to investigate DR’s pathogenesis by analyzing LPS-related genes (LRGs) through bioinformatics.MethodsThe CTD database was utilized to identify LRGs. The datasets associated with DR were acquired from the GEO database. The Venn diagram was used to identify the differentially expressed LRGs (DLRGs), and the putative molecular mechanism of these DLRGs was investigated through functional enrichment analysis. We used WGCNA, Lasso regression, and RF to identify hub DLRGs. The expression levels of these hub DLRGs were validated in an independent dataset (GSE102485) and cell experiments. Employing the CIBERSORT algorithm, we examined the infiltration of 22 distinct immune cell types in DR and assessed the association between key DLRGs and immune infiltrates through correlation analysis.ResultsA total of 71 DLRGs were detected. These genes exhibited significant enrichment in pathways associated with inflammation. In addition, the in-depth analysis uncovered that five hub DLRGs (STK33 and EPHX2) linked to bacterial LPS displayed noteworthy diagnostic potential for individuals diagnosed with DR. The hub DLRGs expression in the high glucose-induced DR model was confirmed by qRT-PCR analysis. Furthermore, examination of immune infiltration indicated a significant association between these five genes and the extent of immune cell infiltration.ConclusionSTK33 and EPHX2 serve as biomarkers related to bacterial LPS. Exploring these genes in-depth could provide innovative ideas and a foundation for comprehending the progression of the disease and developing targeted treatments for DR.

Interleukin-37 promotes wound healing in diabetic mice by inhibiting the MAPK/NLRP3 pathway.

Diabetic foot ulcer (DFU) is a prevalent complication of diabetes characterized by heightened inflammation and impaired wound-healing processes. Interleukin-37 (IL-37) is a natural suppressor of innate inflammation. Here, we aim to investigate the potential of IL-37 in enhancing the healing process of diabetic wounds. The skin samples of DFU and non-diabetic patients during foot and ankle orthopedic surgery were collected. The IL-37 transgenic mice (IL-37Tg) were created using CRISPR/Cas-mediated genome engineering. Mice were administered streptozotocin (STZ, 150 mg/kg) to induce a diabetic model. After 4 weeks, an equidistant full-thickness excisional wound measuring 8 mm was created on the central back of each mouse and allowed to heal naturally. Body weight and blood glucose levels were measured weekly. The wound area was measured, and skin samples were collected on Day 10 for further Quantitative polymerase chain reaction (qPCR) and WB detection and RNA sequencing analysis. The proinflammation cytokines such as TNF-α and IL-1β and the MAPK signaling pathway were significantly increased in the wound margin of DFU patients. Compared with diabetic mice, diabetic IL-37Tg mice showed a significantly accelerated healing process. The enriched signaling pathways in RNA sequencing included cytokine-cytokine receptor interaction, TNF signaling pathway, and NOD-like receptor signaling pathway. Through QPCR and WB detection, we found that IL-37 could inhibit the activated MAPK and NOD-like signaling pathway, reducing TNF-α, IL-1β, and NLRP3 expression in the diabetic wound. IL-37 promotes skin wound healing in diabetic mice, providing a new possible target for treating diabetic wounds.