Cytokine-cytokine Receptor Interaction Research Articles

Cytokine interactions and chemokine dysregulations in mastitis immunopathogenesis: insights from transcriptomic profiling of milk somatic cells in tropical Sahiwal (Bos indicus) cows

IntroductionBovine mastitis causes a significant loss to the dairy industry by affecting the quantity and quality of milk. Addressing this challenge, the present study will leverage advanced omics techniques for early mastitis detection in early lactating Sahiwal cows (Bos indicus). This was the first differential transcriptomic study investigating the alterations in gene expression in milk somatic cells during the progression of naturally occurring mastitis in indigenous Sahiwal cows.MethodsCows were grouped into healthy (H), subclinical mastitis (SCM) and clinical mastitis (CM) groups by thoroughly screening them using the California Mastitis Test (CMT) and milk somatic cell counts (SCC). This was followed by detailed milk composition analysis, differential leukocyte counts (DLC), and microbiological culture.ResultsThe differential gene expression of milk SCs through transcriptome profiling identified 83 and 76, up-regulated and 157 and 192 down-regulated genes in CM vs H and SCM vs H groups (log2 fold change ≥1 and ≤-1, p < 0.05) respectively. Pathway analysis revealed that upregulated genes were enriched in pathways such as phagosome activity, IL-17 signalling, Th1 and Th2 cell differentiation, while downregulated genes were linked to RIG-I-like receptor signalling, NK cell cytotoxicity, and Toll-like receptor signalling and Cytokine-cytokine receptor interactions. Notably, the study underscores the roles of chemokines CCL8, CCL2, and CXCL10 in immune cell recruitment during mastitis, where their downregulation suggests impaired mammary immune defense that governs Chemokine signalling pathways. Further, the comparative analysis with the previously available milk SCs proteome data identified the downregulation of chemokines signalling pathways during mastitis.DiscussionOverall, this research enhances our understanding of mastitis pathogenesis and emphasizes that these targeted chemokines may boost mammary resilience through immunomodulation, genetic selection and genome editing or by utilising adjuvants in vaccine development that restore chemokine signalling offers a potential strategy to improve mastitis resistance in dairy cattle.

Identification and Experimental Validation of NETosis-Mediated Abdominal Aortic Aneurysm Gene Signature Using Multi-omics, Machine Learning, and Mendelian Randomization.

Abdominal aortic aneurysm (AAA) is a life-threatening disorder with limited therapeutic options. Neutrophil extracellular traps (NETs) are formed by a process known as "NETosis" that has been implicated in AAA pathogenesis, yet the roles and prognostic significance of NET-related genes in AAA remain poorly understood. This study aimed to identify key AAA- and NET-related genes (AAA-NETs-RGs), elucidate their potential mechanisms in contributing to AAA, and explore potential therapeutic compounds for AAA therapy. Through bioinformatics analysis of multiomics and machine learning, we identified six AAA-NETs-RGs: DUSP26, FCN1, MTHFD2, GPRC5C, SEMA4A, and CCR7, which exhibited strong diagnostic potential for predicting AAA progression, were significantly enriched in pathways related to cytokine-cytokine receptor interaction and chemokine signaling. Immune infiltration analysis revealed a causal association between AAA-NETs-RGs and immune cell infiltration. Cell-cell communication analysis indicated that AAA-NETs-RGs predominantly function in smooth muscle cells, B cells, T cells, and NK cells, primarily through cytokine and chemokine signaling. Gene profiling revealed that CCR7 and MTHFD2 exhibited the most significant upregulation in AAA patients compared to non-AAA controls, as well as in in vitro AAA models. Notably, genetic depletion of CCR7 and MTHFD2 strongly inhibited Ang II-induced phenotypic switching, functional impairment, and senescence in vascular smooth muscle cells (VSMCs). Based on AAA-NETs-RGs, molecular docking analysis combined with the Connectivity Map (CMap) database identified mirdametinib as a potential therapeutic agent for AAA. Mirdametinib effectively alleviated Ang II-induced phenotypic switching, biological dysfunction, and senescence. These findings provide valuable insights into understanding the pathophysiology of AAA and highlight promising therapeutic strategies targeting AAA-NETs-RGs.

Enrichment analysis of loci associated with psoriasis susceptibility identified in genome-wide association studies.

Psoriasis is a chronic autoimmune skin disease that has been associated with many polymorphic genes based on genome-wide association studies (GWAS). To perform gene ontology and biological pathway analysis of genes associated with psoriasis and also to investigate the degree of commonality of psoriasis-associated loci with susceptibility loci of some other autoimmune diseases, a total of 319 psoriasis-associated polymorphic protein-coding genes were included in the analysis. The web-based Enrichr was used for performing present analysis. Cytokine-cytokine receptor interaction and JAK-STAT signaling were predicted by KEGG analysis. The top biological process and molecular function were positive regulation of cytokine production and cytokine receptor activity, respectively. The present findings revealed that the psoriasis-associated genes were significantly involved in the immune system and its functions, consistent with the autoimmune nature of the disease. The present study revealed that there were 10 genes shared between psoriasis and other 5 autoimmune diseases, interestingly, these genes were significantly enriched in the JAK-STAT pathway (adjusted p-value = 3.75e-5). There were several multifactorial diseases and complex traits that had a statistically significant commonality between their predisposing genes and psoriasis predisposing genes. The current findings suggest that the JAK-STAT pathway is likely involved in the pathogenesis of psoriasis, such as many other autoimmune diseases. Therefore, it is suggested that inhibitors that block the gene transcription of pro-inflammatory cytokines by blocking intracellular signaling pathways mediated by JAK-STAT may be a good model for the treatment of autoimmune diseases, including psoriasis.

Whole transcriptome analysis in oviduct provides insight into microRNAs and ceRNA regulative networks that targeted reproduction of goat (Capra hircus)

BackgroundReproduction traits are crucial for livestock breeding and represent key economic indicators in the domestic goat (Capra hircus) industry. The oviduct, a critical organ in female mammals, plays a pivotal role in several reproductive processes; however, its molecular mechanisms remain largely unknown. Non-coding RNA and mRNAs are essential regulatory elements in reproductive processes; yet their specific roles and regulatory networks in goat oviducts remain unclear.ResultsIn this study, we conducted small RNA sequencing of the oviduct in high- and low-fecundity goats during the follicular (FH and FL groups, n = 10) and luteal (LH and LL groups, n = 10) phase, profiling 20 tissue samples. Combinatorial whole-transcriptome expression profiles were applied to the same samples to uncover the competitive endogenous RNA (ceRNA) regulation network associated with goat fecundity. RT-qPCR was employed to validate the miRNA profiling results, and ceRNA regulatory networks were analyzed through luciferase assay. Gene set enrichment analysis (GSEA) confirmed that the cytokine-cytokine receptor interaction and TGF-β signaling pathway, both related to embryonic development, were enriched in DEM target genes. Additionally, miR-328-3p, a core miRNA, targets SMAD3 and BOP1, which are involved in the negative regulation of cell growth and embryonic development. TOB1 and TOB2, targeted by miR-204-3p, regulate cell proliferation via the protein kinase C-activating G-protein coupled receptor signaling pathway. Analyses of ceRNA regulatory networks revealed that LNC_005981 − miR-328-3p − SMAD3 and circ_0021923 − miR-204-3p − DOT1L may affect goats’ reproduction, findings that were validated using luciferase assay.ConclusionAnalysis of whole-transcriptome profiling of goat oviducts identified several key miRNAs and ceRNAs that may regulate oocyte maturation, embryo development, and the interactions between the oviduct and gametes/early embryos, providing insights into the molecular mechanisms of reproductive regulatory networks.

Identification and validation of prognostic biomarkers related to tumor immune invasion in pancreatic cancer.

The diagnosis and treatment of pancreatic adenocarcinoma (PAAD) remain clinically challenging, and new molecular markers for prognostic assessment and targeted therapy are urgently needed. The tumor microenvironment (TME) and immune invasion play an important role in pancreatic cancer development and progression. Therefore, immunotherapeutic strategies based on the TME and immune invasion may have important clinical value. In this study, we extracted transcriptome and clinicopathological data for 179 PAAD samples from the TCGA database and evaluated the immune composition, stromal composition, and infiltrating immune cell landscape in the tumor samples. Then, we identified relevant differentially expressed genes (DEGs) and performed functional annotation and prognostic correlation analysis to identify prognostic biomarkers for pancreatic cancer, the correlation between biomarkers and tumor immune invasion was analyzed to reveal the molecular immune mechanism of pancreatic cancer. Finally, GEO databases (GES71729), GEPIA, TISIDB, TIMER databases and RT-PCR were used for further analysis. CXCL10 and CXCL11 were highly expressed in pancreatic cancer and associated with poor prognosis of patients through cell adhesion molecules chemokine signaling, cytokine-cytokine receptor interaction, natural killer cell-mediated cytotoxicity, and Toll-like receptor signaling pathways. Finally, the correlation between CXCL10 and CXCL11 and tumor immune invasion was analyzed. The results confirmed that the expression levels of CXCL10 and CXCL11 were positively correlated with the contents of CD8+ T cells. Activated memory CD4+ T cells, M1 macrophages and resting mast cells. The levels of CXCL10 and CXCL11 were related to but negatively correlated with the contents of memory B cells, Tregs and M0 macrophages. Our study demonstrates that CXCL10 and CXCL11 are novel biomarkers of TME and immune cell infiltration in pancreatic cancer by affecting the distribution of immune cells. CXCL10 and CXCL11 may be new targets for molecular targeted therapy and immunotherapy of pancreatic cancer.

Comparison of Deep Learning and Traditional Machine Learning Models for Predicting Mild Cognitive Impairment Using Plasma Proteomic Biomarkers

Mild cognitive impairment (MCI) is a clinical condition characterized by a decline in cognitive ability and progression of cognitive impairment. It is often considered a transitional stage between normal aging and Alzheimer’s disease (AD). This study aimed to compare deep learning (DL) and traditional machine learning (ML) methods in predicting MCI using plasma proteomic biomarkers. A total of 239 adults were selected from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort along with a pool of 146 plasma proteomic biomarkers. We evaluated seven traditional ML models (support vector machines (SVMs), logistic regression (LR), naïve Bayes (NB), random forest (RF), k-nearest neighbor (KNN), gradient boosting machine (GBM), and extreme gradient boosting (XGBoost)) and six variations of a deep neural network (DNN) model—the DL model in the H2O package. Least Absolute Shrinkage and Selection Operator (LASSO) selected 35 proteomic biomarkers from the pool. Based on grid search, the DNN model with an activation function of “Rectifier With Dropout” with 2 layers and 32 of 35 selected proteomic biomarkers revealed the best model with the highest accuracy of 0.995 and an F1 Score of 0.996, while among seven traditional ML methods, XGBoost was the best with an accuracy of 0.986 and an F1 Score of 0.985. Several biomarkers were correlated with the APOE-ε4 genotype, polygenic hazard score (PHS), and three clinical cerebrospinal fluid biomarkers (Aβ42, tTau, and pTau). Bioinformatics analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed several molecular functions and pathways associated with the selected biomarkers, including cytokine-cytokine receptor interaction, cholesterol metabolism, and regulation of lipid localization. The results showed that the DL model may represent a promising tool in the prediction of MCI. These plasma proteomic biomarkers may help with early diagnosis, prognostic risk stratification, and early treatment interventions for individuals at risk for MCI.

Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells.

Chromatin organization regulates transcription to influence cellular plasticity and cell fate. We explored whether chromatin nanoscale packing domains are involved in stemness and response to chemotherapy. Using an optical spectroscopic nanosensing technology we show that ovarian cancer-derived cancer stem cells (CSCs) display upregulation of nanoscale chromatin packing domains compared to non-CSCs. Cleavage under targets and tagmentation (CUT&Tag) sequencing with antibodies for repressive H3K27me3 and active H3K4me3 and H3K27ac marks mapped chromatin regions associated with differentially expressed genes. More poised genes marked by both H3K4me3 and H3K27me3 were identified in CSCs vs. non-CSCs, supporting increased transcriptional plasticity of CSCs. Pathways related to Wnt signaling and cytokine-cytokine receptor interaction were repressed in non-CSCs, while retinol metabolism and antioxidant response were activated in CSCs. Comparative transcriptomic analyses showed higher intercellular transcriptional heterogeneity at baseline in CSCs. In response to cisplatin, genes with low baseline expression levels underwent the highest upregulation in CSCs, demonstrating transcriptional plasticity under stress. Epigenome targeting drugs downregulated chromatin packing domains and promoted cellular differentiation. A disruptor of telomeric silencing 1-like (Dot1L) inhibitor blocked transcriptional plasticity, reversing stemness. These findings support that CSCs harbor upregulated chromatin packing domains, contributing to transcriptional and cell plasticity that epigenome modifiers can target.

Relationship between melanoma vemurafenib tolerance thresholds and metabolic pathway choice and Wnt signaling involvement.

Vemurafenib constitutes an important therapeutic for BRAFV600 mutant melanomas, but despite high initial response rates, resistance to BRAF and MEK inhibitors quickly develops. Here, we performed an integrative analysis of metabolomic consequences and transcriptome alterations to uncover mechanisms involved in adaptive vemurafenib resistance (VemR) development and their relationship with vemurafenib tolerance thresholds. We developed BRAFV600E isogenic models of VemR utilizing M14 and A2058 lines, and patient-derived melanomas with V600E or normal BRAF to verify vemurafenib selectivity. MEK or PI3K inhibitors only partially inhibited VemR cell proliferation, indicating cross-resistance to these inhibitors. MITF and β-catenin levels were induced and treatment with Wnt/β-catenin inhibitor ICG-001 restored vemurafenib sensitivity with concomitant reductions in β-catenin-regulated gene expressions, phospho-ERK1/2, and VemR-induced mitochondrial mass and respiration. Targeted metabolite, MitoPlate-S1, Mito-stress and transcriptome/metabolomic analysis showed that melanoma cells with elevated vemurafenib tolerance thresholds such as A2058 VemR cells utilize Wnt/β-catenin signaling for mitochondrial metabolism while VemR cells with low tolerance such as M14 VemR cells rely on Wnt/β-catenin signaling for pentose phosphate pathway. Pathways associated with cytokine-cytokine receptor, ECM receptor, and neuroactive ligand receptor interactions were similarly enriched in BRAFV600E patient-derived melanoma as M14 and A2058 cells whereas distinct pathways involving cell cycle, DNA replication, Fanconi anemia and DNA repair pathways are upregulated in wild type BRAF expressing patient derived melanoma. These data show for the first time that the metabolic pathway choices made by VemR BRAF mutant melanomas are controlled by vemurafenib tolerance and endurance thresholds and Wnt/β-catenin signaling plays a central role in coordinating expression of genes controlling VemR and metabolic pathway shifts.

Multi-Omics Analysis Reveals the Negative Effects of High-Concentrate Diets on the Colonic Epithelium of Dumont Lambs.

Feeding HC diets has been found to induce metabolic dysregulation in the colon. However, the mechanisms by which changes in colonic flora and metabolites damage the colonic epithelium are poorly studied. Therefore, the present experiment used a multi-omics technique to investigate the mechanism of colonic injury induced by high-concentrate diets in lambs. Twelve male Dumont lambs were randomly split into two groups: a low-concentrate diet (LC = concentrate/forage = 30:70) group and a high-concentrate diet (HC = concentrate/forage = 70:30) group. The results showed that the HC group presented significantly increased lipopolysaccharide (LPS) concentrations in the colonic epithelium and significantly decreased serum total cholesterol (TC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) levels (p < 0.05), which led to cavities and inflammatory cell infiltration in the colonic epithelium. The HC group had significantly lower pH and less VFAs in colon contents, as well as a significantly increased abundance of bacteria of the genera [Eubacterium]_coprostanoligenes_group, Rikenellaceae_RC9_gut_group, Treponema, Clostridia_UCG-014, Alistipes, Ruminococcus, Christensenellaceae_R-7_group, UCG-002, Bacteroidales_RF16_group and Lachnospiraceae_AC2044_group compared to the LC diet group. These microorganisms significantly increased the level of metabolites of cholic acid, chenodeoxycholic acid, LysoPA (P-16:0/0:0), methapyrilene, and fusaric acid. A transcriptome analysis showed that cytokine-cytokine receptor interaction, glutathione metabolism, and the peroxisome signaling pathway were downregulated in the colon epithelium of the lambs fed the HC diet. Therefore, the HC diet caused epithelial inflammation and oxidative damage by affecting the interaction between the microbial flora of the colon and metabolites and the host epithelium, which eventually disrupted colon homeostasis and had a negative impact on sheep health.

Transcriptional and microbial profile of gastric cancer patients infected with Epstein-Barr virus.

Gastric cancer (GC), which has low survival rates and high mortality, is a major concern, particularly in Asia and South America, with over one million annual cases. Epstein-Barr virus (EBV) is recognized as a carcinogen that may trigger gastric carcinogenesis by infecting the stomach epithelium via reactivated B cells, with growing evidence linking it to GC. This study investigates the transcriptional and microbial profiles of EBV-infected versus EBV-non-infected GC patients. Using Illumina NextSeq, cDNA libraries were sequenced, and reads were aligned to the human genome and analyzed with DESeq2. Kegg and differential analyses revealed key genes and pathways. Gene sensitivity and specificity were assessed using ROC curves (p < 0.05, AUC > 0.8). Non-aligned reads were used for microbiome analysis with Kraken2 for bacterial identification. Microbial analysis included LDA score, Alpha and Beta diversity metrics, with significance set at p ≤ 0.05. Spearman's correlation between differentially expressed genes (DEGs) and bacteria were also examined. The data revealed a gene expression pattern in EBV-positive gastric cancer, highlighting immune response, inflammation, and cell proliferation genes (e.g., GBP4, ICAM1, IL32, TNFSF10). ROC analysis identified genes with high specificity and sensitivity for discriminating EBV+ gastric cancer, including GBP5, CMKLR1, GM2A and CXCL11 that play pivotal roles in immune response, inflammation, and cancer. Functional enrichment pointed to cytokine-cytokine receptor interactions, antigen processing, and Th17 immune response, emphasizing the role of the tumor microenvironment, shaped by inflammation and immunomodulation, in EBV-associated GC. Microbial analysis revealed changes in the gastric microbiota in EBV+ samples, with a significant reduction in bacterial taxa. The genera Choristoneura and Bartonella were more abundant in EBV+ GC, while more abundant bacteria in EBV- GC included Citrobacter, Acidithiobacillus and Biochmannia. Spearman's correlation showed a strong link between DE bacterial genera and DEGs involved in processes like cell differentiation, cytokine production, digestion, and cell death. These findings suggest a complex interaction between the host (EBV+ GC) and the microbiota, possibly influencing cancer progression, and offering potential therapeutic targets such as microbiota modulation or gene regulation. Comparing with EBV- samples further highlights the specific impact of EBV and the microbiota on gastric cancer pathogenesis.

Mendelian randomization of plasma proteomics identifies novel ALS-associated proteins and their GO enrichment and KEGG pathway analyses

BackgroundAmyotrophic lateral sclerosis (ALS) is a progressive and fatal neurological disorder with an increasing incidence rate. Despite advances in ALS research over the years, the precise etiology and pathogenic mechanisms remain largely elusive.ObjectiveTo identify novel plasma proteins associated with ALS through Mendelian randomization methods in large-scale plasma proteomics and to provide potential biomarkers and therapeutic targets for ALS treatment.MethodsThis study employed a large-scale plasma proteomic Mendelian randomization approach using genetic data from 80,610 individuals of European ancestry (including 20,806 ALS patients and 59,804 controls) derived from a genome-wide association study (GWAS). Protein quantitative trait loci (pQTLs) data were obtained from Ferkingstad et al. (2021), which measured 4,907 proteins in 35,559 Icelandic individuals. Multiple Mendelian randomization (MR) techniques were utilized, including weighted median, MR-Egger, Wald ratio, inverse-variance weighting (IVW), basic model, and weighted model. Heterogeneity was evaluated using Cochran’s Q test. Horizontal pleiotropy was assessed through the MR-Egger intercept test and MR-PRESSO outlier detection. Sensitivity analysis was performed via leave-one-out analysis.ResultsMR analysis revealed potential causal associations between 491 plasma proteins and ALS, identifying 19 novel plasma proteins significantly linked to the disease. Proteins such as C1QC, UMOD, SLITRK5, ASAP2, TREML2, DAPK2, ARHGEF10, POLM, SST, and SIGLEC1 showed positive correlations with ALS risk, whereas ADPGK, BTNL9, COLEC12, ADGRF5, FAIM, CRTAM, PRSS3, BAG5, and PSMD11 exhibited negative correlations. Reverse MR analyses confirmed that ALS negatively correlates with ADPGK and ADGRF5 expression. Enrichment analyses, including Gene Ontology (GO) functional analysis, indicated involvement in critical biological processes such as external encapsulating structure organization, extracellular matrix organization, chemotaxis, and taxis. KEGG pathway analysis highlighted significant enrichment in the PI3K-Akt signaling pathway, cytokine-cytokine receptor interactions, and axon guidance.ConclusionThis study enhances the understanding of ALS pathophysiology and proposes potential biomarkers and mechanistic insights for therapeutic development. Future research should explore the clinical translation of these findings to improve ALS patient outcomes and quality of life.

Analysis of long Non-Coding RNA and mRNA expression in Clostridium butyricum-Induced apoptosis in SW480 colon cancer cells.

Analysis of long Non-Coding RNA and mRNA expression in Clostridium butyricum-Induced apoptosis in SW480 colon cancer cells.

Genetic parameters and identification of genomic regions and candidate genes associated with vaginal discharge score in Holstein cattle based on genomic and transcriptomic analyses.

Genetic parameters and identification of genomic regions and candidate genes associated with vaginal discharge score in Holstein cattle based on genomic and transcriptomic analyses.

Characterization of a cell-adapted completely attenuated genotype GIIa porcine epidemic diarrhea virus strain.

Characterization of a cell-adapted completely attenuated genotype GIIa porcine epidemic diarrhea virus strain.

Transcriptomic and network analysis identifies shared pathways across Alzheimer’s disease and vascular dementia

Transcriptomic and network analysis identifies shared pathways across Alzheimer’s disease and vascular dementia

Molecular insights into ulcerative colitis and orbital inflammation

Ulcerative colitis (UC) is an increasingly prevalent inflammatory condition affecting the intestinal mucosa, while nonspecific orbital inflammation (NSOI) is a common non-neoplastic orbital disorder. Exploring the molecular interplay between UC and NSOI may help physicians make earlier diagnoses and enhance treatment approaches. We analyzed gene expression datasets (GSE58331, GSE105149, GSE206285, and GSE179285) for UC and NSOI from the GEO database. Using WGCNA and differential expression analysis, we identified genes commonly altered in both diseases. GO enrichment, PPI networks, and transcription factor prediction were performed using Cytoscape plugins (cytoHubba and iRegulon). Machine learning techniques were employed to assess transcription factor activity and evaluate potential therapeutic targets among the hub genes. We conducted an association analysis using the TwoSampleMR package in R to explore potential causal relationships between NSOI and UC. A total of 85 intersecting genes between NSOI and UC were identified, and enrichment analyses revealed their roles in immune and inflammatory processes. Key biomarkers, including CXCL10, CXCR4, CXCL9, CD27, SELL, MMP9, CD79A, CD3E, GZMK, and CCL19, were highlighted, linking them to processes such as leukocyte migration, viral response, and monocyte differentiation. STAT1 was identified as a shared transcription factor influencing both diseases. Machine learning algorithms identified eight potential genes for diagnostic and therapeutic use, with CXCL10 emerging as a key player in the pathogenesis of NSOI and UC. CXCL10 likely regulates CXCR4, LCK, CCR7, and other genes involved in pathways such as cytokine-cytokine receptor interactions, HIV-1 infection, and Epstein-Barr virus infection. This study offers insights into the co-pathogenic mechanisms of UC and NSOI, providing a foundation for further mechanistic research and therapeutic development.

Combined metabolome and transcriptome analysis provides molecular insights into reproductive process in Chuanxiang Black and Landrace pigs.

Testes are crucial for male reproduction, and transcriptomic and metabolomic analyses can help identify genes and pathways linked to reproductive performance differences in pig breeds. The present study was conducted to identify the differentially expressed genes and differentially accumulated metabolites (DAMs) through transcriptomic and metabolomic analyses of testicular tissues in Chuanxiang Black and Landrace pigs. Six testis tissue samples from each pig breed were used for transcriptomic analysis. Further liquid chromatography-mass spectrometry analysis was performed for targeted metabolomic analysis to identify differential metabolites in both breeds. RNA-sequencing data identified a total of 6,233 DEGs, including 3,417 upregulated and 2,816 downregulated genes in Chuanxiang Black compared to Landrace pigs. Comparative pathway enrichment analyses revealed that many DEGs and DAMs were associated with critical reproductive pathways, especially those related to male gametogenesis, spermatogenesis, sexual reproduction, development, and reproductive processes. Three major pathways related to signal transduction (PI3K-Akt, Rap1, and MAPK signaling pathways), lipid metabolism (linoleic acid and arachidonic acid metabolism), and cytokine-cytokine receptor interaction were identified as differentially enriched pathways in Chuanxiang Black pigs. Differential circRNA target gene enrichment analysis revealed 4,179 DEGs, including 3,022 genes involved in biological processes, 477 in cellular components, and 680 in molecular functions. Differential analysis of miRNA between the two groups revealed 2,512 DEGs, including 1,628 upregulated and 884 downregulated genes. Both miRNA and circRNA were involved in enriched KEGG pathways mainly including signaling pathways (cAMP signaling pathways, calcium signaling pathways), endocrine secretion (aldosterone synthesis and secretion and GnRH secretion), and signaling molecules and interaction (ECM-receptor interaction). These findings revealed that both circRNA and miRNA play a crucial role in regulating the differential gene expression related to reproductive processes in Chuanxiang Black compared to Landrace pigs.

T-2 toxin-induced splenic injury by disrupting the gut microbiota-spleen axis via promoting IL-6/JAK/STAT1 signaling-mediated inflammation and apoptosis and its mitigation by elemental nano-selenium.

T-2 toxin is one of the most toxic A trichothecene mycotoxins prevalent in the environment and food chain, which brings severe health hazards to both animals and humans and it can significantly damage immune function. In this study, we comprehensively explained the impact of T-2 toxin on the spleen through gut microbiota-spleen axis by integrating the transcriptome and microbiome. Our results revealed that dietary T-2 toxin ≥ 1.0mg/kg exposure significantly inhibited the growth performance and caused spleen injury in broilers chicks, accompanied by oxidative stress and histopathological damage. Cecal microbiome analysis suggested that T-2 toxin exposure caused gut microbial dysbiosis, especially leading to the decrease of some beneficial bacteria genera that enhanced gut barrier and reduced inflammation, including Blautia, Coprococcus, Lachnospira and Anaerostipes belonging to Lachnospiraceae family. Transcriptome analysis suggested that T-2 toxin exposure directly caused splenic inflammation and immune-related signaling, such as cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway and JAK-STAT signaling pathway. Furthermore, by integrating the transcriptome and microbiome analysis, we found that spleen damage induced by T-2 toxin was associated with the abnormal activation of IL-6/JAK/STAT1 signaling pathway-mediated inflammation and apoptosis, which was further verified by western bolt analysis. Notably, dietary selenium supplementation could protect chicks from T-2 toxin-induced adverse effects on growth performance and spleen injury by inhibiting the expression of the IL-6/JAK/STAT1 signaling-related genes. In summary, our findings provided new insights into the immunotoxicity mechanisms of T-2 toxin in the chickens' spleen and highlighted the potential of selenium to alleviate T-2 toxin-induced immunotoxicity.

An Integrated Network Pharmacology and RNA-seq Approach for Exploring the Protective Effect of Isoquercitrin in Doxorubicin-Induced Cardiotoxicity: Identification of Novel Genes.

Cardiotoxicity, a severe side effect of cytotoxic drugs like doxorubicin (DOX), can lead to cardiomyopathy and heart failure, significantly impacting patient prognosis. This study investigates the molecular mechanisms of DOX-induced cardiotoxicity and explores isoquercitrin (IQC) as a potential therapeutic agent. RNA-sequencing analysis revealed 7855 dysregulated genes in DOX vs. Control and 3853 in DOX + IQC vs. DOX groups. Functional enrichment analysis of upregulated genes in the DOX vs. Control group highlighted cytokine-cytokine receptor interaction and calcium signaling pathways as significant immune-related KEGG pathways. Immune genes were shortlisted based on inflammatory functions, followed by protein-protein interaction analysis and hub gene identification. This process revealed IL6, IL1B, IL10, CCL19, CD27, CSF1R, ADRB2, GDF15, TNFRSF10B, and PADI4 as the top 10 interacting immune hub genes. Validation in the DOX + IQC vs. DOX group showed that IQC downregulated CCL19, IL10, PADI4, and CSF1R genes. Computational drug design techniques, including virtual screening and molecular dynamic simulations, identified promising targets for IQC. These targets were experimentally validated using RT-qPCR in AC16 cell lines under four conditions: control, DOX, low dose DOX + IQC, and high dose DOX + IQC. The study demonstrates that IQC significantly reduces inflammation and oxidative stress in human AC16 cardiomyocyte cell line by downregulating inflammatory and stress pathways induced by DOX. It concludes that CCL19 and PADI4 are crucial immune biomarkers for treating DOX-induced cardiotoxicity using IQC, providing insights into potential therapeutic strategies using plant-based compounds to mitigate the cardiotoxic effects of DOX in cancer treatment.

Molecular Response and Metabolic Reprogramming of the Spleen Coping with Cold Stress in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis).

The Chinese soft-shelled turtle (Pelodiscus sinensis), as a type of warm-water reptile, could be induced to massive death by sharp temperature decline. Hence, the mechanism of spleen tissue responding to cold stress in the P. sinensis was investigated. The present results showed that the superoxide dismutase (SOD) activity declined from 4 to 16 days post-cold-stress (dps), while the catalase (CAT) and glutathione peroxidase (GSH-Px) activities increased, from 4 to 8 dps in the 14 °C (T14) and 7 °C (T7) stress groups. The spleen transcriptome in the T7 group and the control group (CG) at 4 dps obtained 2625 differentially expressed genes (DEGs), including 1462 upregulated and 1663 downregulated genes. The DEGs were enriched mainly in the pathways "intestinal immune network for IgA production" (Pigr, Il15ra, Tnfrsf17, Aicda, and Cd28), "toll-like receptor signaling pathway" (Mapk10, Tlr2, Tlr5, Tlr7, and Tlr8), and "cytokine-cytokine receptor interaction" (Cx3cl1, Cx3cr1, Cxcl14, Cxcr3, and Cxcr4). The metabolomic data showed that esculentic acid, tyrosol, diosgenin, heptadecanoic acid, and 7-ketodeoxycholic acid were obviously increased, while baccatin III, taurohyocholate, parthenolide, enterolactone, and tricin were decreased, in the CG vs. T7 comparison. Integrated analysis of the two omics revealed that "glycine, serine and threonine metabolism", "FoxO signaling pathway", and "neuroactive ligand-receptor interaction" were the main pathways responding to the cold stress. Overall, this work found that low temperature remarkably influenced the antioxidant enzyme activities, gene expression pattern, and metabolite profile in the spleen, indicating that immunity might be weakened by cold stress in P. sinensis.