Gene Ontology Enrichment Analysis Research Articles

Spatial Transcriptomic Profiling Reveals Gene Expression Characteristics in Lymph Node-positive Breast Carcinoma.

Studies on the differences in gene expression characteristics according to lymph node metastasis in breast carcinoma are lacking. This study aimed to compare the spatially resolved transcriptomic profiles between node-positive and negative breast carcinomas. Eight patients with breast carcinoma were included, and digital spatial profiling and bioinformatic analysis were conducted to investigate the spatial transcriptomes. In the epithelial compartment, the top two most up-regulated genes were nuclear receptor subfamily 4 group A member 1 (NR4A1) and Jun proto-oncogene, activating protein-1 transcription factor subunit (JUN). The gene ontology (GO) enrichment analysis of the node-positive group revealed a significant up-regulation of genes associated with myeloid differentiation, mononuclear cell differentiation, and hematopoietic regulation. The gene set enrichment analysis (GSEA) revealed significant enrichment of gene sets associated with the regulation of inflammatory cytokines in both the epithelial and stromal compartments of the node-positive group. Our study highlights significant differences in gene expression profiles and spatially resolved transcriptional activities between node-positive and negative breast carcinomas. These findings underscore the importance of developing personalized treatment strategies for lymph node metastasis of breast carcinoma.

Proteomic insights into the regulatory function of ARID1A in colon cancer cells.

The AT-rich interacting domain-containing protein 1A (ARID1A) is a tumor suppressor gene that has been implicated in several cancers, including colorectal cancer (CRC). The present study used a proteomic approach to elucidate the molecular mechanisms of ARID1A in CRC carcinogenesis. Stable ARID1A-overexpressing SW48 colon cancer cells were established using lentivirus transduction and the successful overexpression of ARID1A was confirmed by western blotting. Label-free quantitative proteomic analysis using liquid chromatography-tandem mass spectrometry identified 705 differentially altered proteins in the ARID1A-overexpressing cells, with 310 proteins significantly increased and 395 significantly decreased compared with empty vector control cells. Gene Ontology enrichment analysis highlighted the involvement of the altered proteins mainly in the Wnt signaling pathway. Western blotting supported these findings, as a decreased protein expression of Wnt target genes, including c-Myc, transcription factor T cell factor-1/7 and cyclin D1, were observed in ARID1A-overexpressing cells. Among the altered proteins involved in the Wnt signaling pathway, the interaction network analysis revealed that ARID1A exhibited a direct interaction with E3 ubiquitin-protein ligase zinc and ring finger 3 (ZNRF3), a negative regulator of the Wnt signaling pathway. Further analyses using the The Cancer Genome Atlas colon adenocarcinoma public dataset revealed that ZNRF3 expression significantly impacted the overall survival of patients with CRC and was positively correlated with ARID1A expression. Finally, an increased level of ZNRF3 in ARID1A-overexpressing cells was confirmed by western blotting. In conclusion, the findings of the present study suggest that ARID1A negatively regulates the Wnt signaling pathway through ZNRF3, which may contribute to CRC carcinogenesis.

Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.

The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome ("arcGaz3") shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome ("arcGaz4_h1"). The new assembly is 2.53Gb long, has a scaffold N50 of 55.6Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of eleven pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling (GERP). We then implemented Gene Ontology (GO) enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the two major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome.

Detection of a Diagnostic Model and Comprehensive Examination of Diabetic Retinopathy Utilizing Genes Linked to Endoplasmic Reticulum Stress.

The aim of this study was to reveal the biological functionalities associated with endoplasmic reticulum stress (ERS)-related genes (ERSGs) in the context of diabetic retinopathy (DR). Differentially expressed genes (DEGs) within the DR group and the Control group were identified and then integrated with ERSGs. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) methodologies were used to investigate potential biological mechanisms. A diagnostic model for ERS and a nomogram were formulated based on biomarkers selected through the Least Absolute Shrinkage and Selection Operator method. The diagnostic efficacy of this model was thoroughly evaluated. ERS-associated subtypes were identified, and the Single-Sample GSEA (ssGSEA) and CIBERSORT algorithms were used to assess immune infiltration. We identified 10 ERS-related DEGs (ERSRDEGs) within the DR Group. Subsequently, a diagnostic model was constructed based on 5 ERS genes, namely CCND1, IGFBP2, TLR4, TXNIP, and VIM. The validation analysis demonstrated the commendable diagnostic performance of the model. Analysis of the ssGSEA immune characteristics revealed a positive correlation in the DR group between myeloid-derived suppressor cells (MDSC), regulatory T cells (Tregs), and CCND1 TXNIP. Furthermore, a significant negative correlation was observed between central memory CD4 T cells and CCND1. In the context of CIBERSORT, the results indicated a positive correlation between macrophages and IGFBP2, as well as Tregs and IGFBP2 in the DR group. Notably, a conspicuous negative correlation was identified between resting mast cells and IGFBP2. The present study provides novel diagnostic biomarkers for DR from an ERS perspective.

Network pharmacology and experimental validation to explore the role and potential mechanism of Liuwei Dihuang Decoction in prostate cancer

ObjectiveTo evaluate the anti-tumor effector of Liuwei Dihuang Decoction (LWDHD) in prostate cancer (PCa) and explore the potential mechanism using experimental validation, network pharmacology, bioinformatics analysis, and molecular docking.MethodsCCK test, Clone formation assay and wound-healing assays were used to determine the effect of LWDHD on prostate cancer growth and metastasis. The active ingredients and targets of LWDHD were obtained from the TCMSP database, and the relevant targets were selected by GeneCards, OMIM and DisGeNET databases for PCa. The cross-targets of drugs and disease were imported into the STRING database to construct protein interactions. The network was also visualized using Cytoscape software and core targets are screened using the Network Analyzer plug-in. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were analyzed using R software. TCGA database was used to analyze the correlation of bioinformatics genes. AutoDock vina was used to predict the molecular docking and binding ability of active ingredients to key targets. Through WB and q-PCR experiments, the above gene targets were detected to verify the effect of LWDHD on PCa.ResultsCCK and scratch tests confirmed that LWDHD could inhibit the proliferation, invasion and migration of prostate cancer cells. Clone formation experiments showed that LWDHD inhibited the long-term proliferative capacity of PC3 cells. LWDHD and PCa had a total of 99 common targets, establishing a “drug-ingredient-common target” network. Through GO and KEGG enrichment analysis, PI3K/AKT, MAPK, TP53 pathway, MYC, TNF pathway and other signaling pathways were found. Bioinformatics analysis showed that MYC gene was highly expressed and CCND1 and MAPK1 were low expressed in prostate cancer tissues. In addition, TP53, AKT1, MYC, TNF and CCND1 were positively correlated with MAPK1, among which AKT1 and CCND1 were most closely correlated with MAPK1. Molecular docking results showed that quercetin, kaempferol, β-sitosterol and other main active ingredients of LWDHD treatment for PCa were combined with core proteins MAPK1 and AKT1 well. WB and q-PCR results showed that LWDHD inhibited the expression of PI3K and AKT in PC3 cells.ConclusionThe mechanism of LWDHD therapy for PCa is a multi-target and multi-pathway complex process, which may be related to the biological processes mediated by MAPK1 and AKT1 pathways, such as cell proliferation and inhibition of metastasis, and the regulation of signaling pathways. The PI3K/AKT signaling pathway may be a central pathway of LWDHD to inhibit prostate cancer proliferation.

GWAS-based polygenic risk scoring for predicting cerebral artery dissection in the Chinese population

ObjectiveCerebral artery dissection (CeAD) is a rare but serious disease. Genetic risk assessment for CeAD is lacking in Chinese population. We performed genome-wide association study (GWAS) and computed polygenic risk score (PRS) to explore genetic susceptibility factors and prediction model of CeAD based on patients in Huashan Hospital.MethodsA total of 210 CeAD patients and 280 controls were enrolled from June 2017 to September 2022 in Department of Neurology, Huashan Hospital, Fudan University. We performed GWAS to identify genetic variants associated with CeAD in 140 CeAD patients and 210 control individuals according to a case and control 1:1.5 design rule in the training dataset, while the other 70 patients with CeAD and 70 controls were used as validation. Then Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analyses were utilized to identify the significant pathways. We constructed a PRS by capturing all independent GWAS SNPs in the analysis and explored the predictivity of PRS, age, and sex for CeAD.ResultsThrough GWAS analysis of the 140 cases and 210 controls in the training dataset, we identified 13 leading SNPs associated with CeAD at a genome-wide significance level of P < 5 × 10− 8. Among them, 10 SNPs were annotated in or near (in the upstream and downstream regions of ± 500Kb) 10 functional genes. rs34508376 (OR2L13) played a suggestive role in CeAD pathophysiology which was in line with previous observations in aortic aneurysms. The other nine genes were first-time associations in CeAD cases. GO enrichment analyses showed that these 10 genes have known roles in 20 important GO terms clustered into two groups: (1) cellular biological processes (BP); (2) molecular function (MF). We used genome-wide association data to compute PRS including 32 independent SNPs and constructed predictive model for CeAD by using age, sex and PRS as predictors both in training and validation test. The area under curve (AUC) of PRS predictive model for CeAD reached 99% and 95% in the training test and validation test respectively, which were significantly larger than the age and sex models of 83% and 86%.ConclusionsOur study showed that ten risk loci were associated with CeAD susceptibility, and annotated functional genes had roles in 20 important GO terms clustered into biological process and molecular function. The PRS derived from risk variants was associated with CeAD incidence after adjusting for age and sex both in training test and validation.

NETWORK TOXICOLOGY FOR THE CARDIOVASCULAR TOXICITY ANALYSIS OF TYROSINE KINASE INHIBITORS

Objective: This study aims to explore potential molecular mechanisms and targets of cardiovascular toxicities caused by tyrosine kinase inhibitors. Therefore, toxicogenomic data mining was conducted focusing on sunitinib, sorafenib, pazopanib, axitinib, and their associations with cardiovascular diseases. Material and Method: Common genes between tyrosine kinase inhibitors and cardiovascular diseases were uncovered via comparative toxicogenomic databases. Additionally, protein-protein and gene-gene interactions were identified using STRING and GeneMANIA, respectively. Subsequently, hub proteins associated with tyrosine kinase inhibitor-induced cardiovascular diseases were determined through Metascape. Transcription factors and microRNAs related to this toxicity were identified using ChEA3 and MIENTURNET, respectively. Finally, gene ontology enrichment analysis and the most associated molecular pathways were identified using the DAVID database and Metascape, respectively. Result and Discussion: Toxicogenomic data mining revealed six genes common between tyrosine kinase inhibitors and cardiovascular diseases, with five of these genes (FLT1, FLT4, KDR, MAPK1, and MAPK3) identified as hub genes. Physical interaction was dominant among these hub genes (77.64%). Sunitinib, sorafenib, pazopanib, and axitinib generally downregulated the activities of these proteins. SOX17 and SOX18 were prominent among transcription factors, while hsa-miR-199a-3p was the most important microRNA associated with this toxicity. Moreover, the Ras signaling pathway was mostly associated with tyrosine kinase inhibitor-induced cardiovascular toxicities. These findings make a substantial contribution to understanding the processes underlying cardiovascular diseases induced by sunitinib, sorafenib, pazopanib, and axitinib. They also reveal novel potential therapeutic targets, including genes, proteins, transcription factors, microRNAs, and pathways.

Comprehensive investigation of tumor immune microenvironment and prognostic biomarkers in osteosarcoma through integrated bulk and single-cell transcriptomic analysis

Osteosarcoma (OS) is an aggressive and highly lethal bone tumor, highlighting the urgent need for further exploration of its underlying mechanisms. In this study, we conducted analyses utilizing bulk transcriptome sequencing data of OS and healthy control samples, as well as single cell sequencing data, obtained from public databases. Initially, we evaluated the differential expression of four tumor microenvironment (TME)-related gene sets between tumor and control groups. Subsequently, unsupervised clustering analysis of tumor tissues identified two significantly distinct clusters. We calculated the differential scores of the four TME-related gene sets for Clusters 1 (C1) and 2 (C2), using Gene Set Variation Analysis (GSVA, followed by single-variable Cox analysis. For the two clusters, we performed survival analysis, examined disparities in clinical-pathological distribution, analyzed immune cell infiltration and immune evasion prediction, assessed differences in immune infiltration abundance, and evaluated drug sensitivity. Differentially expressed genes (DEGs) between the two clusters were subjected to Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA). We conducted Weighted Gene Co-expression Network Analysis (WGCNA) on the TARGET-OS dataset to identify key genes, followed by GO enrichment analysis. Using LASSO and multiple regression analysis we conducted a prognostic model comprising eleven genes (ALOX5AP, CD37, BIN2, C3AR1, HCLS1, ACSL5, CD209, FCGR2A, CORO1A, CD74, CD163) demonstrating favorable diagnostic efficacy and prognostic potential in both training and validation cohorts. Using the model, we conducted further immune, drug sensitivity and enrichment analysis. We performed dimensionality reduction and annotation of cell subpopulations in single cell sequencing analysis, with expression profiles of relevant genes in each subpopulation analyzed. We further substantiated the role of ACSL5 in OS through a variety of wet lab experiments. Our study provides new insights and theoretical foundations for the prognosis, treatment, and drug development for OS patients.

Development of Non-Invasive miRNA Markers for Assessing the Quality of Human Induced Pluripotent Stem Cell-Derived Retinal Organoids

Human retinal organoids (ROs) have emerged as valuable tools for studying retinal development, modeling human retinal diseases, and screening drugs. However, their application is limited primarily due to time-intensive generation, high costs, and low reproducibility. Quality assessment of RO differentiation is crucial for their application in research. However, traditional methods such as morphological evaluation and immunohistochemical analysis have limitations due to their lack of precision and invasiveness, respectively. This study aims to identify non-invasive biomarkers for RO differentiation quality using exosomal microRNAs (miRNAs), which are known to reflect cell-specific functions and development in the retina. We differentiated ROs from human induced pluripotent stem cells (hiPSCs) and classified them into ‘superior’ and ‘inferior’ groups based on morphological and immunohistochemical criteria. Exosomes from the conditioned media were isolated and analyzed for miRNA content. Our findings revealed distinct miRNA profiles between superior and inferior ROs, with superior ROs exhibiting higher miRNA diversity and specifically up- or down-regulated miRNAs. Gene ontology and pathway enrichment analyses indicated that the target genes of these miRNAs are involved in neuron proliferation and differentiation. The study suggests the potential of exosomal hsa-miR-654-3p and hsa-miR-451a as non-invasive biomarkers for real-time monitoring of RO quality, facilitating the development of standardized, efficient, and cost-effective culture methods.

Comparative Transcriptome Analysis Reveals Different Responses in Three Developmental Stages of Mythimna loreyi to Cold Stress.

The loreyi leafworm Mythimna loreyi (Lepidoptera: Noctuidae) is a serious pest of agriculture that causes particular damage to Gramineae crops in Asia, Europe, Australia, Africa, and the Middle East. Low temperature is one of the important environmental factors that limits the survival, distribution, colonization, and abundance of M. loreyi. However, the metabolic synthesis pathways of cold-tolerant substances in M. loreyi and the key genes involved in the regulation under cold stress remain largely unknown. In this study, we sequenced the transcriptomes of three developmental stages (larvae, pupae, and adults) of M. loreyi to discover the molecular mechanisms of their responses to cold stress. In total, sequencing generated 120.64 GB of clean data from 18 samples, of which 19,459 genes and 1740 differentially expressed genes (DEGs) were identified. The enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that many DEGs were mainly enriched in pathways associated with energy metabolism and hormone metabolism. Among these, genes encoding multiple metabolic enzymes, cuticle proteins (CPs), and heat shock proteins (HSPs) were differentially expressed. These results indicate that there are significant differences among the three developmental stages of M. loreyi exposed to cold stress and provide a basis for further studying the molecular mechanisms of cold tolerance in insects.

Small RNA and Degradome Deep Sequencing Reveal Regulatory Roles of MicroRNAs in Response to Sugarcane Mosaic Virus Infection on Two Contrasting Sugarcane Cultivars.

MicroRNAs (miRNAs) play an essential regulatory role in plant-virus interaction. However, few studies have focused on the roles of miRNAs and their targets after sugarcane mosaic virus (SCMV) infection in sugarcane. To address this issue, we conducted small RNA (sRNA) and degradome sequencing on two contrasting sugarcanes (SCMV-resistant 'Fuoguo1' [FG1] and susceptible 'Badila') infected by SCMV at five time points. A total of 1,578 miRNAs were profiled from 30 sRNA libraries, comprising 660 known miRNAs and 380 novel miRNAs. Differential expression analysis of miRNAs revealed that most were highly expressed during the SCMV exponential phase in Badila at 18 h postinfection, with expression profiles positively correlated with virus replication dynamics as observed through clustering. Analysis of degradome data indicated a higher number of differential miRNA targets in Badila compared to FG1 at 18 h postinfection. Gene ontology (GO) enrichment analysis significantly enriched the stimulus-response pathway, suggesting negative regulatory roles to SCMV resistance. Specifically, miR160 upregulated expression patterns and validated in Badila through quantitative real-time PCR (qRT-PCR) in the early stages of SCMV multiplication. Our research provides new insights into the dynamic response of plant miRNA and virus replication and contributes valuable information on the intricate interplay between miRNAs and SCMV infection dynamics. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Dopamine Receptors and TAAR1 Functional Interaction Patterns in the Duodenum Are Impaired in Gastrointestinal Disorders.

Currently, there is a growing amount of evidence for the involvement of dopamine receptors and the functionally related trace amine-associated receptor, TAAR1, in upper intestinal function. In the present study, we analyzed their expression in the duodenum using publicly accessible transcriptomic data. We revealed the expression of DRD1, DRD2, DRD4, DRD5, and TAAR1 genes in different available datasets. The results of the gene ontology (GO) enrichment analysis for DRD2 and especially TAAR1 co-expressed genes were consistent with the previously described localization of D2 and TAAR1 in enteric neurons and secretory cells, respectively. Considering that co-expressed genes are more likely to be involved in the same biological processes, we analyzed genes that are co-expressed with TAAR1, DRD2, DRD4, and DRD5 genes in healthy mucosa and duodenal samples from patients with functional dyspepsia (FD) or diabetes-associated gastrointestinal symptoms. Both pathological conditions showed a deregulation of co-expression patterns, with a high discrepancy between DRDs and TAAR1 co-expressed gene sets in normal tissues and patients' samples and a loss of these genes' functional similarity. Meanwhile, we discovered specific changes in co-expression patterns that may suggest the involvement of TAAR1 and D5 receptors in pathologic or compensatory processes in FD or diabetes accordingly. Despite our findings suggesting the possible role of TAAR1 and dopamine receptors in functional diseases of the upper intestine, underlying mechanisms need experimental exploration and validation.

GAPVD1 Promotes the Proliferation of Triple-Negative Breast Cancer Cells by Regulating the ERK/MAPK Signaling Pathway.

Triple-Negative Breast Cancer (TNBC) accounts for 15-20% of all breast cancers and approximately 50% of breast cancer deaths. Chemotherapy remains the mainstay of systemic treatment due to the lack of effective therapy targets. Thus, more studies are urgently needed to identify new therapeutic targets in TNBC patients. GAPVD1 expression and prognosis value in breast cancer samples were explored in The Cancer Genome Atlas database (TCGA). GAPVD1 knockdown and overexpression TNBC cell lines were constructed. CCK-8 and colony formation assays were performed to detect cell viability. Flow cytometry analysis was performed to detect cell cycle variation. Western blotting was conducted to determine the levels of target genes. Finally, an enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed. GAPVD1 is overexpressed in breast cancer tissues and predicts poor prognosis. In vitro experiments demonstrated that GAPVD1 is correlated with cell proliferation and the cell cycle of TNBC cells. Mechanistically, alteration in GAPVD1 expression was found to be associated with cell cycle-related proteins PCNA, Cyclin A, and the activity of the ERK/MAPK signaling pathway. Consistent with these findings, enrichment analysis of GAPVD1-involving partners and signaling pathways revealed that the cellular biosynthetic process, macromolecule biosynthetic process, and cell cycle signaling are related to GAPVD1. In vivo experiment demonstrated that GAPVD1 inhibition impedes tumor growth and expression of cell cyclerelated proteins. Taken together, our results indicate that GAPVD1 may participate in TNBC cell growth by regulating the cell cycle and ERK/MAPK signaling pathway.

Early changes of microRNAs in blood one month after bariatric surgery

BackgroundChanges in microRNAs (miRNAs) are relevant to bariatric surgery and its comorbidities. The characteristics of changes in miRNAs of the early postoperative period following both bariatric procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB), as well as the factors that related to the effectiveness of early weight loss remain unclear.MethodsWe recruited 18 patients who performed SG and 15 patients who performed RYGB. Their preoperative and 1-month postoperative clinical data and fasting serum samples were collected, and the latter were analyzed by RNA-sequencing. Differential expression analysis of miRNAs was performed by the R-tool. Functional classification annotation and pathway enrichment analysis of targeted genes were analyzed by KOBAS software. The change profiles of miRNAs for both surgeries and their correlation with clinical characteristics and weight loss effectiveness were further analyzed.ResultsA total of 85 differentially expressed miRNAs were identified before and after SG, while a total of 76 were found before and after RYGB. The target genes of these miRNAs were similar in the Gene Ontology enrichment analysis in SG and RYGB, and the enrichment analysis in the Kyoto Encyclopedia of Genes and Genomes was mainly related to metabolic pathways. Hsa-miR-493-5p, hsa-miR-184, and hsa-miR-3199 exhibited similar changes in SG and RYGB, and the former two were correlated with clinical characteristics. Hsa-miR-6729-5p, hsa-miR-4659b-5p, and hsa-miR-2277-5p were correlated with the weight loss effectiveness of SG, while hsa-miR-4662a-5p was correlated with the weight loss effectiveness of RYGB.ConclusionsShort-term metabolic improvement and weight loss occurring after SG and RYGB surgery might be related to changes in miRNAs, which act on multiple biological pathways by regulating genes. In addition, some clinical characteristics and miRNAs were related to the effectiveness of early weight loss after SG and RYGB surgery.Clinical Trial RegistrationChiCTR2200058333.

Proteins from shrews’ venom glands play a role in gland functioning and venom production

Venom production has evolved independently many times in the animal kingdom, although it is rare among mammals. Venomous shrews produce venom in their submandibular salivary glands and use it for food acquisition. Only a few toxins have been identified in shrew venoms thus far, and their modes of action require investigation. The biological and molecular processes relating to venom production and gland functioning also remain unknown. To address this gap, we investigated protein content in extracts from venom glands of two shrew species, Neomys fodiens and Sorex araneus, and interpreted their biological functions. Applying a proteomic approach coupled with Gene Ontology enrichment analysis, we identified 313 and 187 putative proteins in venom glands of N. fodiens and S. araneus, respectively. A search of the UniProt database revealed that most of the proteins found in both shrew species were involved in metabolic processes and stress response, while GO enrichment analysis revealed more stress-related proteins in the glands of S. araneus. Molecules that regulate molecule synthesis, cell cycles, and cell divisions are necessary to enable venom regeneration and ensure its effectiveness in predation and food hoarding. The presence of proteins involved in stress response may be the result of shrews’ high metabolic rate and the costs of venom replenishment. Some proteins are likely to promote toxin spreading during envenomation and, due to their proteolytic action, reinforce venom toxicity. Finally, finding numerous proteins involved in immune response suggests a potential role of shrew venom gland secretions in protection against pathogens. These findings open up new perspectives for studying biological functions of molecules from shrew venom glands and extend our knowledge on the functioning of eulipotyphlan venom systems. Because the majority of existing and putative venomous mammals use oral venom systems to inject venom into target species, the methods presented here provide a promising avenue for confirming or discovering new taxa of venomous mammals.

Network pharmacology- and molecular docking-based exploration of the molecular mechanism underlying Jianpi Yiwei Recipe treatment of gastric cancer.

Traditional Chinese medicine (TCM) is widely used as an important complementary and alternative healthcare system for cancer treatment in Asian countries. Network pharmacology, which utilizes various database platforms and computer software to study the interactions between complex drug components in vivo, is particularly useful for studying the pharmacodynamic mechanisms of multi-pathway and multi-target Chinese medicines. To explore the potential targets and function of Jianpi Yiwei Recipe treatment of gastric cancer (GC) through network pharmacology and molecular docking. Data on the components of Jianpi Yiwei Recipe (Radix Astragali, Radix Codonopsis, Agrimonia eupatoria, Atractylodes macrocephala Koidz., Poria cocos, stir-baked rhizoma dioscoreae, Amomum villosum Lour., fried Fructus Aurantii, pericarpium citri reticulatae, Rhizoma Pinelliae Preparata, and Radix Glycyrrhizae Preparata) were collected and screened by using the TCM systems pharmacology database and analysis platform (TCMSP). Then the targets of these compounds were predicted. GC-related targets were screened using the GeneCards database. Venn diagram was used to identify common targets. An active ingredient-core target interaction network and a protein-protein interaction (PPI) network were built. Moreover, we performed gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses on the core targets and validated them by molecular docking. TCMSP screening revealed 11 active components and 184 targets, whereas GeneCards found 10118 disease-related targets, with 180 shared targets between them. Topology analysis of the PPI network identified 38 targets, including ATK1, TP53, and tumor necrosis factor, as key targets for the treatment of GC by Jianpi Yiwei Recipe. Quercetin, naringenin, luteolin, etc., may be the main active components of Jianpi Yiwei Recipe. GO enrichment analysis identified 2809, 1218, and 553 functions related to biological process, molecular function, and cellular component, respectively. KEGG pathway enrichment analysis revealed 167 related pathways, mainly involved in cancer, endocrine resistance, and AGE-RAGE signaling in diabetic complication. Validation with molecular docking analysis showed docking of key active components with core targets. Jianpi Yiwei Recipe plays a therapeutic role in GC through multiple components, targets, and pathways. These findings form a basis for follow-up exploration of Jianpi Yiwei Recipe in the treatment of GC.

Adipocytes impact on gastric cancer progression: Prognostic insights and molecular features.

Adipocytes, especially adipocytes within tumor tissue known as cancer-associated adipocytes, have been increasingly recognized for their pivotal role in the tumor microenvironment of gastric cancer (GC). Their influence on tumor progression and patient prognosis has sparked significant interest in recent research. The main objectives of this study were to investigate adipocyte infiltration, assess its correlation with clinical pathological features, develop a prognostic prediction model based on independent prognostic factors, evaluate the impact of adipocytes on immune cell infiltration and tumor invasiveness in GC, and identify and validate genes associated with high adipocyte expression, exploring their potential diagnostic and prognostic value. To explore the relationship between increased adipocytes within tumor tissue and prognosis in GC patients as well as the associated mechanisms and potential biomarkers, using public databases and clinical data. Using mRNA microarray datasets from the Gene Expression Omnibus database and clinical samples from Jiangsu Provincial Hospital, survival and regression analyses were conducted to determine the relevant prognostic factors in GC. Feature gene selection was performed using least absolute shrinkage and selection operator and support vector machine recursive feature elimination algorithms, followed by differential gene expression analysis, gene ontology, pathway analysis, and Gene Set Enrichment Analysis. Immune cell infiltration was analyzed using the CIBERSORT algorithm. Tumor adipocyte infiltration correlated with poor prognosis in GC, leading to the development of a highly accurate and discriminative prognostic prediction model. Key genes, ADH1B, SFRP1, PLAC9, and FABP4, were identified as associated with high adipocyte expression in GC. The diagnostic and prognostic potential of these identified genes was validated using independent datasets. Downregulation of immune cells was observed in GC with high adipocyte expression. GC with high intratumoral adipocyte expression demonstrated aggressive tumor biology and a poorer prognosis. The genes ADH1B, SFRP1, PLAC9, and FABP4 have been identified as holding diagnostic and prognostic significance in GC. These findings strongly support the use of adipocyte expression as a valuable indicator of tumor invasiveness and anticipated patient outcomes in GC.

Network pharmacology and molecular dynamics study of the effect of the Astragalus-Coptis drug pair on diabetic kidney disease

BACKGROUND Diabetic kidney disease (DKD) is the primary cause of end-stage renal disease. The Astragalus -Coptis drug pair is frequently employed in the management of DKD. However, the precise molecular mechanism underlying its therapeutic effect remains elusive. AIM To investigate the synergistic effects of multiple active ingredients in the Astragalus-Coptis drug pair on DKD through multiple targets and pathways. METHODS The ingredients of the Astragalus -Coptis drug pair were collected and screened using the TCMSP database and the SwissADME platform. The targets were predicted using the SwissTargetPrediction database, while the DKD differential gene expression analysis was obtained from the Gene Expression Omnibus database. DKD targets were acquired from the GeneCards, Online Mendelian Inheritance in Man database, and DisGeNET databases, with common targets identified through the Venny platform. The protein-protein interaction network and the “disease-active ingredient-target” network of the common targets were constructed utilizing the STRING database and Cytoscape software, followed by the analysis of the interaction relationships and further screening of key targets and core active ingredients. Gene Ontology (GO) function and Kyoto Ency-clopedia of Genes and Genomes (KEGG) pathway enrichments were performed using the DAVID database. The tissue and organ distributions of key targets were evaluated. PyMOL and AutoDock software validate the molecular docking between the core ingredients and key targets. Finally, molecular dynamics (MD) simulations were conducted to simulate the optimal complex formed by interactions between core ingredients and key target proteins. RESULTS A total of 27 active ingredients and 512 potential targets of the Astragalus -Coptis drug pair were identified. There were 273 common targets between DKD and the Astragalus -Coptis drug pair. Through protein-protein interaction network topology analysis, we identified 9 core active ingredients and 10 key targets. GO and KEGG pathway enrichment analyses revealed that Astragalus -Coptis drug pair treatment for DKD involves various biological processes, including protein phosphorylation, negative regulation of apoptosis, inflammatory response, and endoplasmic reticulum unfolded protein response. These pathways are mainly associated with the advanced glycation end products (AGE)-receptor for AGE products signaling pathway in diabetic complications, as well as the Lipid and atherosclerosis. Molecular docking and MD simulations demonstrated high affinity and stability between the core active ingredients and key targets. Notably, the quercetin-AKT serine/threonine kinase 1 (AKT1) and quercetin-tumor necrosis factor (TNF) protein complexes exhibited exceptional stability. CONCLUSION This study demonstrated that DKD treatment with the Astragalus -Coptis drug pair involves multiple ingredients, targets, and signaling pathways. We propose a novel approach for investigating the molecular mechanism underlying the therapeutic effects of the Astragalus -Coptis drug pair on DKD. Furthermore, we suggest that quercetin is the most potent active ingredient and specifically targets AKT1 and TNF, providing a theoretical foundation for further exploration of pharmacologically active ingredients and elucidating their molecular mechanisms in DKD treatment.

Revealing the novel metabolism-related genes in the ossification of the ligamentum flavum based on whole transcriptomic data.

The ossification of the ligamentum flavum (OLF) is one of the major causes of thoracic myelopathy. Previous studies indicated there might be a potential link between metabolic disorder and pathogenesis of OLF. The aim of this study was to determine the potential role of metabolic disorder in the pathogenesis of OLF using the strict bioinformatic workflow for metabolism-related genes and experimental validation. A series of bioinformatic approaches based on metabolism-related genes were conducted to compare the metabolism score between OLF tissues and normal ligamentum flavum (LF) tissues using the single sample gene set enrichment analysis. The OLF-related and metabolism-related differentially expressed genes (OMDEGs) were screened out, and the biological functions of OMDEGs were explored, including the Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and protein-protein interaction. The competing endogenous RNA (ceRNA) network based on pairs of miRNA-hub OMDEGs was constructed. The correlation analysis was conducted to explore the potential relationship between metabolic disorder and immunity abnormality in OLF. In the end, the cell experiments were performed to validate the roles of GBE1 and TNF-α in the osteogenic differentiation of LF cells. There was a significant difference of metabolism score between OLF tissues and normal LF tissues. Forty-nine OMDEGs were screened out and their biological functions were determined. The ceRNA network containing three hub OMDEGs and five differentially expressed miRNAs (DEmiRNAs) was built. The correlation analysis between hub OMDEGs and OLF-related infiltrating immune cells indicated that metabolic disorder might contribute to the OLF via altering the local immune status of LF tissues. The cell experiments determined the important roles of GBE1 expression and TNF-α in the osteogenic differentiation of LF cells. This research, for the first time, preliminarily illustrated the vital role of metabolic disorder in the pathogenesis of OLF using strict bioinformatic algorithms and experimental validation for metabolism-related genes, which could provide new insights for investigating disease mechanism and screening effective therapeutic targets of OLF in the future.

Long-term exposure to dimefluthrin inhibits the growth of Acrossocheilus fasciatus

Dimefluthrin (DIM) is a synthetic pyrethroid insecticide commonly used for the control of pests, particularly for mosquitoes and other flying insects. However, the effects of DIM on non-target aquatic organisms are not known. In this study, we evaluated the long-term effects of DIM on juvenile Acrossocheilus fasciatus (a species of teleost fish) by exposing them to two different concentrations (0.8 μg/L and 4 μg/L) for 60 days. After 60 d of exposure, DIM induced a significant decrease in body weight and irregular, diffused villi in the intestines of A. fasciatus, accompanied by alterations in the expression of immune-related genes. Furthermore, Gene Ontology (GO) enrichment analysis revealed that among the differentially expressed genes (DEGs), all downregulated genes were enriched in processes such as small molecule/cellular amino acid metabolism, generation of precursor metabolites and energy, and phosphatase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the downregulated genes were associated with processes such as cytokine-cytokine receptor interaction, chemokine signaling pathway, JAK-STAT signaling pathway, intestinal immune network for IgA production, natural killer cell-mediated cytotoxicity, and antigen processing and presentation. In contrast, upregulated DEGs were linked to processes such as necroptosis, phototransduction, and Hippo signaling pathway. These results demonstrate the potential toxicity of DIM to non-target aquatic organisms, indicating the broader ecological implications of its use.