KEGG Signaling Pathways Research Articles

Application of Network Pharmacology to Explore the Anti-Aging Molecular Mechanism of Radix notoginseng

Objective: To study the anti-aging effects of Radix Notoginseng and to explore its molecular network mechanism. Methods: Aging and Radix notoginseng gene targets were searched and downloaded from the Genecards website, then Venn intersection analysis was performed to find common genes for diseases and drugs to explore candidate targets for Radix notoginseng in the treatment of aging. Bioinformatics was then used to analyze the biological processes, cellular components, molecular functions, and KEGG signaling pathways of the shared target network. Protein molecular network construction was carried out to find the core molecular network genes of the drug Radix notoginseng for the treatment of aging. A final PubMed literature comparison was performed to assess the value of the potential role of core network genes. Results: The keywords “Aging” and “Radix notoginseng” were queried in Genecards and 25,000 aging-related targets were obtained, 17 for Radix notoginseng. GO and KEGG analysis of the intersecting genes obtained from the Venn intersection analysis then showed that the BP with the highest potential to be associated with disease and drugs is positive regulation of protein phosphorylation, CC is macromolecular complex and MF is identical protein binding. The KEGG with the higher correlation is lipid and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, and proteoglycans in cancer. A total of 10 hub genes were identified in the PPI network construction, including EGFR, MMP9, TNF, VEGFA, RHOA, CDKN1A, CASP3, CCND1, AKT1, and IL1B. Among these, it found that a large number of MMP9 and TNF genes were reported in the literature, with the remaining hub genes less frequently reported in the literature. Conclusion: This study uses bioinformatics and network pharmacology to explain the core network mechanisms of the drug Radix notoginseng in the treatment of aging using the latest databases. The results show that hub genes such as CDKN1A, EGFR, and AKT1 are involved in the core biological processes of aging. The results of the study provide an important reference for resolving the core molecular network mechanism of anti-aging properties and provide a validation basis for future experimental validation.

Abstract 6217: Differential genome-wide gene regulatory networks for lung cancer

Abstract Background: Lung cancer remains the leading cause of cancer death worldwide due to the fact that most cases are diagnosed at distant stages, and treatment is less effective. During the past two decades, much effort has been devoted to understanding tumor biology and developing targeted therapeutics, which have significantly improved patient survival. With the increasingly available multi-omics data from healthy controls and lung cancer patients, we constructed gene regulatory networks for the two main subtypes of non-small-cell lung cancer (NSCLC), the most common type of lung cancer. In addition, differential networks were constructed by integrative analysis of data from lung cancer tissue and tissues from healthy lungs. Methods: Transcriptomics and genomic data were obtained from the patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissue available in The Cancer Genome Atlas (TCGA) project, and both types of omics data of normal lung tissue were downloaded from The Genotype-Tissue Expression (GTEx) consortium. The networks for each subtype and the differential networks were constructed by utilizing our newly developed machine learning tools, two-stage penalized least square (2SPLS) approach, and analysis of variance of directed networks (NetANOVA), respectively. Results: For the top three identified subnetworks of LUAD, we identified some well-known genes associated with lung cancer, such as EGFR, IRF1, KRAS, ERBB2, PIK3CA, MYC, at bootstrap frequency >90%. Based on the top three subnetworks with a bootstrap frequency of 100%, results from the Ingenuity Pathway Analysis (IPA) indicated several significant pathways, primary immunodeficiency signaling and communication between innate and adaptive immune cells. GO enrichment analysis showed statistically significant biological processes, including immune response, extracellular matrix organization, and significant KEGG pathways such as Hematopoietic cell lineage. The differential networks between LUAD, LUSC, and healthy lungs showed the same regulations across all three groups, such as the regulation between EEF2 and RACK1, the perturbations between LUAD and healthy (two-way regulations between HIGD2A and ARL10), and LUSC and healthy (GRB14 regulates EIF3E) respectively. In addition, we identified the differences between LUAD and LUSC, such as bi-directional regulations between CLTB and ARL10. Conclusion: Although all groups share most regulations, we identified differential gene regulations between healthy lung tissue and lung cancer tissue and between LUAD and LUSC of NSCLC. Using multi-omics data generated from lung tissues, coupled with advanced machine learning methods, the causal relationships between genome-wide genes from the analysis will help us understand the molecular mechanism of lung cancer and facilitate the development of personalized treatment strategies. Citation Format: Min Zhang, Zhongli Jiang, Dabao Zhang. Differential genome-wide gene regulatory networks for lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6217.

Blended-protein changes body weight gain and intestinal tissue morphology in rats by regulating arachidonic acid metabolism and secondary bile acid biosynthesis induced by gut microbiota.

The impact of dietary nutrients on body growth performance and the composition of gut microbes and metabolites is well-established. In this study, we aimed to determine whether dietary protein can regulate the physiological indexes and changes the intestinal tissue morphology in rats, and if dietary protein was a crucial regulatory factor for the composition, function, and metabolic pathways of the gut microbiota. A total of thirty male Sprague Dawley (SD) rats (inbred strain, weighted 110 ± 10g) were randomly assigned to receive diets containing animal-based protein (whey protein, WP), plant-based protein (soybean protein, SP), or a blended protein (soybean-whey proteins, S-WP) for a duration of 8weeks. To investigate the effects of various protein supplement sources on gut microbiota and metabolites, we performed a high throughput 16S rDNA sequencing association study and fecal metabolomics profiling on the SD rats. Additionally, we performed analyses of growth indexes, serum biochemical indexes, and intestinal morphology. The rats in S-WP and WP group exhibited a significantly higher body weight and digestibility of dietary protein compared to the SP group (P < 0.05). The serum total protein content of rats in the WP and S-WP groups was significantly higher (P < 0.05) than that in SP group, and the SP group exhibited significantly lower (P < 0.05) serum blood glucose levels compared to the other two groups. The morphological data showed the rats in the S-WP group exhibited significantly longer villus height and shallower crypt depth (P < 0.05) than the SP group. The gut microbial diversity of the SP and S-WP groups exhibited a higher level than that of the WP group, and the microbiomes of the WP and S-WP groups are more similar compared to those of the SP group. The Arachidonic acid metabolism pathway is the most significant KEGG pathway when comparing the WP group and the SP group, as well as when comparing the SP group and the S-WP group. The type of dietary proteins exerted a significant impact on the physiological indices of SD rats. Intake of S-WP diet can enhance energy provision, improve the body's digestion and absorption of nutrients, as well as promote intestinal tissue morphology. In addition, dietary protein plays a crucial role in modulating fecal metabolites by regulating the composition of the gut microbiota. Metabolomics analysis revealed that the changes in the levels of arachidonic acid metabolites and secondary bile acid metabolite induced by Clostridium_sensu_stricto_1 and [Eubacterium]_coprostanoligenes_group maybe the primarily causes of intestinal morphological differences.

Mechanism of Qingchang compound against coccidiosis based on network pharmacology-molecular docking.

The aim of this study was to investigate the anti-Eimeria tenella mechanism of Qingchang Compound (QCC) and provide a basis for its clinical application. The active ingredients, active ingredient-disease intersection targets, and possible pathways of QCC for the treatment of chicken coccidiosis were analyzed, the binding ability of pharmacodynamic components and target proteins was determined by network pharmacology and the molecular docking, and a model of infection with coccidiosis was constructed to verify and analyze the mechanism of action of QCC against coccidiosis. Among the 57 components that met the screening conditions, the main bioactive components were quercetin, dichroine, and artemisinin, with IL-1β, IL-6, IL-10, IFN-γ, and IL-8 as the core targets. Simultaneously, the KEGG signaling pathway of QCC anti-coccidiosis in chickens was enriched, including cytokine-cytokine receptor interactions. The results showed that the main pharmacodynamic components of QCC and the core targets could bind well; artemisinin and alpine possessed the largest negative binding energies and presented the most stable binding states. In addition, in vivo studies showed that QCC reduced blood stool in chickens with coccidiosis, restored cecal injury, and significantly reduced the mRNA and protein expression levels of IL-1β, IL-10, and IFN-γ in ceca (p < 0.01). Our results suggest that the main active ingredients of QCC are artemisinin and alpine and its mechanism of action against coccidiosis may be related to the reduction of the inflammatory response by acting on specific cytokines.

Molecular mechanism of resveratrol promoting differentiation of preosteoblastic MC3T3-E1 cells based on network pharmacology and experimental validation

The purpose of this study was to investigate the mechanism by which resveratrol (Res) inhibits apoptosis and promotes proliferation and differentiation of pre-osteoblastic MC3T3-E1 cells, laying the groundwork for the treatment of osteoporosis (OP). The TCMSP database was used to find the gene targets for Res. The GeneCards database acquire the gene targets for OP. After discovering the potential target genes, GO, KEGG, and Reactome enrichment analysis were conducted. Verifying the major proteins involved in apoptosis can bind to Res using molecular docking. CCK8 measured the proliferative activity of mouse pre-osteoblasts in every group following Res intervention. Alkaline phosphatase staining (ALP) and alizarin red staining to measure the ability of osteogenic differentiation. RT-qPCR to determine the expression levels of Runx2 and OPG genes for osteogenic differentiation ability of cells. Western blot to measure the degree of apoptosis-related protein activity in each group following Res intervention. The biological processes investigated for GO of Res therapeutic OP involved in cytokine-mediated signaling pathway, negative regulation of apoptotic process, Aging, extrinsic apoptotic signaling pathway in absence of ligand, according to potential therapeutic target enrichment study. Apoptosis, FoxO signaling pathway, and TNF signaling pathway are the primary KEGG signaling pathways. Recactome pathways are primarily engaged in Programmed Cell Death, Apoptosis, Intrinsic Apoptotic Pathway, and Caspase activation via extrinsic apoptotic signaling pathways. This research established a new approach for Res treatment of OP by demonstrating how Res controls the apoptosis-related proteins TNF, IL6, and CASP3 to suppress osteoblast death and increase osteoclastogenesis.

Discussion on the mechanism of Danggui Sini decoction in treating diabetic foot based on network pharmacology and molecular docking and verification of the curative effect by meta-analysis.

The main active components and mechanism of Danggui Sini decoction (DSD) in treating diabetic foot (DF) were studied and verified by network pharmacology and molecular docking. Evidence-based medicine was used to prove its efficacy. The TCMSP systematic pharmacology platform screened out DSD's practical components and targets-screening disease targets in GeneCards database, using Cytoscape 3.7.2 to draw DSD-active ingredient-target network diagram, and drawing the protein interaction network diagram through STRING database. The Metascape platform was used to analyze the GO function enrichment and KEGG signal pathway. The molecular docking experiment was carried out by using Auto Dock vina 4.2. The related literature on DSD in treating DF in China Zhiwang, Wanfang, Weipu, and China Biomedical Literature Database was searched. The literature was screened, data was extracted, and quality was evaluated according to the inclusion and exclusion criteria. Then, a meta-analysis was performed using RevMan 5.3 software. A total of 256 targets of all effective components of DSD were obtained. Among 1,272 disease targets, there are 113 common targets. The GO analysis received 6,179 entries, and the KEGG pathway enrichment analysis found 251 related pathways. The molecular docking results of the main targets of diabetic foot and the active substances of DSD all showed a high docking activity. The meta-analysis included six literature, all of which were randomized controlled experiments. The quality grade of the literature was C, and the results showed that the total effective rate of clinical efficacy in the experimental group was significantly higher than that in the control group. DSD may treat DF by participating in biological processes such as cell proliferation regulation, inflammatory reaction, oxidative stress reaction, and promotion of angiogenesis. DSD treats DF through AKT1, TP53, IL6, TNF, VEGFA, and other targets. DSD plays a role in treating DF mainly through the AGE-RAGE signaling pathway and PI3K-AKT signaling pathway. The molecular docking results of AKT1, TP53, IL-6, TNF, and VEGFA with the active substances of DSD show that they all have a high docking activity; among them, VEGFA has a higher docking activity. Compared with conventional treatment, DSD has a high effective rate, short wound healing time, large wound healing area, and high ABI index.

Differential gene expression patterns in ST-elevation Myocardial Infarction and Non-ST-elevation Myocardial Infarction

The ST-elevation Myocardial Infarction (STEMI) and Non-ST-elevation Myocardial Infarction (NSTEMI) might occur because of coronary artery stenosis. The gene biomarkers apply to the clinical diagnosis and therapeutic decisions in Myocardial Infarction. The aim of this study was to introduce, enrich and estimate timely the blood gene profiles based on the high-throughput data for the molecular distinction of STEMI and NSTEMI. The text mining data (50 genes) annotated with DisGeNET data (144 genes) were merged with the GEO gene expression data (5 datasets) using R software. Then, the STEMI and NSTEMI networks were primarily created using the STRING server, and improved using the Cytoscape software. The high-score genes were enriched using the KEGG signaling pathways and Gene Ontology (GO). Furthermore, the genes were categorized to determine the NSTEMI and STEMI gene profiles. The time cut-off points were identified statistically by monitoring the gene profiles up to 30 days after Myocardial Infarction (MI). The gene heatmaps were clearly created for the STEMI (high-fold genes 69, low-fold genes 45) and NSTEMI (high-fold genes 68, low-fold genes 36). The STEMI and NSTEMI networks suggested the high-score gene profiles. Furthermore, the gene enrichment suggested the different biological conditions for STEMI and NSTEMI. The time cut-off points for the NSTEMI (4 genes) and STEMI (13 genes) gene profiles were established up to three days after Myocardial Infarction. The study showed the different pathophysiologic conditions for STEMI and NSTEMI. Furthermore, the high-score gene profiles are suggested to measure up to 3 days after MI to distinguish the STEMI and NSTEMI.

The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery

BackgroundRetinitis pigmentosa is the prevailing genetic cause of blindness in developed nations with no effective treatments. In the pursuit of unraveling the intricate dynamics underlying this complex disease, mechanistic models emerge as a tool of proven efficiency rooted in systems biology, to elucidate the interplay between RP genes and their mechanisms. The integration of mechanistic models and drug-target interactions under the umbrella of machine learning methodologies provides a multifaceted approach that can boost the discovery of novel therapeutic targets, facilitating further drug repurposing in RP.MethodsBy mapping Retinitis Pigmentosa-related genes (obtained from Orphanet, OMIM and HPO databases) onto KEGG signaling pathways, a collection of signaling functional circuits encompassing Retinitis Pigmentosa molecular mechanisms was defined. Next, a mechanistic model of the so-defined disease map, where the effects of interventions can be simulated, was built. Then, an explainable multi-output random forest regressor was trained using normal tissue transcriptomic data to learn causal connections between targets of approved drugs from DrugBank and the functional circuits of the mechanistic disease map. Selected target genes involvement were validated on rd10 mice, a murine model of Retinitis Pigmentosa.ResultsA mechanistic functional map of Retinitis Pigmentosa was constructed resulting in 226 functional circuits belonging to 40 KEGG signaling pathways. The method predicted 109 targets of approved drugs in use with a potential effect over circuits corresponding to nine hallmarks identified. Five of those targets were selected and experimentally validated in rd10 mice: Gabre, Gabra1 (GABARα1 protein), Slc12a5 (KCC2 protein), Grin1 (NR1 protein) and Glr2a. As a result, we provide a resource to evaluate the potential impact of drug target genes in Retinitis Pigmentosa.ConclusionsThe possibility of building actionable disease models in combination with machine learning algorithms to learn causal drug-disease interactions opens new avenues for boosting drug discovery. Such mechanistically-based hypotheses can guide and accelerate the experimental validations prioritizing drug target candidates. In this work, a mechanistic model describing the functional disease map of Retinitis Pigmentosa was developed, identifying five promising therapeutic candidates targeted by approved drug. Further experimental validation will demonstrate the efficiency of this approach for a systematic application to other rare diseases.

DIA proteomics analysis reveals the mechanism of folic acid-induced acute kidney injury and the effects of icariin

The complexities of acute kidney injury (AKI), a multifaceted pathological occurrence, are not fully understood. At present, there is a lack of effective pharmaceutical treatments in clinical practice. Studies have shown that icariin has beneficial effects in models of acute kidney injury (AKI) caused by cisplatin and lipopolysaccharide (LPS). The aim is to explore the mechanisms that cause folic acid (FA)-induced AKI and examine the protective effects of icariin against this condition. To establish a mouse model of AKI, FA was administered via intraperitoneal injection. Icariin was used as the drug intervention. The model and the impact of drug intervention were assessed using measurements of renal function parameters, staining with hematoxylin and eosin, and Q-PCR. The analysis of protein expression changes in the control, model, and icariin treatment groups was conducted using proteomics. KEGG signaling pathway analysis indicates that differential expressed proteins are enriched in the component and coagulation cascades signaling pathway. Through protein-protein interaction network analysis, it was found that compared to the normal group, the expression of Fibrinogen and other proteins was significantly upregulated at the center of the protein interaction network in the model group. After drug treatment, the expression of these proteins was significantly downregulated. The validation experiment supports the above results. In conclusion, this study clarified the molecular mechanism of FA induced acute renal injury from the proteomics level, and provided target selection for AKI; At the same time, the mechanism of icariin in the treatment of AKI was analyzed from the proteomics level.

Identification of Differentially Expressed mRNAs and miRNAs and Related Regulatory Networks in Cumulus Oophorus Complexes Associated with Fertilization.

Cumulus oophorus complexes (COCs) are the first extracellular barriers that sperm must pass through to fuse with oocytes, which have an important role in oocyte maturation and fertilization. However, little is known about the molecular mechanisms of COCs involved in fertilization. In this study, COCs were collected and then randomly divided into a test group that interacted with sperm and a control group that did not interact with sperm. Then, the total RNA was extracted; RNA transcriptome and small RNA libraries were prepared, sequenced, and analyzed. The results showed that 1283 differentially expressed genes (DEGs), including 560 upregulated and 723 downregulated genes. In addition, 57 differentially expressed miRNAs (DEMIs) with 35 upregulated and 22 downregulated were also detected. After the RNA-seq results were verified by RT-qPCR, 86 effective DEGs and 40 DEMIs were finally screened and a DEMI-DEG regulatory network was constructed. From this, the top ten hub target genes were HNF4A, SPN, WSCD1, TMEM239, SLC2A4, E2F2, SIAH3, ADORA3, PIK3R2, and GDNF, and they were all downregulated. The top ten hub DEMIs were miR-6876-5p, miR-877-3p, miR-6818-5p, miR-4690-3p, miR-6789-3p, miR-6837-5p, miR-6861-5p, miR-4421, miR-6501-5p, and miR-6875-3p, all of which were upregulated. The KEGG signaling pathway enrichment analysis showed that the effective DEGs were significantly enriched in the calcium, AMPK, and phospholipase D signaling pathways. Our study identified several DEGs and DEMIs and potential miRNA-mRNA regulatory pathways in COCs and these may contribute to fertilization. This study may provide novel insights into potential biomarkers for fertilization failure.

Study on the Anti-Periodontitis Mechanism of Eucommia ulmoides Based on Network Pharmacology

Periodontitis is a chronic inflammation of periodontal support tissue caused by local factors. Eucommia ulmoides, a traditional Chinese medicinal herb, has a significant therapeutic effect on periodontitis, but its mechanism of action is still unclear. In this study network pharmacology method was used to deeply elucidate the pharmacological substance basis and mechanism of Eucommia ulmoides in treating periodontitis. The protein interaction network (PPI) was constructed using the STRING database. The GO and KEGG signal pathway enrichment analyses of the intersected targets were performed using the DAVID database to predict the mechanism of action. The results indicate that Eucommia ulmoides exerted its therapeutic effect on periodontitis through a synergistic mechanism of multiple components, targets, and pathways. The top 8 therapeutic targets were identified, including EGFR, HIF1A, MMP9, ESR1, JUN, PPARG, AKT1, and SRC. Prolactin and HIF-1 signaling pathway may be the key mechanism of Eucommia ulmoides in treating periodontitis.

Decreased expression of LncRNA CRYM-AS1 promotes apoptosis through the Hippo-YAP1 signaling pathway leading to diabetic erectile dysfunction.

Long non-coding RNAs (lncRNAs) primarily engage with mRNA, DNA, proteins, and microRNAs (miRNAs), thereby regulating gene expression; however, its specific role in diabetic erectile dysfunction (DED) has not been studied. This study aims to investigate the effects and mechanisms of LncRNA CRYM-AS1 in DED. The differential target gene LncRNA CRYM-AS1 was identified in the penile tissues of rats with DED through bioinformatics analyses. A KEGG signaling pathway enrichment analysis suggested a potential association between LncRNA CRYM-AS1 and the Hippo-YAP1 pathway. Real-time fluorescent quantitative PCR (RT-qPCR) results indicated a significantly lower expression of LncRNA CRYM-AS1 in the penile tissue of DED rats compared to the control group. Western Blot and immunohistochemistry (IHC) staining results demonstrated significantly elevated protein expression levels of YAP1, Caspase3, BAX, and Bcl-2, with a decreased Bcl-2/BAX ratio. CCK8 cell viability results showed a significant decrease in cell viability in the high glucose group at 4 days of modeling, and compared with the normal glucose group, RT-qPCR results showed that the expression of LncRNA CRYM-AS1 in the high glucose group in human umbilical vein endothelial cells (HUVECs) was significantly reduced; Western Blot results showed that the protein expression of YAP1, Cleaved-caspase3 and BAX was significantly up-regulated, and the protein expression of Bcl-2 was significantly down-regulated in the high glucose group. Compared with the empty vector group, RT-qPCR results after transfection of siLncRNA CRYM-AS1 showed that the expression of LncRNA CRYM-AS1 was down-regulated, the mRNA and protein expression of YAP1, Caspase3, Cleaved-caspase3, BAX, and Bcl-2 were significantly up-regulated, and the Bcl-2/BAX ratio decreased. Flow cytometry results showed that the apoptosis rate of HUVECs increased after interference. Low expression of LncRNA CRYM-AS1 may activate the Hippo-YAP1 signaling pathway to regulate apoptosis in HUVECs, leading to ED development, and the discovery of new target genes may provide new therapeutic targets to regulate diabetic erectile disfunction.

Expression of interleukin-34 in tongue squamous cell carcinoma and its clinical implications

To investigate the expression of interleukin- 34 (IL-34) in tongue squamous cell carcinoma (TSCC) and its clinical implications. Serum IL-34 level was detected in 36 patients with TSCC and 36 healthy individuals using enzymelinked immunosorbent assay (ELISA). The expressions of IL-34 mRNA and protein levels in TSCC and adjacent tissues were examined in 41 patients using real-time fluorescence quantitative PCR (qRT-PCR) and immunohistochemistry (IHC), and their correlation with the clinicopathological features of the patients was further analyzed. Informatic analysis of the differentially expressed genes related with IL-34 in TSCC was carried out based on String database, LinkedOmics database and GEO database, and GO functional analysis and KEGG signaling pathway enrichment analysis were performed using Webgestalt database. The serum level of IL-34 was significantly lower in TSCC patients than in the healthy individuals (P < 0.001), and its expression level was also significantly lower in the tumor tissues than in the adjacent tissues (P < 0.001). The expression level of IL-34 in TSCC tissues was related with lymph node metastasis and TNM staging (P < 0.05), but not with age, gender, smoking, drinking, or tumor size (P > 0.05). Informatic analysis suggested that IL-34 had the strongest correlation with CSF1R and PTPRJ. IL-34 and its related genes in TSCC were enriched mainly in bone marrow cell differentiation, collagen-containing extracellular matrix, and cytokine binding and signal receptor activator activity. KEGG signaling pathway enrichment showed that IL-34 and the related differentially expressed genes were involved mainly in osteoclast differentiation, protein polysaccharide in cancer, and the MAPK signaling pathway. IL-34 is lowly expressed in TSCC and participates in the occurrence and progression of TSCC, and can be potentially used as a new diagnostic biomarker and therapeutic target for TSCC.

Combining Network Pharmacology, Molecular Docking and Preliminary Experiments to Explore the Mechanism of Action of FZKA Formula on Non-small Cell Lung Cancer.

Clinically, Fuzhengkangai formulation (FZKA) has been proven to have significant therapeutic effects on non-small lung cancer (NSCLC), although the mechanism is unknown. We aimed to explore the potential mechanism of FZKA in the treatment of NSCLC in this study. We obtained the active components and targets of FZKA by TCMSP. The target genes of NSCLC were searched from OMIM, GEO (GSE18842), and GeneCards database. Cytoscape (3.7.2) software was used to construct a "drug-compound-cross-target interaction" interaction network, and the STING database was used to analyze previous cross-target interactions. Meanwhile, the results were visualized and processed by performing GO enrichment analysis and KEGG signaling pathway enrichment analysis at the target site. The core targets were docked with active components through AutoDockTools-1.5.6 software. Finally, we used cellular experiments to validate the bioinformatics predictions. There were 40 active and 465 potential genes from the TCMSP database. Key active chemicals, namely Quercetin, Kaempferol, Luteolin, and Tanshinone IIA, and 176 targets were deemed as targets of FZKA against NSCLC by PPI network analysis. GO and KEGG enrichment analyses suggest that FZKA acts primarily through the PI3K-AKT and MAPK signaling pathways in the treatment of NSCLC. Moreover, cellular assays showed that Quercetin, Kaempferol, Luteolin, and Tanshinone IIA not only reduced the viability of A549 cells and promoted apoptosis but also significantly decreased the p-AKT/AKT and p-ERK1/2/ERK1/2 ratios. Our data suggested that FZKA can be involved in the treatment of NSCLC through multiple components, targets and pathways.

Effects of Xiaoyao San on exercise capacity and liver mitochondrial metabolomics in rat depression model

ObjectiveThis study aimed to investigate the therapeutic effects of Xiaoyao San (XYS), a herbal medicine formula, on exercise capacity and liver mitochondrial metabolomics in a rat model of depression induced by chronic unpredictable mild stress (CUMS). MethodsA total of 24 male SD rats were randomly divided into four groups: control group (C), CUMS control group (M), Venlafaxine positive treatment group (V), and XYS treatment group (X). Depressive behaviour and exercise capacity of rats were assessed by body weight, sugar-water preference test, open field test, pole test, and rotarod test. The liver mitochondria metabolomics were analyzed by using liquid chromatography-mass spectrometry (LC-MS) method. TCMSP database and GeneCards database were used to screen XYS for potential targets for depression, and GO and KEGG enrichment analyses were performed. ResultsCompared with C group, rats in M group showed significantly lower body weight, sugar water preference rate, number of crossing and rearing in the open field test, climbing down time in the pole test, and retention time on the rotarod test (P < 0.01). The above behaviors and exercise capacity indices were significantly modulated in rats in V and X groups compared with M group (P < 0.05, 0.01). Compared with C group, a total of 18 different metabolites were changed in the liver mitochondria of rats in M group. Nine different metabolites and six metabolic pathways were regulated in the liver mitochondria of rats in X group compared with M group. The results of network pharmacology showed that 88 intersecting targets for depression and XYS were obtained, among which 15 key targets such as IL-1β, IL-6, and TNF were predicted to be the main differential targets for the treatment of depression. Additionally, a total of 1 553 GO signaling pathways and 181 KEGG signaling pathways were identified, and the main biological pathways were AGE-RAGE signaling pathway, HIF-1 signaling pathway, and calcium signaling pathway. ConclusionXYS treatment could improve depressive symptoms, enhance exercise capacity, positively regulate the changes of mitochondrial metabolites and improve energy metabolism in the liver of depressed rats. These findings suggest that XYS exerts antidepressant effects through multi-target and multi-pathway.

Extensive CXCR4-MAPK Signaling Activation in the Novel B Cell Acute Lymphoblastic Subtype of CDX2/Ubtf

Background B-cell acute lymphoblastic leukemia (B-ALL) is a genetically heterogeneous group of acute leukemia with novel subtypes emerging. Since we first reported a novel subgroup B-ALL with half cases possessing CXCR4 truncated mutations and abnormal expression of CDX2 in all cases, the genomic features were further elucidated by different research groups that concurrent focal deletions lead to both upstream enhancer hijacking by CDX2 and UBTF::ATXN7L3 fusion transcript. But the molecular characterization and underlying mechanism beyond the novel subtype B-ALL remain ambiguous. Methods In order to comprehensively elucidate the molecular features, we adopt whole genome sequencing to reveal the genomic abnormalities, including snv, indel, copy number variant, and structural variation. Then, the signaling transduction and functional effect of differentially expressed genes were conducted by transcriptome analysis. Furthermore, we constructed a weighted gene co-expression network (WGCNA) and transcriptional regulons network to unravel the hub genes or transcriptional factors in the subtype. Results We retrospectively identify 2.4% (n=12) cases belonging to a novel subtype among 503 B-ALL cases with available transcriptome data by unsupervised clustering, and this subtype is characterized by CXCR4 truncated mutations or high expression of FLNA which could enhance CXCR4 signaling. Among these patients, only one male was affected showing a strong sex tendency towards females. Uniformly, all cases harbor both focal deletions encompassing between PAN3 and FLT3 located upstream of CDX2, and between UBTF and ATXN7L3, unraveled by whole genome sequencing (n=10). The focal deletions lead to overexpression of CDX2 by enhancer hijacking of upstream PAN3 and fusion transcript UBTF::ATXN7L3, respectively. In addition, 80% (n=8) cases also occurred with 1q+ which is regarded as a factor contributing to poor prognosis in leukemia and lymphoma. Transcriptomic analysis of the differentially expressed genes (DEGs) for this subtype confirmed the critical role of oncogenic MAPK signaling. Enhanced MAPK signaling was further supported by the function of the hub genes including KIAA1549 and KIAA1549L, which belong to oncogenic MAPK signaling, derived from WGCNA analysis. According to the functional enrichment analysis of DEGs, axon guidance was the only significant enriched KEGG pathway. The hub genes NTN3 from WGCNA analysis and regulon CDX2 both confirmed the functional involvement of axon guidance in this subtype. Furthermore, we prospectively identify 8 more cases by RT-PCR screening of the UBTF::ATXN7L3 transcript. Totally, twenty patients have been found in our cohort, and interestingly, there exist two cases among this subtype accumulated with multiple subclones characterized by different CXCR4 mutations, which strengthen the genotoxic stress over CXCR4 signaling. Discussion Although genomic characterization of this novel subtype has been revealed by our and others' research. The functional effect and underlying mechanism have never been elucidated. Here, we emphasize that enhanced CXCR4 signaling in this subtype may act as an upstream driver event, and it could be supplied as a therapeutic target.

The mechanism of action of limonoids of Citri Reticulatae Semen against MCF-7 breast cancer cells

Limonoids (LMD), particularly limonin, possess significant anti-breast cancer (BC) potential. However, their precise anti- breast cancer mechanisms remain unelucidated. In this study, we aimed to identify potential biomarkers associated with BC development and metastasis and to investigate LMD anti-BC activity. Key LMD components were analyzed using UPLC-QQQ-MS/MS, with various bioinformatics tools utilized for additional analysis. These included ADME and toxicity prediction, Weighted Gene Co-expression Network Analysis (WGCNA), and construction of protein-protein interaction (PPI) and “LMD-Hub-gene-BC” models. A total of 1898 DEGs were obtained including 622 up-regulated and 1276 down-regulated genes. The WGCNA identified 4 significant modules. The 11 hub genes were identified by NTA. The results of enrichment analysis showed that 631 significant GO conditions and 34 significant KEGG pathways were enriched, of which cell cycle, p53 signaling pathway and Prostate cancer might be the main regulatory pathways for its anti-BC. The gene expression and immunohistochemistry of the result suggests that most of the hub genes expression has significant differences (P < 0.05). KM-plotter results revealed that most of the hub genes were associated with prognosis and clinical progression of BC (P < 0.05). The molecular docking suggests that the active ingredients have a high affinity with hub gene. The proliferation results suggest that limonin inhibits MCF-7 cells in a dose- and time-dependent manner. The results suggest that limonin may induce cell cycle arrest in the G2-M phase, allowing apoptosis to occur. Immunofluorescence and western blot results indicate that it exerts anti-tumour effects by down-regulating the expression of these proteins. This study identified potential biomarkers of LMD against BC. Notably, LMD can exert anti-tumour effects by inhibiting the proliferation of MCF-7 cells, down-regulating the expression levels of CCNB1 and AHURKA proteins, inducing cell cycle arrest in the G2-M phase, leading to apoptosis, and regulating the p53 signaling pathway. It is expected to provide certain guiding significance for the further exploration of potential markers and molecular regulation mechanisms for the diagnosis and prognosis of BC patients with LMD.

Thyroid Transcriptomics Revealed the Reproductive Regulation of miRNA in the Follicular and Luteal Phases in Small-Tail Han Sheep with Different FecB Genotypes.

MicroRNA (miRNA) is a type of endogenous short-stranded ncRNA that influences many biological processes such as animal growth, development and metabolism. The thyroid gland is an important endocrine gland in sheep, and an increasing number of studies have shown that the thyroid gland plays an important role in animal reproduction, but the molecular mechanisms of the thyroid gland in sheep reproduction are poorly understood. In this study, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between the follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) small-tail Han (STH) sheep, respectively, and to identify differentially expressed miRNAs (DEMs) associated with reproduction. Bioinformatic analysis of the target genes of these DEMs revealed that they can be enriched in multiple GO terms associated with the reproductive process in animals and in the KEGG signaling pathway. The miRNA-mRNA coexpression network revealed that oar-miR-133 and oar-miR-370-3p may play an important role in sheep reproduction. The results of the dual-luciferase reporter assay suggest a possible targeting relationship between novel-51 and TARBP2. These results provided a novel resource for elucidating regulatory mechanisms underlying STH sheep prolificacy.

Effect and molecular mechanism of Sulforaphane alleviates brain damage caused by acute carbon monoxide poisoning:Network pharmacology analysis, molecular docking, and experimental evidence.

Sulforaphane (SFN) has attracted much attention due to its ability on antioxidant, anti-inflammatory, and anti-apoptotic properties, while its functional targets and underlying mechanism of action on brain injury caused by acute carbon monoxide poisoning (ACOP) have not been fully elucidated. Herein, we used a systematic network pharmacology approach to explore the mechanism of SFN in the treatment of brain damage after ACOP. In this study, the results of network pharmacology demonstrated that there were a total of 81 effective target genes of SFN and 36 drug-disease targets, which were strongly in connection with autophagy-animal signaling pathway, drug metabolism, and transcription disorders in cancer. Upon the further biological function and KEGG signaling pathway enrichment analysis, a large number of them were involved in neuronal death, reactive oxygen metabolic processes and immune functions. Moreover, based on the results of bioinformatics prediction associated with multiple potential targets and pathways, the AMP-activated protein kinase (AMPK) signaling pathway was selected to elucidate the molecular mechanism of SFN in the treatment of brain injury caused by ACOP. The following molecular docking analysis also confirmed that SFN can bind to AMPKα well through chemical bonds. In addition, an animal model of ACOP was established by exposure to carbon monoxide in a hyperbaric oxygen chamber to verify the predicted results of network pharmacology. We found that the mitochondrial ultrastructure of neurons in rats with ACOP was seriously damaged, and apoptotic cells increased significantly. The histopathological changes were obviously alleviated, apoptosis of cortical neurons was inhibited, and the number of Nissl bodies was increased in the SFN group as compared with the ACOP group (p < .05). Besides, the administration of SFN could increase the expressions of phosphorylated P-AMPK and MFN2 proteins and decrease the levels of DRP1, Caspase3, and Casapase9 proteins in the brain tissue of ACOP rats. These findings suggest that network pharmacology is a useful tool for traditional Chinese medicine (TCM) research, SFN can effectively inhibit apoptosis, protect cortical neurons from the toxicity of carbon monoxide through activating the AMPK pathway and may become a potential therapeutic strategy for brain injury after ACOP.

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep.

Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.