GO Functional Analysis Research Articles

Mechanism of Olibanum-Myrrha in treatment of rheumatoid arthritis based on network pharmacology and molecular docking

In this paper, network pharmacology method and molecular docking technique were used to investigate the target genes of Olibanum and Myrrha compatibility and the possible mechanism of action in the treatment of rheumatoid arthritis(RA). Our team obtained the main active components of Olibanum-Myrrha based on literatures study, relevant traditional Chinese medicine systematic pharmacological databases and literature retrieval, and made target prediction of the active components through SwissTargetPrediction database. At the same time, RA-related targets were collected through DrugBank, GeneCards and Therapeutic Target Database(TDD) databases; and VENNY 2.1 was use to collect intersection targets to map common targets of drug and disease of Venn diagram online. The team used STRING database to construct PPI protein interaction network diagram, and screen out core targets according to the size of the interaction, and Cytoscape 3.6.0 software was used to construct network models of "traditional Chinese medicine-component-target" "traditional Chinese medicine-component-target-disease" and core target interaction network model. The intersection target was analyzed by using DAVID 6.8 online database for GO function analysis and KEGG pathway enrichment analysis, and Pathon was used to visualization. AutoDock Vina and Pymol were used to connect the core active components with the core targets. Sixteen active components of Olibanum-Myrrha pairs were found and collected in the laboratory, and 320 relevant potential targets, 468 RA-related targets and 62 intersection targets were obtained through the Venn diagram. It mainly acted on multiple targets, such as IL6, TNF, IL1 B and MAPK1, involving TNF signaling pathway and Toll-like receptor signaling pathway in RA treatment. Finally, in this study, possible targets and signaling pathways of Olibanum-Myrrha compatibility therapy for RA were discussed, and molecular docking between core targets and core active components was conducted, which could provide scientific basis for the study on the mechanism of Olibanum-Myrrha compatibility.

Evaluation of 3,4,4,9-trichlorocarbanilide to zebrafish developmental toxicity based on transcriptomics analysis

Triclocarban (TCC), considered an endocrine-disrupting, persistent, and bioaccumulating organic matter, has attracted a great deal of attention for its pollution and health risks. However, studies on its toxicological mechanism, especially for embryo development are limited. This article explores the cardiac developmental toxicity induced in zebrafish embryos after exposure to different TCC concentrations. First, liquid chromatography-tandem mass spectrometry was used in detecting TCC in embryos in vivo after exposure to various TCC. Results showed that embryonic TCC content reached 9.23 ng after exposure to 300 μg/L TCC, the heart rates of the embryos markedly decreased, heart abnormalities significantly increased. In addition, obvious pericardial effusion was observed in the larvae. Through transcriptome sequencing, 200 differential gene expression (DGE) patterns were detected in the TCC (300 μg/L) experimental and control groups. The results of GO function analysis and KEGG pathway of DGE showed that aryl hydrocarbon receptor (AhR) activation and cyp-related genes (cyp1a, cyp1b1 and cyp1c) were significantly up-regulated. these affected the normal development of zebrafish embryonic heart, tissue edema, and hemorrhage. TCC exhibited strong cardiac teratogenic effects and developmental toxicity, which is partly related to AhR activation. Transcriptome-based results are helpful in precisely determining the risk of TCC exposure. The potential mechanism between TCC and AhR should be further investigated.

Toxic effects of metal copper stress on immunity, metabolism and pathologic changes in Chinese mitten crab (Eriocheir japonica sinensis).

Copper (Cu2+), which represents a major physiological challenge for crab culture, is ubiquitous in the aquatic culture environment, and gills are the first organs that come into direct contact with the environment. However, the molecular basis of the response of crabs to Cu2+ stress remains unclear. Here, we conducted a transcriptome and differential expression analysis on the gills from Chinese mitten crab unexposed and exposed to Cu2+ for 24 h. The comparative transcriptome analysis identified 2486 differentially expressed genes (DEGs). GO functional analysis and KEGG pathway analysis revealed some DEGs, which were mostly related to immunity, metabolism, osmotic regulation, Cu2+ homeostasis regulation, antioxidant activity, and detoxification process. Some pathways related to humoral and cellular immunity, such as phagosome, peroxisome, lysosome, mTOR signaling pathway, PI3K-Akt signaling pathway, Toll-like receptor signaling pathway, and T cell receptor signaling pathway were enhanced under Cu2+ stress. In addition, Cu2+ stress altered the expression patterns of key phagocytosis and apoptosis genes (lectin, cathepsin L, Rab7, and HSP70), confirming that Cu2+ can induce oxidative stress and eventually even apoptosis. Histological analysis revealed that the copper can induce damage at the cellular level. This comparative transcriptome analysis provides valuable molecular information to aid future study of the immune mechanism of Chinese mitten crab in response to Cu2+ stress and provides a foundation for further understanding of the effects of metal toxicity.

Five candidate biomarkers associated with the diagnosis and prognosis of cervical cancer.

Purpose: Cervical cancer (CC) is one of the most general gynecological malignancies and is associated with high morbidity and mortality. We aimed to select candidate genes related to the diagnosis and prognosis of CC.Methods: The mRNA expression profile datasets were downloaded. We also downloaded RNA-sequencing gene expression data and related clinical materials from TCGA, which included 307 CC samples and 3 normal samples. Differentially expressed genes (DEGs) were obtained by R software. GO function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed in the DAVID dataset. Using machine learning, the optimal diagnostic mRNA biomarkers for CC were identified. We used qRT-PCR and Human Protein Atlas (HPA) database to exhibit the differences in gene and protein levels of candidate genes.Results: A total of 313 DEGs were screened from the microarray expression profile datasets. DNA methyltransferase 1 (DNMT1), Chromatin Assembly Factor 1, subunit B (CHAF1B), Chromatin Assembly Factor 1, subunit A (CHAF1A), MCM2, CDKN2A were identified as optimal diagnostic mRNA biomarkers for CC. Additionally, the GEPIA database showed that the DNMT1, CHAF1B, CHAF1A, MCM2 and CDKN2A were associated with the poor survival of CC patients. HPA database and qRT-PCR confirmed that these genes were highly expressed in CC tissues.Conclusion: The present study identified five DEmRNAs, including DNMT1, CHAF1B, CHAF1A, MCM2 and Kinetochore-related protein 1 (KNTC1), as potential diagnostic and prognostic biomarkers of CC.

Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions

As the polyploidy progenitor of modern sugarcane, Saccharum spontaneum is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported on the mechanism of drought tolerance in S. spontaneum. Herein, the physiological changes of S. spontaneum GXS87-16 at three water-deficit levels (mild, moderate, and severe) and after re-watering during the elongation stage were investigated. RNA sequencing was utilized for global transcriptome profiling of GXS87-16 under severe drought and re-watered conditions. There were significant alterations in the physiological parameters of GXS87-16 in response to drought stress and then recovered differently after re-watering. A total of 1569 differentially expressed genes (DEGs) associated with water stress and re-watering were identified. Notably, the majority of the DEGs were induced by stress. GO functional annotations and KEGG pathway analysis assigned the DEGs to 47 GO categories and 93 pathway categories. The pathway categories were involved in various processes, such as RNA transport, mRNA surveillance, plant hormone signal transduction, and plant-pathogen interaction. The reliability of the RNA-seq results was confirmed by qRT-PCR. This study shed light on the regulatory processes of drought tolerance in S. spontaneum and identifies useful genes for genetic improvement of drought tolerance in sugarcane.

New insight into LncRNA-mRNA regulatory network associated with lipid biosynthesis using Hi-C data in seeds of tung tree (Vernicia fordii Hemsl.)

Tung tree (Vernicia fordii Hemsl.), widely distributed in China, is a major potential source of biofuel. Exploration of the lipid biosynthesis regulatory network is essential for increasing tung tree lipid yield and its economic value. LncRNAs play significant regulatory roles in many different biological processes in plants. In this study, the profile and differential expression of lncRNAs and mRNAs were evaluated in tung tree seeds in two lipid accumulation phases using high-throughput sequencing technologies. GO function analysis of the protein-coding genes revealed that the majority of up-regulated genes were enriched in the categories of carbohydrate transport (GO:0008643), positive regulation of seed germination (GO:0010030), seed oilbody biogenesis (GO:0010344) and lipid metabolic process (GO:0006629). Network analysis showed that 177 up-regulated lncRNAs might regulate 1290 target genes. GO function analysis was performed on the lncRNA up-regulated target genes, revealed that the lipid particle organization (GO:0034389) was enriched in the biological process. Associated chromatin interactions between lncRNAs and mRNAs were conducted according to Hi-C data. A total of 68 lncRNAs and 46 genes were included in the lipid biosynthesis regulatory network, which provides useful information to reveal the interaction between lncRNAs and coding genes related to lipid biosynthesis in tung tree.

Comparative transcriptome analysis of different developmental stage of Bactrocera minax (Diptera: Tephritidae): Implication of the molecular basis of its obligatory diapause induction

The Chinese citrus fruit fly, Bactrocera minax (Enderlein), a devastating pest in citrus, has an obligatory diapause at the pupal stage. Although the physiology of obligatory diapause has been well described, the molecular mechanisms underlying the process remain unknow. Here we investigated the molecular mechanisms of obligatory diapause induction in B. minax using high-throughput RNA-Seq data from second-instar larva (2L), third-instar larva (3L) and pupa (P) stages. A total of 116,402 unigenes were obtained, of which 54,781 unigenes were successfully annotated in public databases, and the differentially expressed genes in the 3L vs 2L, P vs 2L, and P vs 3L comparisons were identified. The cluster co-expression patterns of the differentially expressed genes revealed that significantly differentially-expressed genes in the pupal stage were predicted to be related to diapause induction. All differentially expressed genes were investigated by GO functional and KEGG pathway analysis, and the results showed that genes involved in processes such as 20-hydroxyecdysone (20E) biosynthesis, cell cycle and metabolic pathways are likely related to obligatory diapause induction in B. minax. These results provide important information on the transcriptome of the Chinese citrus fruit fly that can be used for further functional studies as well as contributing to our understanding of the molecular basis of obligatory diapause induction and suggesting potential molecular targets for the control of this pest.

Hippophae rhamnoides mediate gene expression profiles against keratinocytes infection of Staphylococcus aureus.

Staphylococcus aureus causes a wide range of skin diseases such as bacterial keratitis, follicles, psoriasis, cellulitis and atopic dermatitis. This study aims to investigate the S. aureus mediated molecular modulation, and the effect of HR in reversing the deleterious impact of S. aureus in keratinocytes. Human keratinocyte (HaCaT) cells were cultured in DMEM, supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Subcultures were divided into three flasks: control with no S. aureus and extract (C), S. aureus infected (SA) and S. aureus infected cells and extract (SE). RNA was isolated and microarray analysis was performed. The data was annotated using GO functional analysis and DAVID functional annotation. For each comparison group, significant probes were filtered out at significant cut off by fold change (P < 0.05 and/or > twofold change). For SA vs control, SE vs control, and SE vs SA, 204, 9369, 9900 probes were filtered respectively. In SA vs control, TNF signaling, NOD-like receptor and chemokine receptor signaling pathways were upregulated with key genes such as CCL2, CCL20 and BIRC3. The SE vs SA, showed significant expression variations of a number of important genes. Molecular pathways associated with ILs, TNFs, TGFs, IFNs, FGFs, MAPKs, MMPs, caspases and Wnts were either up regulated or downregulated. This effect was reversed by the extract, possibly through downregulating various proinflammatory cytokines and apoptotic pathways. Our study reveals that S. aureus inserts a negative impact on the regulation of various key genes which is apparently reversed by the HR extract.

Analyses of plantaricin Q7 synthesis by Lactobacillus plantarum Q7 based on comparative transcriptomics

Plantaricin Q7 was a bacteriocin with broad-spectrum antibacterial activity and biosafety produced by Lactobacillus plantarum Q7. However, the low yield of plantaricin Q7 was the main limitation to its industrialization. To understand the plantaricin Q7 production at the level of transcription, the biosynthesis of plantaricin Q7 from L. plantarum Q7 was investigated by transcriptomics. It was found that there were four critical time points in plantaricin Q7 synthesis stage. Plantaricin Q7 entered the synthesis period at 2 h, and the largest synthesis rate was observed at 6 h. The highest production of plantaricin Q7 reached at 12 h, and the production began to decrease at 16 h. The transcriptomics results of GO function and KEGG pathway analyses at those four time points showed that oppD encoding ABC oligopeptide transporter, pedC encoding bacteriocin ABC transport accessory protein, agrC encoding histidine protein kinase, and groL as well as groS encoding heat shock protein and accessory protein played a key role in the synthesis of plantaricin Q7. In addition, clpL and clpP encoding protease could cause the degradation of plantaricin Q7. When environmental induction was used to regulate the express of the heat shock protein, plantaricin Q7 yield was increased by 33.33% when 2% NaCl as inducer, and groS was significantly up-regulated. It was suggested that groS could be a critical gene for the synthesis of plantaricin Q7. These findings provided new regulated targets to improve the production of bacteriocins.

Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba

Gastric cancer (GC) is one of the most common types of malignancy. Its potential molecular mechanism has not been clarified. In this study, we aimed to explore potential biomarkers and prognosis-related hub genes associated with GC. The gene chip dataset GSE79973 was downloaded from the GEO datasets and limma package was used to identify the differentially expressed genes (DEGs). A total of 1269 up-regulated and 330 down-regulated genes were identified. The protein-protein interactions (PPI) network of DEGs was constructed by STRING V11 database, and 11 hub genes were selected through intersection of 11 topological analysis methods of CytoHubba in Cytoscape plug-in. All the 11 selected hub genes were found in the module with the highest score from PPI network of all DEGs by the molecular complex detection (MCODE) clustering algorithm. In order to explore the role of the 11 hub genes, we performed GO function and KEGG pathway analysis for them and found that the genes were enriched in a variety of functions and pathways among which cellular senescence, cell cycle, viral carcinogenesis and p53 signaling pathway were the most associated with GC. Kaplan-Meier analysis revealed that 10 out of the 11 hub genes were related to the overall survival of GC patients. Further, seven of the 11 selected hub genes were verified significantly correlated with GC by uni- or multivariable Cox model and LASSO regression analysis including C3, CDK1, FN1, CCNB1, CDC20, BUB1B and MAD2L1. C3, CDK1, FN1, CCNB1, CDC20, BUB1B and MAD2L1 may serve as potential prognostic biomarkers and therapeutic targets for GC.

LAPTM5 Plays a Key Role in the Diagnosis and Prognosis of Testicular Germ Cell Tumors.

Objective Testicular germ cell tumors (TGCT) are a serious malignant tumor with low early diagnosis rates and high mortality. Methods To investigate novel biomarkers to predict the diagnosis and prognosis of this cancer, bioinformatics analysis was used as an accurate, efficient, and economical method. Results Our study detected 39 upregulated and 589 downregulated differentially expressed genes (DEGs) using the GEO and TCGA databases. To identify the function of DEGs, GO functional analysis, three pathway analysis (KEGG, REACTOME, and PANTHER), and protein-protein interaction network were performed using the KOBAS website, as well as the String database. After a series of analyses in GEPIA and TIMER, including differential expression, we found one candidate gene related to the prognosis and diagnosis of TGCT. LAPTM5 was also associated with CD8+ T cell and PDCD1 expression, which suggests that it may affect immune infiltration. Conclusions LAPTM5 was identified as a hub gene, which could be used as a potential biomarker for TGCT diagnosis and prognosis.

A network pharmacology based approach for predicting active ingredients and potential mechanism of Lianhuaqingwen capsule in treating COVID-19.

The outbreak of severe respiratory disease caused by SARS-CoV-2 has led to millions of infections and raised global health concerns. Lianhuaqingwen capsule (LHQW-C), a traditional Chinese medicine (TCM) formula widely used for respiratory diseases, shows therapeutic efficacy in the application of coronavirus disease 2019 (COVID-19). However, the active ingredients, drug targets, and the therapeutic mechanisms of LHQW-C in treating COVID-19 are poorly understood. In this study, an integrating network pharmacology approach including pharmacokinetic screening, target prediction (targets of the host and targets from the SARS-CoV-2), network analysis, GO enrichment analysis, KEGG pathway enrichment analysis, and virtual docking were conducted. Finally, 158 active ingredients in LHQW-C were screen out, and 49 targets were predicted. GO function analysis revealed that these targets were associated with inflammatory response, oxidative stress reaction, and other biological processes. KEGG enrichment analysis indicated that the targets of LHQW-C were highly enriched to several immune response-related and inflammation-related pathways, including the IL-17 signaling pathway, TNF signaling pathway, NF-kappa B signaling pathway, and Th17 cell differentiation. Moreover, four key components (quercetin, luteolin, wogonin, and kaempferol) showed a high binding affinity with SARS-CoV-2 3-chymotrypsin-like protease (3CL pro). The study indicates that some anti-inflammatory ingredients in LHQW-C probably modulate the inflammatory response in severely ill patients with COVID-19.

Bioinformatics analysis identified hub genes in prostate cancer tumorigenesis and metastasis.

Prostate cancer (PCa) is the most frequent cancer found in males worldwide, and its mortality rate is increasing every year. To discover key molecular changes in PCa development and metastasis, we analyzed microarray data of localized PCa, metastatic PCa and normal prostate tissue samples from clinical specimens. Gene expression profiling datasets of PCa were analyzed online. The DAVID was used to perform GO functional and KEGG pathway enrichment analyses. CytoHubba in Cytoscape software was applied to identify hub genes. Survival data were downloaded from GEPIA. Gene expression data were obtained from ONCOMINE and UALCAN. We obtained 4 sets of differentially expressed genes (DEGs), DEGs 1: a comparison of the gene expression between 4 normal prostate and 5 localized PCa samples in GSE27616; DEGs 2: a comparison of the gene expression between 6 normal prostate and 7 localized PCa samples in GSE3325; DEGs 3: a comparison of the gene expression between 5 localized PCa and 4 metastatic PCa samples in GSE27616; DEGs 4: a comparison of the gene expression between 7 localized PCa and 6 metastatic PCa samples in GSE3325. A comparison of these 4 sets of genes revealed 51 overlapped genes. GO function analysis revealed enrichment of the 51 DEGs in functions related to the proteinaceous extracellular matrix and centrosome, protein homodimerization activity and chromatin binding were the main functions of these genes, which participated in regulating cell division, mitotic nuclear division, proteinaceous extracellular matrix, cell adhesion and apoptotic process. KEGG pathway analysis indicated that these identified DEGs were mainly enriched in progesterone-mediated oocyte maturation, oocyte meiosis and cell cycle. We defined the 16 genes with the highest degree of connectivity as the hub genes in the 51 overlapped DEGs. Cox regression revealed TOP2A, CCNB2, BUB1, CDK1 and EZH2 were related to Disease-free survival (DFS). The expression levels of the 5 genes were 2.232-, 1.786-, 2.303-, 1.699-, and 1.986-fold higher in PCa than the levels in normal tissues, respectively (P < 0.05). We obtained 20 hub genes from DEGs by the comparison of normal prostate tissue vs. localized cancer tissue. Among them, KIF20A, CDKN3, PBK and CDCA2, were expressed higher in PCa than in normal tissues, and were associated with the DFS of PCa patients. Meanwhile, we obtained 20 hub genes from DEGs by the comparison of localized cancer tissue vs. metastatic cancer tissue. Cox regression revealed PLK1, CCNA2 and CDC20, were associated with both the DFS and overall survival of PCa patients. The results suggested that the functions of KIF20A, CDKN3, PBK and CDCA2 may contribute to PCa development and the functions of PLK1, CCNA2 and CDC20 may contribute to PCa metastasis. Meanwhile, the functions of TOP2A, CCNB2, BUB1, CDK1 and EZH2 may contribute to both PCa development and metastasis.

Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis.

Pancreatic adenocarcinoma (PAAD) is one of the most common malignant tumors with high mortality rates and a poor prognosis. There is an urgent need to determine the molecular mechanism of PAAD tumorigenesis and identify promising biomarkers for the diagnosis and targeted therapy of the disease. Three GEO datasets (GSE62165, GSE15471 and GSE62452) were analyzed to obtain differentially expressed genes (DEGs). The PPI networks and hub genes were identified through the STRING database and MCODE plugin in Cytoscape software. GO and KEGG enrichment pathways were analyzed by the DAVID database. The GEPIA database was utilized to estimate the prognostic value of hub genes. Furthermore, the roles of MMP14 and COL12A1 in immune infiltration and tumor-immune interaction and their biological functions in PAAD were explored by TIMER, TISIDB, GeneMANIA, Metascape and GSEA. A total of 209 common DEGs in the three datasets were obtained. GO function analysis showed that the 209 DEGs were significantly enriched in calcium ion binding, serine-type endopeptidase activity, integrin binding, extracellular matrix structural constituent and collagen binding. KEGG pathway analysis showed that DEGs were mainly enriched in focal adhesion, protein digestion and absorption and ECM-receptor interaction. The 14 genes with the highest degree of connectivity were defined as the hub genes of PAAD development. GEPIA revealed that PAAD patients with upregulated MMP14 and COL12A1 expression had poor prognoses. In addition, TIMER analysis revealed that MMP14 and COL12A1 were closely associated with the infiltration levels of macrophages, neutrophils and dendritic cells in PAAD. TISIDB revealed that MMP14 was strongly positively correlated with CD276, TNFSF4, CD70 and TNFSF9, while COL12A1 was strongly positively correlated with TNFSF4, CD276, ENTPD1 and CD70. GSEA revealed that MMP14 and COL12A1 were significantly enriched in epithelial mesenchymal transition, extracellular matrix receptor interaction, apical junction, and focal adhesion in PAAD development. Our study revealed that overexpression of MMP14 and COL12A1 is significantly correlated with PAAD patient poor prognosis. MMP14 and COL12A1 participate in regulating tumor immune interactions and might become promising biomarkers for PAAD.

Gender Differences in Rheumatoid Arthritis: Interleukin-4 Plays an Important Role.

Introduction Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by symmetrical peripheral polyarthritis. A large number of studies have shown that RA is characterized by gender differences in clinical manifestations. The purpose of this study is to identify the key molecules of gender differences in patients with RA and to provide new molecular targets for personalized therapy. Material and Methods. The data from GSE55457 were downloaded from the comprehensive gene expression comprehensive database, and two groups (RA vs. No-RA groups, Male-RA vs. Female-RA groups) of differentially expressed genes (EDGs) were obtained by GEO2R. The GO function and KEGG pathway analyses of DEGs were carried out through the plug-in ClueGO in Cytoscape. Based on the STRING online, a protein-protein interaction (PPI) network was constructed. Hub genes were selected from CytoHubba. Through the intersection of the top 10 hub genes in two sets of EDGs, the key genes and related KEGG pathways were found. Quantitative Real-Time PCR and Western blotting analysis were performed for verification. Results 1230 DEGs were screened between RA and No-RA groups, and 306 DEGs were screened between male and female RA groups. The common key gene of the two groups is IL-4. Between RA group and No-RA group, interleukin-4 (IL-4) participates in cytokine-cytokine receptor interaction, Th1 and Th2 cell differentiation, Th17 cell differentiation, T cell receptor signaling pathway, etc. Conclusion This study contributes to the molecular biological mechanism of gender differences in RA. IL-4 may have played an important role.

Identification of an Immune-Related Gene Signature to Improve Prognosis Prediction in Colorectal Cancer Patients.

BackgroundDespite recent advance in immune therapy, great heterogeneity exists in the outcomes of colorectal cancer (CRC) patients. In this study, we aimed to analyze the immune-related gene (IRG) expression profiles from three independent public databases and develop an effective signature to forecast patient’s prognosis.MethodsIRGs were collected from the ImmPort database. The CRC dataset from The Cancer Genome Atlas (TCGA) database was used to identify a prognostic gene signature, which was verified in another two CRC datasets from the Gene Expression Omnibus (GEO). Gene function enrichment analysis was conducted. A prognostic nomogram was built incorporating the IRG signature with clinical risk factors.ResultsThe three datasets had 487, 579, and 224 patients, respectively. A prognostic six-gene-signature (CCL22, LIMK1, MAPKAPK3, FLOT1, GPRC5B, and IL20RB) was developed through feature selection that showed good differentiation between the low- and high-risk groups in the training set (p < 0.001), which was later confirmed in the two validation groups (log-rank p < 0.05). The signature outperformed tumor TNM staging for survival prediction. GO and KEGG functional annotation analysis suggested that the signature was significantly enriched in metabolic processes and regulation of immunity (p < 0.05). When combined with clinical risk factors, the model showed robust prediction capability.ConclusionThe immune-related six-gene signature is a reliable prognostic indicator for CRC patients and could provide insight for personalized cancer management.

Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

BackgroundBased on therapy with syndrome differentiation and clinical studies on Xiaochaihu decoction (XCHD), we hypothesize that Modified Xiaochaihu Decoction (MXD) has an ability to ameliorate non-alcoholic fatty liver disease (NAFLD). This study aims to elucidate the pharmacological efficacy of MXD and its mechanism in the treatment of NAFLD by network pharmacology and experimental validation.MethodsThe active ingredients in MXD and their potential targets were identified using network analysis followed by experimental validation. First, we used data on the ingredients and targets obtained from professional database and related literature to do PPI network analysis, GO functional analysis, and KEGG pathway enrichment analysis. Core targets identified by network pharmacology were then tested in natural ageing female rats model. Indexes of lipid and glucose homeostasis were determined enzymatically and/or histologically. Gene expression was analyzed by real-time PCR and/or Western blot (WB).ResultsIn total, 4009 NAFLD-related targets and 1953 chemical ingredients of MXD were obtained. In-depth network analysis of 140 common targets indicated that MXD played a critical role in anti-NAFLD via multiple targets and pathways. Based on the data of PPI analysis, GO functional enrichment analysis, KEGG pathway enrichment analysis, and literatures on the mechanism of NAFLD, we chose the core targets related to lipid metabolism (SREBP-1c, ChREBP, FASN, PPARα, and ACACA) and inflammation (IL-6 and NF-κB) to do further study. Significantly, in further animal verification experiment we using naturally ageing rats with NAFLD as a model, we found that MXD administration ameliorated age-related NAFLD and mechanistically down-regulated the mRNA/protein expression of core targets in lipid metabolism and inflammation related pathways such as FASN, ACACA, IL-6, and NF-κB. In addition, 12 of 24 potential ingredients acting on verified targets came from BC, and 11 of 24 potential ingredients acting on verified targets were derived from SM, implying that both BC and SM served as the key role in MXD against NAFLD.ConclusionThe bioinformatics data and in vivo experimental results suggest that the MXD-induced amelioration of NAFLD may be predominantly related to modulation of lipid metabolism and inflammation. Both BC and SM serve as the key role in MXD against NAFLD. These results may provide novel evidence for clinical implication of MXD.

Mechanism of "Scutellaria barbata-Hedyotis diffusa" against breast cancer based on network pharmacology

To explore the mechanism of Scutellaria barbata-Hedyotis diffusa against breast cancer based on network pharmacological methods. The active components and corresponding target proteins of S. barbata and H. diffusa were screened by using Traditional Chinese Medicine Systems Pharmacology Database(TCMSP), and the targets of breast cancer were screened through the Genecards and OMIM databases. Venn online software was used to obtain the common targets of drugs and the disease, and then the &quot;compound-target-disease&quot; network diagram was constructed by using Cytoscape 3.7.2 software. The STRING database was used to draw the protein-protein interaction(PPI) network, and the David database was used to perform GO function and KEGG pathway enrichment analysis on effective targets. The results showed that 29 S. barbata compounds, 7 H. diffusa compounds, and 109 effective targets were screened. The 59 common targets for drugs and disease were obtained through Venn diagrams. The PPI network showed that MYC, CCND1, EGFR, ESR1, CASP3, VEGFA, etc. might be the key targets for &quot;S. barbata-H. diffusa&quot; in the treatment of breast cancer. In the GO function analysis, 88 entries were found, involving the regulation of transcription factor activity, receptor activity, cytokine activity, enzyme activity, and biosynthetic processes. In KEGG pathway analysis, 37 entries related to cancer, cell cycle, apoptosis, angioge-nesis and other pathways were found, including p53 signaling pathway, ErbB signaling pathway, nod like receptor signaling pathway, MAPK signaling pathway, VEGF signaling pathway, Wnt signaling pathway and mTOR signaling pathway and other classic signaling pathways. This study preliminarily revealed the key targets, biological processes and signal pathway of &quot;S. barbata-H. diffusa&quot; against breast cancer. It was found that its function was in a multi-target and multi-channel manner, which laid a foundation for future molecular biological experiments.

Abstract LB-131: Profile of glucose metabolism in bladder cancer patients and the inhibitory effect of sulforaphane on bladder cancer glycolysis by regulating microRNA expression

Abstract Object: We are committed to studying the characteristics of energy metabolism in bladder cancer patients, and to investigate the regulation of sulforaphane (SFN) on glucose metabolism in bladder cancer cells. Methods: Real-time PCR was used to detect the gene level of glycolysis key rate-limiting enzymes in bladder tumors, and para-carcinoma tissues as control. We also measured the activity of glycolysis enzymes in patient serum and bladder cancer cells by ELISA. Then we measured microRNAs level by microarray after SFN treatment. GO function and KEGG pathway enrichment analyses were used to gain insights into the biological roles and the potential pathway of different expression microRNAs. Results: Gene expression results showed that the level of PFK-1 was highly increased in tumor tissues. However, there is no significant differential in serum activity of PFK-1 as compared with control group. SFN obviously elevated microRNA expression related to glucose metabolism, including miR-200c, miR-34a and let-7. The activity of HK2, which can be blocked by miR-34a, was strongly inhibited in bladder cancer cells by incubating with 20 μmol/L SFN for 24 h. Furthermore, functional annotation analysis results suggest that miR-200c target genes were mainly enriched in 82 GO terms and 17 pathways (P &amp;lt; 0.05), including mTOR signaling (p = 0.0154) and AMPK signaling (p = 0.0158), which also involved in the regulation of energy metabolism. Conclusion: Aberrant gene expression of PFK-1 is one of most important causes of glucose metabolic disorders in bladder cancer patients. SFN can significantly down-regulate glucose metabolism in bladder cancer cells by regulating the expression of glycolysis related-microRNAs. Citation Format: Yujuan Shan, Lei Huang. Profile of glucose metabolism in bladder cancer patients and the inhibitory effect of sulforaphane on bladder cancer glycolysis by regulating microRNA expression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-131.

Comparative transcriptome profiling reveals a mechanism of Streptococcus agalactiae resistance to florfenicol

Florfenicol is widely used to control diseases in aquatic animals, and is used extensively to treat streptococcosis—caused by Streptococcus agalactiae—in the commercially important fish tilapia. There are known issues with the development of florfenicol resistance in Streptococcus agalactiae, but the underlying resistance mechanisms are not clear, a situation currently preventing optimal deployment of antibiotics. Here, we examined the induction of resistance by successively increasing the concentrations of florfenicol, and then used RNA-sequencing (RNA-Seq) to characterize changes in the transcriptomes of a florfenicol-resistant strain (H51-R) and a florfenicol-sensitive strain (H51–S). We obtained a total of 18,418,068 sequence reads in H51-R and 16,070,122 sequence reads in H51–S, from which a total of 1940 unigenes were assembled. In total, 376 unigenes were found to be differently expressed genes (DEGs). After florfenicol treatment, 181 genes were upregulated and 195 genes were downregulated. GO functional analysis of the DEGs indicated that the most strongly enriched GO terms included metabolic process (152 genes), catalytic activity (146), and binding (133), with terms including membrane, membrane part, and transporter activity also showing enrichment. KEGG pathway enrichment analysis highlighted that ribosomes were prominently involved in the transcriptional changes associated with florfenicol resistance. This study demonstrates that florfenicol treatment affects multiple biological functions of Streptococcus agalactiae, suggests that florfenicol resistance in Streptococcus agalactiae is closely related to the reduction of intracellular drug accumulation caused by ATP-binding cassette (ABC) transporters, and highlights the potential involvement of altered ribosomal function in florfenicol resistance.