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1.
Article | IMSEAR | ID: sea-236649

ABSTRACT

Noscapinoids, synthetic derivatives of noscapine, have been identified as potential anticancer drugs in cervical cancer. This study aimed to understand the mechanism of action of noscapinoids by comparing the gene expression profiles of treated and untreated Hela cells using RNA-seq. A total of 4926 differentially expressed genes (DEGs) were identified, including BAG2, BCL2L11, HSPA4, CASP14, CASP12, CASP8, CASP10, CASP1, and CFLAR. Pathway analysis revealed 20 enriched pathways from up and downregulated DEGs, including endoproteases, cysteine-type endopeptidase activity, TNF, IL-17 signaling pathway, Mitophagy, and Shigellosis. A detailed investigation into DEGs using annotations for cellular components, molecular functions, and biological processes identified different 20 regulating activities from both up and downregulating DEGs. To determine the 50 most functional genes from each group, a protein-protein interaction network was built. These genes were then subjected to further testing by reverse transcription polymerase chain reaction. It was discovered that the downregulated genes that were the focus of the investigation were related to tumor cell invasion, migration and motility, and cell survival and proliferation. The study suggests that these DEGs could be targeted for therapeutic purposes and may serve as potential biomarkers for developing novel therapeutic approaches in cancer treatment. The research sheds light on the mechanism of action of noscapinoids and highlights their potential as a new class of anticancer drugs.

2.
Braz. j. med. biol. res ; 57: e13482, fev.2024. graf
Article in English | LILACS-Express | LILACS | ID: biblio-1581903

ABSTRACT

Both embryonic stem cells (ESCs) and the successful reprogramming of induced pluripotent stem cells (iPSCs) offer an unprecedented therapeutic potential for Parkinson's disease (PD), allowing for the replacement of depleted neurons in PD-affected brain regions, thereby achieving therapeutic goals. This study explored the differences in cell types between iPSCs and ESCs in the PD brain to provide a feasible theoretical basis for the improved use of iPSCs as a replacement for ESCs in treating PD. Signal cell RNA sequencing data and microarray data of ESCs and iPSCs were collected from the GEO database. scRNA-seq data were subjected to quality control, clustering, and identification using the Seurat R package to determine cell types and proportions in ESCs and iPSCs. Differential expression analysis was performed to identify differentially expressed genes between ESCs and iPSCs, and PPI network analysis was conducted using String. Based on scRNA-seq data, we identified 13 cell clusters in ESCs and 13 cell clusters in iPSCs. iPSCs were predominantly composed of immune cells and lacked astrocytes, neurons, and dopamine neurons compared to ESCs. iPSCs also exhibited lower cell type diversity compared to ESCs. At the gene level, iPSCs lacked key genes, such as TH and GAP43 for nerve growth and development. At the metabolic level, the difference between ESCs and iPSC was mainly reflected in nerve cells and was closely related to the tumor-proliferation signature. iPSCs can be promoted to differentiate into cell types closer to or even replace ESCs, providing a better therapeutic option for PD treatment.

3.
Article in Chinese | WPRIM | ID: wpr-1039069

ABSTRACT

Chimeric RNA is a fusion transcript comprising of exon fragments from different genes. There are three splicing types: chromosome rearrangements, trans-splicing, cis-splicing, and the recently mentioned circular chimeric RNA. The traditional methods for the detection of chimeric RNA includes chromosome karyotype analysis, FISH, DNA microarray, etc., but their specificity, sensitivity and accuracy for the detection of chimeric RNA are poorly understood. With the development of sequencing technology, second-generation sequencing technology has shown strong data processing capabilities and can detect chimeric RNA through high-throughput sequence analysis. Currently, detection methods making use of high-throughput sequencing datasets includes FusionCatcher, SOAPfuse, EricScript, etc. For validation of the detected chimeric RNA, the commonly used methods include PCR, RPA, agarose gel electrophoresis, sanger sequencing, etc. The development of newly introduced techniques has led to the discovery of different novel chimeric RNA, the third and fourth generation sequencing has also been developed and nearly mature, and the sequencing technology taking PacBio as an example has also brought a new dawn to the discovery of chimeric RNA, but each of them has its advantages and disadvantages, mainly focusing on its cost, false positive rate, detection time, etc. This paper basically describes various different techniques that can be utilized for the detection and validation of chimeric RNA.

4.
Chongqing Medicine ; (36): 481-486, 2024.
Article in Chinese | WPRIM | ID: wpr-1017483

ABSTRACT

Objective To investigate the transcriptome differences of ovarian cancer cells after cisplatin(DDP)resistance,and to find potential antagonists based on this screening.Methods DDP-resistant cell line A2780-DDP was constructed with A2780 cells as the research object.Through transcriptome sequencing anal-ysis,the key factors of DDP resistance were found and verified by quantitative real-time PCR(qPCR)and Western blot experiments.Through the screening of small molecule inhibitors,CCK-8 cell viability assay was used to find potential antagonists.Results A2780-DDP were successfully constructed,and it was found that there was no difference in cell proliferation after drug resistance,but the ability of cell invasion and migration was enhanced.Through transcriptome sequencing analysis,it was found that ITGB7 and Akt may be the key genes of A2780-DDP,and qPCR and Western blot showed that they were highly expressed in A2780-DDP.CCK-8 results showed that triptolide(TPL)and Olaparib had good inhibitory effects in DDP-resistant cell lines.Conclusion The ITGB7/Akt pathway plays an important role in DDP resistance,and potential DDP re-sistance antagonists such as TPL can provide new ideas for the treatment of ovarian cancer.

5.
Journal of Army Medical University ; (semimonthly): 359-368, 2024.
Article in Chinese | WPRIM | ID: wpr-1017570

ABSTRACT

Objective To preliminarily investigate the anti-tumor effects of phytosphingosine(PHS)and the involvement of inducing apoptosis of leukemia cells.Methods Cellular model of leukemia was established in leukemia cell lines K562 and SUP-B15.CCK-8 assay and EdU assay were used to measure the viability and DNA synthesis of K562 and SUP-B15 cells.RNA-seq was carried out to verify the differentially expressed genes(DEGs)after PHS treatment.Gene Ontology(GO)enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were applied to analyze the involved functions and signaling pathways.Comparative Toxicogenomics Database(CTD)and Discovery Studio software were employed to predict the underlying targets of PHS and molecular docking.Cell apoptosis was detected by flow cytometry,mitochondrial membrane potential was evaluated by JC-1 probe,and protein expression of key molecules was validated by Western blotting.Results PHS inhibited the proliferation of K562 and SUP-B15 cells in a time-and dose-dependent manner.The half-maximal inhibitory concentration(IC50)of K562 cells was 17.67 and 12.52 pmol/L for 24 and 48 h,respectively,and the IC50 value of SUP-B15 cells was 17.58 and 14.86 μmol/L for 24 and 48 h,respectively.PHS treatment at a dose of 20 μmol/L for 48 h resulted in significant inhibition of DNA synthesis.GO enrichment analysis of the K562 cells showed that PHS might be involved in positive regulation of apoptotic process,plasma membrane and its integral components,and protein kinase binding and activity.Reverse predictive analysis showed that BCL-2 protein was the most likely target of PHS.PHS significantly increased the apoptotic rate of leukemia cells(P<0.05)in a dose-dependent manner,reduced the mitochondrial membrane potential,and down-regulated BCL-2 level(P<0.05)and up-regulated the levels of Cleaved caspase-3 and Cleaved caspase-9(P<0.05).Conclusion PHS may inhibit the proliferation of leukemia cells by inducing mitochondria-dependent apoptosis,possibly through PHS and BCL-2 interaction.

6.
Chinese Journal of Biotechnology ; (12): 150-162, 2024.
Article in Chinese | WPRIM | ID: wpr-1008086

ABSTRACT

Photosynthesis in plants directly affects the synthesis and accumulation of organic matter, which directly influences crop yield. RNA-binding proteins (RBPs) are involved in the regulation of a variety of physiological functions in plants, while the functions of RBPs in photosynthesis have not been clearly elucidated. To investigate the effect of a glycine-rich RNA-binding protein (SlRBP1) in tomato on plant photosynthesis, a stably inherited SlRBP1 silenced plant in Alisa Craig was obtained by plant tissue culture using artificial small RNA interference. It turns out that the size of the tomato fruit was reduced and leaves significantly turned yellow. Chlorophyll(Chl) content measurement, Chl fluorescence imaging and chloroplast transmission electron microscopy revealed that the chloroplast morphology and structure of the leaves of tomato amiR-SlRBP1 silenced plants were disrupted, and the chlorophyll content was significantly reduced. Measurement of photosynthesis rate of wild-type and amiR-SlRBP1 silenced plants in the same period demonstrated that the photosynthetic rate of these plants was significantly reduced, and analysis of RNA-seq data indicated that silencing of SlRBP1 significantly reduced the expression of photosynthesis-related genes, such as PsaE, PsaL, and PsbY, and affected the yield of tomato fruits through photosynthesis.


Subject(s)
RNA , Solanum lycopersicum/genetics , Photosynthesis/genetics , Chlorophyll , RNA-Binding Proteins/genetics
7.
J. appl. oral sci ; J. appl. oral sci;32: e20240031, 2024. tab, graf
Article in English | LILACS-Express | LILACS | ID: biblio-1569297

ABSTRACT

Abstract This study aimed to assess the influence of smoking on the subgingival metatranscriptomic profile of young patients affected by stage III/IV and generalized periodontal disease. Methodology In total, six young patients, both smokers and non-smokers (n=3/group), who were affected by periodontitis were chosen. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting were followed. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from the biofilm and sequenced via Illumina HiSeq. Differential expression analysis used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R, with a statistical cutoff of ≤0.05. Results This study found 3351 KEGGs in the subgingival biofilm of both groups. Smoking habits altered the functional behavior of subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Smoking also altered antibiotic resistance gene levels in subgingival biofilm by significantly overexpressing genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. Conclusion Due to the limitations of a small sample size, our data suggest that smoking may influence the functional behavior of subgingival biofilm, modifying pathways that negatively impact the behavior of subgingival biofilm, which may lead to a more virulent community.

8.
Article in Chinese | WPRIM | ID: wpr-1023085

ABSTRACT

Hepatotoxicity induced by bioactive constituents in traditional Chinese medicines or herbs,such as bavachin(BV)in Fructus Psoraleae,has a prolonged latency to overt drug-induced liver injury in the clinic.Several studies have described BV-induced liver damage and underlying toxicity mechanisms,but little attention has been paid to the deciphering of organisms or cellular responses to BV at no-observed-adverse-effect level,and the underlying molecular mechanisms and specific indicators are also lacking during the asymptomatic phase,making it much harder for early recognition of hepatotoxicity.Here,we treated mice with BV for 7 days and did not detect any abnormalities in biochemical tests,but found subtle steatosis in BV-treated hepatocytes.We then profiled the gene expression of hepatocytes and non-parenchymal cells at single-cell resolution and discovered three types of hepatocyte subsets in the BV-treated liver.Among these,the hepa3 subtype suffered from a vast alteration in lipid metabolism,which was characterized by enhanced expression of apolipoproteins,carboxylesterases,and stearoyl-CoA desaturase 1(Scd1).In particular,increased Scd1 promoted monounsaturated fatty acids(MUFAs)syn-thesis and was considered to be related to BV-induced steatosis and polyunsaturated fatty acids(PUFAs)generation,which participates in the initiation of ferroptosis.Additionally,we demonstrated that mul-tiple intrinsic transcription factors,including Srebf1 and Hnf4a,and extrinsic signals from niche cells may regulate the above-mentioned molecular events in BV-treated hepatocytes.Collectively,our study deciphered the features of hepatocytes in response to BV insult,decoded the underlying molecular mechanisms,and suggested that Scd1 could be a hub molecule for the prediction of hepatotoxicity at an early stage.

9.
Article in Chinese | WPRIM | ID: wpr-1030729

ABSTRACT

Objective The transcriptome sequencing results of brain tissues of olanzapine-treated mice were analyzed to screen out differentially-expressed genes and explore potential targets of atypical antipsychotics leading to body weight gain.Methods Twenty female C57BL/6 mice were randomly divided into control group (Ctrl) and Olanzapine administration group (Olz), which were given saline and Olanzapine solution by gavage, respectively. The whole brain tissues were collected 8 weeks later for Transcriptome sequencing (RNA-Seq). The possible targets of olanzapine-induced body weight gain were identified by the Gene Ontology (GO) functional annotation analysis, the Kyoto Encyclopedia of Genes and Gnomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis. Differential expression levels of mRNAs were further verified by real-time quantitative fluorescence PCR (RT-qPCR).Results Compared with Ctrl group, 591 differentially expressed genes were screened in Olz group, including 251 up-regulated genes and 340 down-regulated genes. GO analysis showed that differential genes were widely involved in transcriptional process, among which the expression of genes related to the regulation of digestive system and cold-induced thermogenesis were significantly enriched. KEGG analysis showed that differential genes were widely involved in the interaction between neuroactive ligands and receptors, and the differential genes were significantly enriched in oxytocin signaling, fat digestion and absorption, and cholesterol metabolism pathways. RT-qPCR were performed to verify the expression levels of genes enriched in feeding regulation, gastric kinesis, thermogenesis, fat metabolism and other processes (Oxt, Trpv1, Adipoq, Phox2b, Abcg5, Mogat2, Dbh, Plac8 and Neurog1) as well as hub genes in PPI network (Fos, Dusp1 and Egr2), and the results were consistent with the trend of RNA-Seq.Conclusion Olanzapine administration resulted in changes in central feeding regulation, gastrointestinal motility, thermogenesis and other physiological processes in mice, which might be involved in body weight gain induced by olanzapine.

10.
Zhongguo Zhong Yao Za Zhi ; (24): 1908-1915, 2023.
Article in Chinese | WPRIM | ID: wpr-981410

ABSTRACT

This study aimed to analyze the biological foundation and biomarkers of stable coronary heart disease(CHD) with phlegm and blood stasis(PBS) syndrome based on RNA-seq and network pharmacology. Peripheral blood nucleated cells from five CHD patients with PBS syndrome, five CHD patients with non-PBS syndrome, and five healthy adults were collected for RNA-seq. The specific targets of CHD with PBS syndrome were determined by differential gene expression analysis and Venn diagram analysis. The active ingredients of Danlou Tablets were screened out from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, and the "component-target" prediction was completed through PubChem and SwissTargetPrediction. The "drug-ingredient-target-signaling pathway" network of Danlou Tablets against CHD with PBS syndrome was optimized by Cytoscape software. After the target biomarkers were identified, 90 participants were enrolled for diagnostic tests, and 30 CHD patients with PBS syndrome were included in before-and-after experiment to determine the therapeutic effect of Danlou Tablets on those targets. As revealed by RNA-seq and Venn diagram analysis, 200 specific genes were identified for CHD with PBS syndrome. A total of 1 118 potential therapeutic targets of Danlou Tablets were predicted through network pharmacology. Through integrated analysis of the two gene sets, 13 key targets of Danlou Tablets in the treatment of CHD with PBS syndrome were screened out, including CSF1, AKR1C2, PDGFRB, ARG1, CNR2, ALOX15B, ALDH1A1, CTSL, PLA2G7, LAP3, AKR1C3, IGFBP3, and CA1. They were presumably the biomarkers of CHD with PBS syndrome. The ELISA test further showed that CSF1 was significantly up-regulated in the peripheral blood of CHD patients with PBS syndrome, and was significantly down-regulated after Danlou Tablets intervention. CSF1 may be a biomarker for CHD with PBS syndrome, and it is positively correlated with the severity of the disease. The diagnostic cut-off of CSF1 for CHD with PBS syndrome was 286 pg·mL~(-1).


Subject(s)
Adult , Humans , Network Pharmacology , RNA-Seq , Coronary Disease/genetics , Drugs, Chinese Herbal/therapeutic use , Medicine, Chinese Traditional , Biomarkers , Syndrome , Tablets , Molecular Docking Simulation
11.
The Journal of Practical Medicine ; (24): 3169-3174, 2023.
Article in Chinese | WPRIM | ID: wpr-1020673

ABSTRACT

Objective To analyze the regulation of gene expression by adenosine deaminase RNA specific 1(ADAR1)in cervical cancer cell line Hela using RNA-seq technology and provide theoretical basis for understanding the role of ADAR1 in the occurrence and progression of cervical cancer.Methods RNA-seq sequencing of normal and ADAR1 knockdown Hela cell lines to identify differentially expressed genes.By conducting enrichment analysis using KEGG Pathway,GO cellular,and GSEA,the study analyzes the relevant signaling pathways and biological processes involving ADAR1 in Hela cell lines.Results Differentially expressed genes are mainly enriched in immune and inflammation-related signaling pathways(such as TNF-α/NF-κB,NIK/NF-κB,Jak/Stat-IL-6),Hippo signaling pathway,TGF-β signaling pathway,and are involved in interferon response,cellular amino acid metabo-lism regulation,protein ubiquitination/deubiquitination,viral transcription,and other biological processes.Further analysis of the NF-κB signaling pathway revealed a significant increase in the mRNA expression levels of NF-κB1 and TRAF5 after ADAR1 knockdown.Conclusion ADAR1 may regulate the expression of NF-κB signaling pathway-related factors and thereby regulate the occurrence and development of cervical cancer.

12.
China Tropical Medicine ; (12): 462-2023.
Article in Chinese | WPRIM | ID: wpr-979731

ABSTRACT

@#Abstract: Objective In order to explore the application prospects of the phenyl pyrazole insecticide fipronil for mosquito control and identify potential target genes involved in the resistance of Aedes aegypti to fipronil, and lay the foundation for an in-depth study of the resistance mechanism of Aedes aegypti to fipronil. Methods Using Aedes aegypti sensitive strains as experimental materials, Aedes aegypti larvae were treated with fipronil, and the differences in gene expression of Aedes aegypti larvae before and after drug administration were compared at the transcriptome level using transcriptome sequencing combined with bioinformatics analysis, and the differential genes were analyzed. Results A total of 757 differentially expressed genes were identified between the fipronil-treated group and control group, including 217 and 540 up- and down-regulated genes, respectively. Among these, the expression of glutamate-gated chloride channel (GluCls) genes varied significantly before and after treatment. Gene ontology analysis revealed that differentially expressed genes were enriched in catalytic activity, binding, metabolic processes, and membrane-related functions, while KEGG pathway analysis indicated enrichment in biosynthesis, metabolism, and life regulation processes, while the glutathione metabolic pathway was enriched in 15 differentially expressed genes. Conclusions The transcriptome results revealed that GST gene expression was significantly upregulated in fipronil-treated Aedes aegypti larvae, indicating that GST gene is involved in the development of fipronil resistance in Aedes aegypti larvae. In addition, GluCls gene expression was also significantly different before and after treatment, suggesting that GluCls migh be a potential target receptor for fipronil resistance in Aedes aegypti. As GluCls is an ideal target receptor found only in invertebrates, this discovery provides a reference and basis for further exploration of the toxicological mechanism of fipronil on Aedes aegypti.

13.
Chin. j. integr. med ; Chin. j. integr. med;(12): 600-607, 2023.
Article in English | WPRIM | ID: wpr-982297

ABSTRACT

OBJECTIVE@#To investigate the protective mechanisms of Chinese medicine Shexiang Tongxin Dropping Pills (STDP) on heart failure (HF).@*METHODS@#Isoproterenol (ISO)-induced HF rat model and angiotensin II (Ang II)-induced neonatal rat cardiac fibroblast (CFs) model were used in the present study. HF rats were treated with and without STDP (3 g/kg). RNA-seq was performed to identify differentially expressed genes (DEGs). Cardiac function was evaluated by echocardiography. Hematoxylin and eosin and Masson's stainings were taken to assess cardiac fibrosis. The levels of collagen I (Col I) and collagen III (Col III) were detected by immunohistochemical staining. CCK8 kit and transwell assay were implemented to test the CFs' proliferative and migratory activity, respectively. The protein expressions of α-smooth muscle actin (α-SMA), matrix metalloproteinase-2 (MMP-2), MMP-9, Col I, and Col III were detected by Western blotting.@*RESULTS@#The results of RNA-seq analysis showed that STDP exerted its pharmacological effects on HF via multiple signaling pathways, such as the extracellular matrix (ECM)-receptor interaction, cell cycle, and B cell receptor interaction. Results from in vivo experiments demonstrated that STDP treatment reversed declines in cardiac function, inhibiting myocardial fibrosis, and reversing increases in Col I and Col III expression levels in the hearts of HF rats. Moreover, STDP (6, 9 mg/mL) inhibited the proliferation and migration of CFs exposed to Ang II in vitro (P<0.05). The activation of collagen synthesis and myofibroblast generation were markedly suppressed by STDP, also the synthesis of MMP-2 and MMP-9, as well as ECM components Col I, Col III, and α-SMA were decreased in Ang II-induced neonatal rats' CFs.@*CONCLUSIONS@#STDP had anti-fibrotic effects in HF, which might be caused by the modulation of ECM-receptor interaction pathways. Through the management of cardiac fibrosis, STDP may be a compelling candidate for improving prognosis of HF.


Subject(s)
Rats , Animals , Matrix Metalloproteinase 2/metabolism , Matrix Metalloproteinase 9/metabolism , RNA-Seq , Transcriptome/genetics , Heart Failure/drug therapy , Collagen , Collagen Type I/metabolism , Fibrosis , Myocardium/pathology
14.
Acta Universitatis Medicinalis Anhui ; (6): 1795-1800,1806, 2022.
Article in Chinese | WPRIM | ID: wpr-1039213

ABSTRACT

Objective @#To reveal the effect of lipopolysaccharide-binding protein (lbp) gene on sepsis in rats and its important regulatory mechanism.@*Methods @#The acute liver inflammatory injury model was induced by lipopo- lysaccharide (LPS) .The levels of serum alanine aminotransferase ( ALT) and aspartate aminotransferase ( AST) were detected by biochemical analyzer to evaluate the liver injury,and the proinflammatory factors TNF-α and IL-6 were detected by RT-PCR to evaluate the level of inflammation,liver hematoxylin-eosin staining was used to ob- serve the infiltration of inflammatory cells and hepatocyte injury in liver tissue. RNA-Seq was performed to compare the transcriptome expression differences between lbp gene knockout (lbp -/ -) rats and wild-type (WT) rats to ex- cavate the downstream genes regulated by lbp in LPS induced liver inflammatory injury.The biological process and signal pathway were explored by GO function annotation and KEGG enrichment analysis. RT-PCR was used to veri- fy the mRNA expression level of differential genes. @*Results @#Compared with WT group,the levels of ALT,AST and pro-inflammatory factors in serum of lbp -/ - rats decreased (P <0. 05) ,and histological observation showed that the infiltration of inflammatory cells decreased.Transcriptomic analysis of liver tissue showed that 168 genes were differentially expressed after lbp -/ - (P<0. 05) ,among which Cyp7a1、Cyp4a2 and other up-regulated genes were enriched in peroxisome proliferator activated receptor ( PPAR) signal pathway and steroid hormone synthesis pathway (P<0. 05) .@*Conclusion @# lbp -/ - may participate in biological processes such as bacterial clearance and lipid metabolism by promoting PPAR signal pathway,so as to reduce liver inflammatory injury and slow down the occurrence and development of sepsis.

15.
Article in Chinese | WPRIM | ID: wpr-1011575

ABSTRACT

【Objective】 To investigate the relationship between differential expressions of lncRNAs and mRNAs and Hespintor’s possible anti-tumor mechanism using transcriptome sequencing technology. 【Methods】 First, a nude mouse model of human hepatoma tumors was established. The tumor tissue mass was collected after 4 weeks of group treatment. The cDNA libraries of tumor tissues were established in the Hespintor treatment group and the solvent control group, and transcriptome sequencing was performed. Based on RNA-seq data, the differentially expressed lncRNA and mRNA genes were screened, and the functional enrichment and interaction analysis were performed. The network module division approach was utilized to identify the target genes of Hespintor and build its regulatory network. 【Results】 The Hespintor treatment group yielded a high-confidence differentially expressed gene collection of 2 003 lncRNAs (DEGs lncRNA) and 1 038 mRNAs (DEGs mRNA). Target mRNAs regulated by DEGs lncRNA were mainly enriched in PIP3 to activate the Akt signal, p53 signal pathway, FOXO-mediated transcription, and cell cycle, among other things. DEGs mRNA were primarily enriched in chemokine signaling pathways, extracellular matrix receptor interactions, complement, and coagulation cascades. Both of them were related in three ways: cell behavior, transcriptional regulation, and cell cycle. 【Conclusion】 The PI3K/Akt signaling pathway may play a key role in the inhibitory effect of Hespintor on tumor, inducing G1/S phase cell cycle arrest and apoptosis.

16.
Article in Chinese | WPRIM | ID: wpr-1015677

ABSTRACT

Cholangiocarcinoma (CCA) is a highly invasive type of cancer with insidious onset and high mortality. Polypyrimidine tract-binding protein 1 (PTBP1) is highly over-expressed in various types of tumor tissues, which contributes to cancer progression. But the role of PTBP1 in CCA has not been explored yet. In this study, we aim to investigate the function of PTBP1 in CCA. Therefore, we used publicly available data from the cancer genome atlas (TCGA) to evaluate the dysregulation of PTBP1 in CCA. The results showed that the PTBP1 is significantly up-regulated in CCA tissues compared to the matched non-tumor tissues (P < 0. 05). We assessed the effects of PTBP1 on the growth of CCA cell lines RBE and HuH28 by performing CCK-8 and plate colony formation assays. The results showed that overexpression of PTBP1 significantly promoted the growth (P < 0. 01) of CCA cells, whereas knockdown of PTBP1 exhibited opposite effects. Transwell and Invasion assays revealed that overexpression of PTBP1 significantly promotes the migration and invasion of CCA cells (P < 0. 001), whereas knockdown of PTBP1 exhibited opposite effects (P < 0. 001). The RNA sequencing (RNA-seq) analysis in PTBP1-depleted cells showed that the up-regulated genes are significantly enriched in p53 signaling pathway, while the down-regulated genes are represented by cholesterol metabolism, Rho GTPase and TGF-β pathways. Then, the alternative splicing analysis revealed that inhibition of PTBP1 led to series of aberrant alternative splicing events, including several cancer-associated ones, such as splicing events within the TGF-β regulator TGIF1 and the p53 activity-correlated gene GNAS. These results indicate that PTBP1 promotes the progression of CCA likely by regulating the transcriptome alternative splicing to influence multiple cancer-associated signaling pathways.

17.
Article in Chinese | WPRIM | ID: wpr-1015692

ABSTRACT

Heme peroxidase EfeB in E. coli belongs to the dye-decolorizing peroxidase (DyP) superfamily. Peroxidases in this superfamily have a good ability in degradation of synthetic dyes, but their physiological functions in organisms are unclear. In order to further understand the physiological function of EfeB, the mutant strain EcoΔefeB was constructed by homologous recombination. The differences between parental strain E. coli BL21 and EcoΔefeB at genome transcription level as well as cell growth under different conditions were compared. The response of efeB to iron ion was also investigated. The results showed that the deletion of efeB gene caused the differential expression of 1 765 genes, which were mainly related to cell metabolic pathway, cell membrane synthesis and flagellum movement. There was no significant difference in cell growth between BL21 and EcoΔefeB at pH 7. 0, but the growth of BL21 was much better than that of EcoΔefeB at pH 4. 5. The functional expression of efeB may support the survival of E. coli at low pH. EfeB was significantly up-regulated when Fe

18.
Chinese Journal of Biotechnology ; (12): 287-302, 2022.
Article in Chinese | WPRIM | ID: wpr-927712

ABSTRACT

As a non-essential metal, cadmium (Cd) pollution poses severe threats to plant growth, environment, and human health. Phytoextraction using nursery stocks prior to their transplantation is a potential useful approach for bioremediation of Cd contaminated soil. A greenhouse pot experiment was performed to investigate the growth, Cd accumulation, profiles of transcriptome as well as root-associated microbiomes of Photinia frase in Cd-added soil, upon inoculation of two types of arbuscular mycorrhizal fungi (AMF) Sieverdingia tortuosa and Funneliformis mosseae. Compared with the control, inoculation of F. mosseae increased Cd concentrations in root, stem and leaf by 57.2%, 44.1% and 71.1%, respectively, contributing to a total Cd content of 182 μg/plant. KEGG pathway analysis revealed that hundreds of genes involved in 'Mitogen-activated protein kinase (MAPK) signaling pathway', 'plant hormone signal transduction', 'biosynthesis of secondary metabolites' and 'glycolysis/gluconeogenesis' were enriched upon inoculation of F. mosseae. The relative abundance of Acidobacteria was increased upon inoculation of S. tortuosa, while Chloroflexi and Patescibacteria were increased upon inoculation of F. mosseae, and the abundance of Glomerales increased from 23.0% to above 70%. Correlation analysis indicated that ethylene-responsive transcription factor, alpha-aminoadipic semialdehyde synthase, isoamylase and agmatine deiminase related genes were negatively associated with the relative abundance of Glomerales operational taxonomic units (OTUs) upon inoculation of F. mosseae. In addition, plant cysteine oxidase, heat shock protein, cinnamoyl-CoA reductase and abscisic acid receptor related genes were positively associated with the relative abundance of Patescibacteria OTUs upon inoculation of F. mosseae. These finding suggested that AMF can enhance P. frase Cd uptake by modulating plant gene expression and altering the structure of the soil microbial community. This study provides a theoretical basis for better understanding the relationship between root-associated microbiomes and root transcriptomes of P. frase, from which a cost-effective and environment-friendly strategy for phytoextraction of Cd in Cd-polluted soil might be developed.


Subject(s)
Humans , Cadmium , Microbiota , Mycorrhizae , Photinia , Soil Pollutants , Transcriptome
19.
Chinese Journal of Biotechnology ; (12): 820-830, 2022.
Article in Chinese | WPRIM | ID: wpr-927747

ABSTRACT

Studies of cellular dynamic processes have shown that cells undergo state changes during dynamic processes, controlled mainly by the expression of genes within the cell. With the development of high-throughput sequencing technologies, the availability of large amounts of gene expression data enables the acquisition of true gene expression information of cells at the single-cell level. However, most existing research methods require the use of information beyond gene expression, thus introducing additional complexity and uncertainty. In addition, the prevalence of dropout events hampers the study of cellular dynamics. To this end, we propose an approach named gene interaction network entropy (GINE) to quantify the state of cell differentiation as a means of studying cellular dynamics. Specifically, by constructing a cell-specific network based on the association between genes through the stability of the network, and defining the GINE, the unstable gene expression data is converted into a relatively stable GINE. This method has no additional complexity or uncertainty, and at the same time circumvents the effects of dropout events to a certain extent, allowing for a more reliable characterization of biological processes such as cell fate. This method was applied to study two single-cell RNA-seq datasets, head and neck squamous cell carcinoma and chronic myeloid leukaemia. The GINE method not only effectively distinguishes malignant cells from benign cells and differentiates between different periods of differentiation, but also effectively reflects the disease efficacy process, demonstrating the potential of using GINE to study cellular dynamics. The method aims to explore the dynamic information at the level of single cell disorganization and thus to study the dynamics of biological system processes. The results of this study may provide scientific recommendations for research on cell differentiation, tracking cancer development, and the process of disease response to drugs.


Subject(s)
Cell Differentiation/genetics , Entropy , Gene Regulatory Networks , High-Throughput Nucleotide Sequencing , Single-Cell Analysis/methods
20.
Chinese Journal of Orthopaedics ; (12): 776-785, 2022.
Article in Chinese | WPRIM | ID: wpr-957068

ABSTRACT

Objective:To explore the key pathways and genes involved in microglia inflammation through transcriptome sequencing and bioinformatics analysis.Methods:BV2 cells were stimulated by lipopolysaccharide to establish microglia inflammation model. The levels of IL-6 and TNF-α were detected by ELISA and RT-qPCR. The established microglia inflammation model was sequenced by transcriptome sequencing, and the differentially expressed genes were screened by bioinformatics method. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes were performed. The protein-protein interaction network of differentially expressed genes was constructed by using string database, and the protein-protein interaction network was visualized by using Cytoscape software. The protein interaction network module was extracted by using MCODE app. The hub gene was extracted by using cytohubba app and was verified through RT-qPCR. We conducted enrichment analysis of hub genes, predicted their targeted miRNAs and interacting drugs.Results:The microglia inflammation model was successfully established and verified by ELISA and RT-qPCR. We screened 434 differentially expressed genes by bioinformatics analysis of transcriptome sequencing results. GO analysis showed that these differentially expressed genes were mainly concentrated in cellular response to cytokine stimulus, inflammatory response, regulation of response to external stimulation. KEGG analysis showed that these differentially expressed genes were mainly concentrated in Chemokine signaling pathway, TNF signaling pathway, IL-17 signaling pathway. We constructed the protein interaction network of these differentially expressed genes, and carried out module analysis and extraction of hub genes. Most of hub genes are located in module 1, and the seed gene of module 1 is S1pr1. Hub genes include S1pr1, Cxcr4, Cx3cl1, Cx3cr1, Cxcl10, Cxcl2, Ccl4, Ccl5, Ccl9, Fpr1. RT-qPCR results showed that compared with the culture medium group, the mRNA expressions of S1pr1, Cxcr4, Cx3cl1 and Cx3cr1 were down-regulated, and the mRNA expressions of Cxcl10, Cxcl2, Ccl4, Ccl5, Ccl9 and Fpr1 were up-regulated in the LPS group. The enrichment analysis of hub genes mainly focused on chemokine-mediated signaling pathway, Class A/1 (Rhodopsin-like receptors), cell chemotaxis and so on. Drugs and miRNAs that may interact with hub genes were predicted. Conclusion:Through transcriptome sequencing and bioinformatics analysis of microglia inflammation model, differentially expressed genes were screened, hub genes and seed genes were extracted, which will help us further understand the molecular mechanism of microglia inflammation and provide potential targets for the treatment of related diseases.

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