Effects of Erythrodiol on the Antioxidant Response and Proteome of HepG2 Cells

Erythrodiol (EO) is a pentacyclic triterpenic alcohol found in olive tree leaves and olive oil, and it has important effects on the health properties and quality of olive oil. In this study, we characterized the cytotoxic effects of EO on human hepatocarcinoma (HepG2) cells by studying changes in cell viability, reactive oxygen species (ROS) production, antioxidant defense systems, and the proteome. The results reveal that EO markedly decreased HepG2 cell viability without changing ROS levels. The concentrations of glutathione and NADPH were significantly reduced, with selective changes in the activity of several antioxidant enzymes: glutathione peroxidase, glutathione reductase, glucose 6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase. Proteomic data reveal that EO led to the complete elimination or decreased abundance of 41 and 3 proteins, respectively, and the abundance of 29 proteins increased. The results of functional enrichment analysis show that important metabolic processes and the nuclear transport of mature mRNA were impaired, whereas AMP biosynthesis and cell cycle G2/M phase transition were induced. The transcription factors and miRNAs involved in this response were also identified. These potent antiproliferative effects make EO a good candidate for the further analysis of its hepatic antitumor effects in in vivo studies.

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Viral miRNAs Confer Survival in Host Cells by Targeting Apoptosis Related Host Genes

10.1101/2020.06.10.144469 ◽

2020 ◽

Author(s):

Md. Sajedul Islam ◽

Abul BMMK Islam

Keyword(s):

Target Genes ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Host Cells ◽

Viral Mirnas ◽

Expression Of Genes ◽

Apoptosis Process ◽

Eukaryotic Organisms

AbstractBackgroundmiRNAs are small non-coding RNAs that regulate the expression of genes by RNA silencing method. Like eukaryotic organisms, some viruses also produce miRNAs. While contribution of host miRNA in the prevention of viral pathogenesis has been studied, it is not known very well how viral miRNA can confer its survival in the host. Here we hypothesized that viral miRNAs can bind to the host target genes to confer their pathogenicity by down-regulating specific pathways and related genes that otherwise pose threat to cell survival.Methods and ResultsUsing targets of 168 viral miRNAs from 13 different viruses overrepresentation analysis was done. Functional enrichment analysis of the genes targeted by the miRNAs indicates that viruses target specific immune system and host defense related pathways via miRNA mediated gene silencing. Integration and analysis of the publicly available experimental host gene expression data by RNA-seq provided insight that viruses target host apoptosis process by switching off related genes through miRNA induced mechanisms and thus probably ensure their survival.ConclusionsAs switching off the apoptosis of host cells would provide the viruses with selective advantages in surviving inside host, our findings therefore envisage an important function of viral miRNA which demands further in vivo experiments for better understanding in this regard.

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Pueraria Flos Alleviates Alcoholic Liver Injury Via Regulation of PPARα and MAOA: Deciphering the Effective Forms and Potential Mechanism Based on a Bioinformatics-Integrated Metabolic Profile Strategy and Experimental Validation

10.21203/rs.3.rs-1055239/v1 ◽

2021 ◽

Author(s):

Jialin Qu ◽

Qiuyue Chen ◽

Tianfu Wei ◽

Ning Dou ◽

Dong Shang ◽

...

Keyword(s):

Liver Injury ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Rat Plasma ◽

Functional Enrichment ◽

Network Pharmacology ◽

Potential Mechanism ◽

Effective Form ◽

High Level

Abstract Background: Pueraria Flos, a representative medicinal and edible antidote for alcoholism, has rich clinical experience and remarkable curative effect in the treatment of alcoholic liver disease (ALD). However, its effective forms and hepatoprotective mechanism are remained unknown. Methods: A strategy based on UPLC-QTOF-MS combined with mass defect filtering technique was established for comprehensively identifying prototypes and metabolites absorbed and excreted into rat plasma, urine, bile and feces after oral administration. Then, the absorbed constituents with a relative high level were subjected to the network pharmacology, functional enrichment analysis and molecular docking to clarify the potential mechanism in the treatment of ALD. Furthermore, the therapeutic effect of PF on ALD and predicted mechanisms was further evaluated using a rat model of alcohol-induced liver injury and Western blot analysis. Results: 25 absorbed prototype constituents and 82 metabolites were identified or tentatively characterized with glucuronidation, sulfation, methylation, hydroxylation and reduction as their major metabolic pathways. The constructed absorbed constituent-target-pathway-disease network and docking analysis revealed that 4 metabolic components Te-7XG, genistein-7G-4'S, tectoridin-4'S and Te-7XG-4'S, 2 targets MAOA and PPARA, and 6 pathways related to lipid regulation and amino acid metabolism may play crucial roles in the PF mediated protection against ALD. An in vivo validation in rat further demonstrated that PF alleviated liver injury via activating and suppressing the PPARA and MAOA expression, respectively. Conclusions: The present results not only increase the understanding on the effective form and molecular mechanism of PF mediated protection against ALD, but also promote better application of PF as supplement food and herbal medicine for the treatment of ALD.

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Phosphorylation Targets of DNA-PK and Their Role in HIV-1 Replication

Cells ◽

10.3390/cells9081907 ◽

2020 ◽

Vol 9 (8) ◽

pp. 1907

Author(s):

Andrey Anisenko ◽

Marina Kan ◽

Olga Shadrina ◽

Anna Brattseva ◽

Marina Gottikh

Keyword(s):

Protein Kinase ◽

Kinase Activity ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Dna Double Strand Breaks ◽

Cellular Processes ◽

Hiv 1

The DNA dependent protein kinase (DNA-PK) is a trimeric nuclear complex consisting of a large protein kinase and the Ku heterodimer. The kinase activity of DNA-PK is required for efficient repair of DNA double-strand breaks (DSB) by non-homologous end joining (NHEJ). We also showed that the kinase activity of DNA-PK is essential for post-integrational DNA repair in the case of HIV-1 infection. Besides, DNA-PK is known to participate in such cellular processes as protection of mammalian telomeres, transcription, and some others where the need for its phosphorylating activity is not clearly elucidated. We carried out a systematic search and analysis of DNA-PK targets described in the literature and identified 67 unique DNA-PK targets phosphorylated in response to various in vitro and/or in vivo stimuli. A functional enrichment analysis of DNA-PK targets and determination of protein–protein associations among them were performed. For 27 proteins from these 67 DNA-PK targets, their participation in the HIV-1 life cycle was demonstrated. This information may be useful for studying the functioning of DNA-PK in various cellular processes, as well as in various stages of HIV-1 replication.

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Comprehensive analysis of LncRNAs expression profiles in an in vitro model of steatosis treated with Exendin-4

Journal of Translational Medicine ◽

10.1186/s12967-021-02885-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Khaoula Errafii ◽

Neyla S. Al-Akl ◽

Olfa Khalifa ◽

Abdelilah Arredouani

Keyword(s):

Hepg2 Cells ◽

Expression Profiles ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Alcoholic Fatty Liver ◽

Critical Pathways ◽

Hepatic Lipid Accumulation

Abstract Background and aims The hallmark of non-alcoholic fatty liver disease (NAFLD) is the excessive hepatic lipid accumulation. Currently, no pharmacotherapy exists for NAFLD. However, the glucagon-like peptide-1 receptor agonists have recently emerged as potential therapeutics. Here, we sought to identify the long non-coding RNAs (LncRNAs) associated with the steatosis improvement induced by the GLP-1R agonist Exendin-4 (Ex-4) in vitro. Methods Steatosis was induced in HepG2 cells with oleic acid. The transcriptomic profiling was performed using total RNA extracted from untreated, steatotic, and Ex-4-treated steatotic cells. We validated a subset of differentially expressed LncRNAs with qRT-PCR and identified the most significantly enriched cellular functions associated with the relevant LncRNAs. Results We confirm that Ex-4 improves steatosis in HepG2 cells. We found 379 and 180 differentially expressed LncRNAs between untreated and steatotic cells and between steatotic and Ex-4-treated steatotic cells, respectively. Interestingly, 22 upregulated LncRNAs in steatotic cells became downregulated with Ex-4 exposure, while 50 downregulated LncRNAs in steatotic cells became upregulated in the presence of Ex-4. Although some LncRNAs, such as MALAT1, H19, and NEAT1, were previously associated with NAFLD, the association of others with steatosis and the positive effect of Ex-4 is being reported for the first time. Functional enrichment analysis identified many critical pathways, including fatty acid and pyruvate metabolism, and insulin, PPAR, Wnt, TGF-β, mTOR, VEGF, NOD-like, and Toll-like receptors signaling pathways. Conclusion Our results suggest that LncRNAs may play essential roles in the mechanisms underlying steatosis improvement in response to GLP-1R agonists and warrant further functional studies.

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Proteomics analysis of human intestinal organoids during hypoxia and reoxygenation as a model to study ischemia-reperfusion injury

Cell Death and Disease ◽

10.1038/s41419-020-03379-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Anna M. Kip ◽

Zita Soons ◽

Ronny Mohren ◽

Annet A. M. Duivenvoorden ◽

Anjali A. J. Röth ◽

...

Keyword(s):

Molecular Mechanisms ◽

Ischemia Reperfusion Injury ◽

Profile Analysis ◽

Ischemia Reperfusion ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Intestinal Organoids

AbstractIntestinal ischemia-reperfusion (IR) injury is associated with high mortality rates, which have not improved in the past decades despite advanced insight in its pathophysiology using in vivo animal and human models. The inability to translate previous findings to effective therapies emphasizes the need for a physiologically relevant in vitro model to thoroughly investigate mechanisms of IR-induced epithelial injury and test potential therapies. In this study, we demonstrate the use of human small intestinal organoids to model IR injury by exposing organoids to hypoxia and reoxygenation (HR). A mass-spectrometry-based proteomics approach was applied to characterize organoid differentiation and decipher protein dynamics and molecular mechanisms of IR injury in crypt-like and villus-like human intestinal organoids. We showed successful separation of organoids exhibiting a crypt-like proliferative phenotype, and organoids exhibiting a villus-like phenotype, enriched for enterocytes and goblet cells. Functional enrichment analysis of significantly changing proteins during HR revealed that processes related to mitochondrial metabolism and organization, other metabolic processes, and the immune response were altered in both organoid phenotypes. Changes in protein metabolism, as well as mitophagy pathway and protection against oxidative stress were more pronounced in crypt-like organoids, whereas cellular stress and cell death associated protein changes were more pronounced in villus-like organoids. Profile analysis highlighted several interesting proteins showing a consistent temporal profile during HR in organoids from different origin, such as NDRG1, SDF4 or DMBT1. This study demonstrates that the HR response in human intestinal organoids recapitulates properties of the in vivo IR response. Our findings provide a framework for further investigations to elucidate underlying mechanisms of IR injury in crypt and/or villus separately, and a model to test therapeutics to prevent IR injury.

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Enrichment analysis on regulatory subspaces: a novel direction for the superior description of cellular responses to SARS-CoV-2

10.1101/2021.12.15.472466 ◽

2021 ◽

Author(s):

Pedro P. Rodrigues ◽

Rafael S. Costa ◽

Rui Henriques

Keyword(s):

Machine Learning ◽

Cell Lines ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Learning Approaches ◽

Transcriptional Responses ◽

Kegg Pathways ◽

Regulatory Processes

Statement: The enrichment analysis of discriminative cell transcriptional responses to SARS-CoV-2 infection using biclustering produces a broader set of superiorly enriched GO terms and KEGG pathways against alternative state-of-the-art machine learning approaches, unraveling novel knowledge. Motivation and methods: The comprehensive understanding of the impacts of the SARS-CoV-2 virus on infected cells is still incomplete. This work identifies and analyses the main cell regulatory processes affected and induced by SARS-CoV-2, using transcriptomic data from several infectable cell lines available in public databases and in vivo samples. We propose a new class of statistical models to handle three major challenges, namely the scarcity of observations, the high dimensionality of the data, and the complexity of the interactions between genes. Additionally, we analyse the function of these genes and their interactions within cells to compare them to ones affected by IAV (H1N1), RSV and HPIV3 in the target cell lines. Results: Gathered results show that, although clustering and predictive algorithms aid classic functional enrichment analysis, recent pattern-based biclustering algorithms significantly improve the number and quality of the detected biological processes. Additionally, a comparative analysis of these processes is performed to identify potential pathophysiological characteristics of COVID-19. These are further compared to those identified by other authors for the same virus as well as related ones such as SARS-CoV-1. This approach is particularly relevant due to a lack of other works utilizing more complex machine learning tools within this context.

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IMMU-28. IMMUNOGENOMIC ANALYSIS REVEALS LGALS1 CONTRIBUTES TO THE IMMUNE HETEROGENEITY AND IMMUNOSUPPRESSION IN GLIOMA

Neuro-Oncology ◽

10.1093/neuonc/noaa222.382 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii365-iii365

Author(s):

Qun Chen ◽

Jinquan Cai ◽

Bo Han ◽

Xiangqi Meng

Keyword(s):

Prognostic Significance ◽

Suppressor Cells ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Genomic Variation ◽

Functional Enrichment ◽

Immunosuppressive Microenvironment

Abstract Mutualistic and dynamic communication between tumour cells and the surrounding microenvironment accelerates the initiation, progression, chemoresistance and immune evasion of glioblastoma (GBM). However, the immunosuppressive mechanisms of GBM has not been thoroughly elucidated to date. We enrolled six microenvironmental signatures to identify glioma microenvironmental genes. The functional enrichment analysis such as ssGSEA, ESTIMATE algorithm, Gene Ontology, Pathway analysis is conducted to discover the potential function of microenvironmental genes. In vivo and in vitro experiments are used to verify the immunologic function of LGALS1 in GBM. We screen eight glioma microenvironmental genes from glioma databases, and discover a key immunosuppressive gene (LGALS1 encoding Galectin-1) exhibiting obviously prognostic significance among glioma microenvironmental genes. Gliomas with different LGALS1 expression have specific genomic variation spectrums. Immunosuppression is a predominate characteristic in GBMs with high expression of LGALS1. Knockdown of LGALS1 remodels the GBM immunosuppressive microenvironment by down regulating M2 macrophages and myeloid-derived suppressor cells (MDSCs), and inhibiting immunosuppressive cytokines. Our results thus implied an important role of microenvironmental regulation in glioma malignancy and provided evidences of LGALS1 contributing to immunosuppressive environment in glioma and that targeting LGALS1 could remodel immunosuppressive microenvironment of glioma.

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Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Current Bioinformatics ◽

10.2174/1574893614666190204152500 ◽

2019 ◽

Vol 14 (7) ◽

pp. 591-601 ◽

Cited By ~ 1

Author(s):

Aravind K. Konda ◽

Parasappa R. Sabale ◽

Khela R. Soren ◽

Shanmugavadivel P. Subramaniam ◽

Pallavi Singh ◽

...

Keyword(s):

Expression Pattern ◽

Gene Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Wrky Transcription Factor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Callose Deposition ◽

Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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The Antitumor Effects of Britanin on Hepatocellular Carcinoma Cells and its Real-Time Evaluation by In Vivo Bioluminescence Imaging

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520620666200227092623 ◽

2020 ◽

Vol 20 (9) ◽

pp. 1147-1156

Author(s):

Hanrui Li ◽

GeTao Du ◽

Lu Yang ◽

Liaojun Pang ◽

Yonghua Zhan

Keyword(s):

Hepatocellular Carcinoma ◽

Western Blot ◽

Blot Analysis ◽

Tumor Size ◽

Hepg2 Cells ◽

Western Blot Analysis ◽

Bioluminescence Imaging ◽

Antitumor Effects ◽

In Vivo Bioluminescence Imaging

Background: Hepatocellular carcinoma is cancer with many new cases and the highest mortality rate. Chemotherapy is the most commonly used method for the clinical treatment of hepatocellular carcinoma. Natural products have become clinically important chemotherapeutic drugs due to their great potential for pharmacological development. Many sesquiterpene lactone compounds have been proven to have antitumor effects on hepatocellular carcinoma. Objective: Britanin is a sesquiterpene lactone compound that can be considered for the treatment of hepatocellular carcinoma. The present study aimed to investigate the antitumor effect of britanin. Methods: BEL 7402 and HepG2 cells were used to study the cytotoxicity and antitumor effects of britanin. Preliminary studies on the nuclear factor kappa B pathway were conducted by western blot analysis. A BEL 7402-luc subcutaneous tumor model was established for the in vivo antitumor studies of britanin. In vivo bioluminescence imaging was conducted to monitor changes in tumor size. Results: The results of the cytotoxicity analysis showed that the IC50 values for britanin in BEL 7402 and HepG2 cells were 2.702μM and 6.006μM, respectively. The results of the colony formation demonstrated that the number of cells in a colony was reduced significantly after britanin treatment. And the results of transwell migration assays showed that the migration ability of tumor cells was significantly weakened after treatment with britanin. Tumor size measurements and staining results showed that tumor size was inhibited after britanin treatment. The western blot analysis results showed the inhibition of p65 protein expression and reduced the ratio of Bcl-2/Bax after treatment. Conclusion: A series of in vitro and in vivo experiments demonstrated that britanin had good antitumor effects and provided an option for hepatocellular carcinoma treatment.

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Structural variations in papaya genomes

BMC Genomics ◽

10.1186/s12864-021-07665-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhenyang Liao ◽

Xunxiao Zhang ◽

Shengcheng Zhang ◽

Zhicong Lin ◽

Xingtan Zhang ◽

...

Keyword(s):

Agronomic Traits ◽

Enrichment Analysis ◽

Copy Number Variant ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Structural Variations ◽

Reproduction Traits ◽

Depth Study ◽

Environmental Adaptability ◽

The Impact

Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. Results We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. Conclusions SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.

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