scholarly journals Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen

2017 ◽  
Vol 114 (40) ◽  
pp. E8498-E8507 ◽  
Author(s):  
Hackwon Do ◽  
Nishanth Makthal ◽  
Arica R. VanderWal ◽  
Mandy Rettel ◽  
Mikhail M. Savitski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Bacterial Pathogen ◽  
Global Gene Expression ◽  
Intercellular Signaling ◽  
Human Pathogen ◽  
Unknown Peptide ◽  
Peptide Secretion ◽  
Complex Signaling

Successful pathogens use complex signaling mechanisms to monitor their environment and reprogram global gene expression during specific stages of infection. Group A Streptococcus (GAS) is a major human pathogen that causes significant disease burden worldwide. A secreted cysteine protease known as streptococcal pyrogenic exotoxin B (SpeB) is a key virulence factor that is produced abundantly during infection and is critical for GAS pathogenesis. Although identified nearly a century ago, the molecular basis for growth phase control of speB gene expression remains unknown. We have discovered that GAS uses a previously unknown peptide-mediated intercellular signaling system to control SpeB production, alter global gene expression, and enhance virulence. GAS produces an eight-amino acid leaderless peptide [SpeB-inducing peptide (SIP)] during high cell density and uses the secreted peptide for cell-to-cell signaling to induce population-wide speB expression. The SIP signaling pathway includes peptide secretion, reimportation into the cytosol, and interaction with the intracellular global gene regulator Regulator of Protease B (RopB), resulting in SIP-dependent modulation of DNA binding and regulatory activity of RopB. Notably, SIP signaling causes differential expression of ∼14% of GAS core genes. Several genes that encode toxins and other virulence genes that enhance pathogen dissemination and infection are significantly up-regulated. Using three mouse infection models, we show that the SIP signaling pathway is active during infection and contributes significantly to GAS pathogenesis at multiple host anatomic sites. Together, our results delineate the molecular mechanisms involved in a previously undescribed virulence regulatory pathway of an important human pathogen and suggest new therapeutic strategies.

scholarly journals Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8276 ◽  
Author(s):  
Yichong Zhang ◽  
Yuanbo Zhan ◽  
Yuhui Kou ◽  
Xiaofeng Yin ◽  
Yanhua Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Text Mining ◽  
Heterotopic Ossification ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Egf Receptor ◽  
Enrichment Analysis ◽  
Biological Pathways ◽  
Specific Gene ◽  
Cord Injury

Background Neurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO. Methods In this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO. Results We identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO. Conclusions These results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies.

scholarly journals Identifying Main Genes and Pathways by Using Gene Expression Profiling in Primary Immunodeficiency HOIL-1/RBCK1 Disorder Patients

2021 ◽  
Author(s):  
Khyber Shinwari ◽  
Guojun Liu ◽  
Mikhail Bolkov ◽  
Monib Ullah ◽  
Irina Tuzankina
Keyword(s):  
Gene Expression ◽  
Cell Adhesion ◽  
Signaling Pathway ◽  
Focal Adhesion ◽  
Molecular Mechanisms ◽  
Kegg Pathway ◽  
Wnt Signaling Pathway ◽  
Negative Regulation ◽  
Coagulation Cascade ◽  
Bacterial Disease

HOIL-1/RBCK1 deficiency is a new autosomal receiving disorder with dysfunctional cellular responses to pro-inflammatory cytokines, leading to auto-inflammation, pyogenic bacterial disease, and muscle amylopectinosis growth. Our study with integrated bioinformatics studies of the feature genes and the correlative gene functions, investigated the molecular mechanisms of RBCK1 deficiency. GSE31064 dataset expression profile was downloaded from the Omnibus Gene Expression database. Between RBCK1, MYDK88, NEMO deficient fibroblast, and healthy fibroblast specimens, differentially expressed genes (DEGs) were defined. Gene ontology (GO) gene role enrichment analysis and the Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Annotation, Visualization and Integrated Discovery Database (DAVID). The protein-protein interaction (PPI) of these DEGs was visualized using Cytoscape. GO analysis revealed that the “Skeletal system development, Extracellular matrix organization, Positive regulation of cell migration, Negative regulation of canonical Wnt signaling pathway, Cell adhesion, Angiogenesis and Negative regulation of BMP signaling pathway, Serine-type carboxypeptidase activity, Polysaccharide binding, Calcium ion binding, frizzled binding, Neuropilin binding, and cell adhesion molecule binding, extracellular exosome, extracellular space, extracellular region, lysosomal lumen, endoplasmic reticulum lumen, cell surface and focal adhesion to BP, MF, and CC, respectively. The study of the KEGG pathway showed that the complement and coagulation cascade, interactions of the ECM receptor, PI3K-Akt signaling pathway, PPAR signaling pathway, TGF-beta signaling pathway, cancer pathway, viral carcinogenesis and focal adhesion pathway were closely correlated with the incidence of RBCK1 deficiency. Importantly, it has been predicted that TK1, AURKB, CDCA2, UBE2C, KIFC1, CEP55, CDCA3, GINS2, MCM6 and CDC45 are significantly associated with RCBK1 deficiency. Our study offers a record of damaged genes and pathways in RCBK1, which will boost the understanding of RBCK1 deficiency pathogenesis and other inherent immunodeficiency diseases. This research has the potential and can possibly use in the clinic for diagnosis and targeted therapy of HOIL-1/RBCK1 disorder and other inherent immunodeficiencies.

scholarly journals Global transcriptome analysis of rat hypothalamic arcuate nucleus demonstrates reversal of hypothalamic gliosis following surgically and diet induced weight loss

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pernille Barkholt ◽  
Kristoffer T. G. Rigbolt ◽  
Mechthilde Falkenhahn ◽  
Thomas Hübschle ◽  
Uwe Schwahn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Weight Loss ◽  
Molecular Mechanisms ◽  
Arcuate Nucleus ◽  
Gene Expression Signature ◽  
Global Gene Expression ◽  
Metabolic Effects ◽  
Expression Of Genes ◽  
Hypothalamic Arcuate Nucleus ◽  
Laser Capture

Abstract The central mechanisms underlying the marked beneficial metabolic effects of bariatric surgery are unclear. Here, we characterized global gene expression in the hypothalamic arcuate nucleus (Arc) in diet-induced obese (DIO) rats following Roux-en-Y gastric bypass (RYGB). 60 days post-RYGB, the Arc was isolated by laser-capture microdissection and global gene expression was assessed by RNA sequencing. RYGB lowered body weight and adiposity as compared to sham-operated DIO rats. Discrete transcriptome changes were observed in the Arc following RYGB, including differential expression of genes associated with inflammation and neuropeptide signaling. RYGB reduced gene expression of glial cell markers, including Gfap, Aif1 and Timp1, confirmed by a lower number of GFAP immunopositive astrocyte profiles in the Arc. Sham-operated weight-matched rats demonstrated a similar glial gene expression signature, suggesting that RYGB and dietary restriction have common effects on hypothalamic gliosis. Considering that RYGB surgery also led to increased orexigenic and decreased anorexigenic gene expression, this may signify increased hunger-associated signaling at the level of the Arc. Hence, induction of counterregulatory molecular mechanisms downstream from the Arc may play an important role in RYGB-induced weight loss.

scholarly journals Trisomy 21 and Down syndrome: a short review

2008 ◽  
Vol 68 (2) ◽  
pp. 447-452 ◽  
Author(s):  
CA. Sommer ◽  
F. Henrique-Silva
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Short Review ◽  
Complex Disorder ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Chromosome Segments

Even though the molecular mechanisms underlying the Down syndrome (DS) phenotypes remain obscure, the characterization of the genes and conserved non-genic sequences of HSA21 together with large-scale gene expression studies in DS tissues are enhancing our understanding of this complex disorder. Also, mouse models of DS provide invaluable tools to correlate genes or chromosome segments to specific phenotypes. Here we discuss the possible contribution of HSA21 genes to DS and data from global gene expression studies of trisomic samples.

scholarly journals Retinal Genomic Fabrics Remodeling after Optic Nerve Injury

2021 ◽  
Author(s):  
Pedro Henrique Victorino ◽  
Camila Marra ◽  
Dumitru Andrei Iacobas ◽  
Sanda Iacobas ◽  
David C Spray ◽  
...  
Keyword(s):  
Gene Expression ◽  
Optic Nerve ◽  
Notch Signaling ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Notch Signaling Pathway ◽  
Complement Cascade ◽  
Gene Expressions ◽  
Nerve Crush ◽  
Individual Gene

Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the Genomic Fabric Paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers for the expression of each gene 3 independent characteristics: level, variability and correlation with each other gene. Thus, the 17,657 quantified genes our study generated a total of 155,911,310 values to analyze. This represents 8,830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with DiI. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted Protein-Protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among up-regulated genes. Enrichment analysis showed that Complement Cascade and Notch Signaling Pathway, as well as Oxidative Stress and Kit Receptor Pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pair-wise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in Complement Cascade and Notch Signaling Pathway. This deep bioinformatic study provides novel insights beyond the regulation of individual gene expression and discloses changes in the control of expression of Complement Cascade and Notch Signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.

scholarly journals Identification of Key Genes and Pathways Associated with Mast Cells Resting in Meningioma

2020 ◽  
Author(s):  
Hui Xie ◽  
Xiao-hui Ding ◽  
Ce Yuan ◽  
Jin-jiang Li ◽  
Zhao-yang Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mast Cells ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Risk Model ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Receptor Interaction ◽  
Key Genes

Abstract Background: To identify candidate key genes and pathways related to mast cells resting in meningioma and the underlying molecular mechanisms of meningioma.Methods: Gene expression profiles of GSE43290 and GSE16581 datasets were obtained from the Gene Expression Omnibus (GEO) database. GO and KEGG pathway enrichments of DEGs were analyzed using the ClusterProfiler package in R. The protein-protein interaction network (PPI), and TF-miRNA- mRNA co-expression networks were constructed. Further, the difference in immune infiltration was investigated using the CIBERSORT algorithm.Results: A total of 1499 DEGs were identified between tumor and normal controls. The analysis of the immune cell infiltration landscape showed that the probability of distribution of memory B cells, regulatory T cells (Tregs), and resting mast cells in tumor samples were significantly higher than those in the controls. Moreover, through WGCNA analysis, the module related to mast cells resting contained 158 DEGs, and KEGG pathway analysis revealed that the DEGs were dominant in the TNF signaling pathway, cytokine-cytokine receptor interaction, and IL-17 signaling pathway. Survival analysis of hub genes related to mast cells resting showed that the risk model was constructed based on 9 key genes. The TF-miRNA- mRNA co-regulation network, including MYC-miR-145-5p, TNFAIP3-miR-29c-3p, and TNFAIP3-hsa-miR-335-3p, were obtained. Further, 36 nodes and 197 interactions in the PPI network were identified. Conclusions: The results of this study revealed candidate key genes, miRNAs, and pathways related to mast cells resting involved in meningioma development, providing potential therapeutic targets for meningioma treatment.

scholarly journals Transcriptome Changes in the Mink Uterus during Blastocyst Dormancy and Reactivation

2019 ◽  
Vol 20 (9) ◽  
pp. 2099
Author(s):  
Xinyan Cao ◽  
Jiaping Zhao ◽  
Yong Liu ◽  
Hengxing Ba ◽  
Haijun Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Embryo Implantation ◽  
Global Gene Expression ◽  
Gene Clusters ◽  
Protein Protein Interaction ◽  
Kegg Pathways ◽  
Maternal Regulation

Embryo implantation in the mink follows the pattern of many carnivores, in that preimplantation embryo diapause occurs in every gestation. Details of the gene expression and regulatory networks that terminate embryo diapause remain poorly understood. Illumina RNA-Seq was used to analyze global gene expression changes in the mink uterus during embryo diapause and activation leading to implantation. More than 50 million high quality reads were generated, and assembled into 170,984 unigenes. A total of 1684 differential expressed genes (DEGs) in uteri with blastocysts in diapause were compared to the activated embryo group (p < 0.05). Among these transcripts, 1527 were annotated as known genes, including 963 up-regulated and 564 down-regulated genes. The gene ontology terms for the observed DEGs, included cellular communication, phosphatase activity, extracellular matrix and G-protein couple receptor activity. The KEGG pathways, including PI3K-Akt signaling pathway, focal adhesion and extracellular matrix (ECM)-receptor interactions were the most enriched. A protein-protein interaction (PPI) network was constructed, and hub nodes such as VEGFA, EGF, AKT, IGF1, PIK3C and CCND1 with high degrees of connectivity represent gene clusters expected to play an important role in embryo activation. These results provide novel information for understanding the molecular mechanisms of maternal regulation of embryo activation in mink.

scholarly journals Blood Gene Expression Profile Study Revealed the Activation of Apoptosis and p53 Signaling Pathway May Be the Potential Molecular Mechanisms of Ionizing Radiation Damage and Radiation-Induced Bystander Effects

Dose-Response ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 155932582091418
Author(s):  
Guangyao He ◽  
Anzhou Tang ◽  
Mao Xie ◽  
Wei Xia ◽  
Pengcheng Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Ionizing Radiation ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
P53 Signaling ◽  
Gene Correlation ◽  
Radiation Induced ◽  
P53 Signaling Pathway

Radiotherapy is an effective treatment for local solid tumors, but the mechanism of damage to human body caused by radiation therapy needs further study. In this study, gene expression profiles of human peripheral blood samples exposed to different doses and rates of ionizing radiation (IR) were used for bioinformatics analysis to investigate the mechanism of IR damage and radiation-induced bystander effect (RIBE). Differentially expressed genes analysis, weighted gene correlation network analysis, functional enrichment analysis, hypergeometric test, gene set enrichment analysis, and gene set variation analysis were applied to analyze the data. Moreover, receiver operating characteristic curve analysis was performed to identify core genes of IR damage. Weighted gene correlation network analysis identified 3 modules associated with IR damage, 2 were positively correlated and 1 was negatively correlated. The analysis showed that the positively correlated modules were significantly involved in apoptosis and p53 signaling pathway, and ESR1, ATM, and MYC were potential transcription factors regulating these modules. Thus, the study suggested that apoptosis and p53 signaling pathway may be the potential molecular mechanisms of IR damage and RIBE, which could be driven by ESR1, ATM, and MYC.

Transcriptional gene expression profile in hepatocarcinoma cells induced by acetylsalicylic acid (ASA) in hepatitis C virus (HCV)-subgenomic replicon system.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e22016-e22016
Author(s):  
Clara Patricia Rios Ibarra ◽  
Barbara Verduzco Garza ◽  
Rocio Ortiz Lopez ◽  
Yohann Grondin ◽  
Sonia Lozano Sepulveda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Expression Profile ◽  
Molecular Mechanisms ◽  
Antiviral Effect ◽  
Subgenomic Replicon ◽  
Expression Of Genes ◽  
Antioxidant Agents ◽  
Hepatocarcinoma Cells

e22016 Background: It has been demonstrated that ASA treatment could down-regulate in vitro HCV expression in hepatocarcinoma cells (~50%, p 0.05). However, the signaling pathway induced during ASA antiviral effect has not been elucidated. We analyzed the transcriptional expression profile of Huh-7-HCV-subgenomic replicon cells in presence or absence of ASA in order to identify the signaling pathway and the molecular mechanisms involved in the antiviral effect induced by ASA on HCV expression. Methods: Huh-7-HCV-replicon cells (hepatocarcinoma) were exposed to 4 mM ASA from 24 to 72 hours. Total RNA was isolated, quantified and validated by capillary electrophoresis. After that, we performed a retrotranscription in vitro. Synthesized transcripts were marked with biotin, purified, fragmentized and hybridized in HG-U133 Plus 2 Gene Expression. Hybridization signals were captured with Gen Chip 3000 7G Scanner and analyzed by Expression Console and Dchit Software. Results: After normalization, we obtained hierarchical maps with differentially-expressed genes. Among genetic targets over-expressed, the following stood out CCAAT-enhancer-binding proteins (C/EBP), interleukine-8 (IL-8), cytochrome P450 (CyP450) and methallothioneins (MT) genes were found. Among down-regulated genes we identified ribonucleotide reductase (RR) and superoxide dismutase (SOD) genes. Some of these genes have been previously associated with oxidative stress regulation. All results were validated by real time PCR. Conclusions: We observed that ASA modulates the expression of genes associated with antioxidant role as SOD and methallothioneins. Antioxidant agents can inhibit virus proliferation. HCV decreased antioxidant defense, which promotes the development of hepatic complications caused by HCV infection, including liver cancer. Therefore, ASA could be inducing an antioxidant environment regulating HCV replication. This study provides a tool for identifying novel host factors in hepatocarcinoma cells involved in the antiviral effect regulated by ASA against HCV and improves our understanding of the regulatory mechanism of HCV replication.

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