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Dong WW, Feng Z, Zhang YQ, Ruan ZS, Jiang L. Potential mechanism and key genes involved in mechanical ventilation and lipopolysaccharide‑induced acute lung injury. Mol Med Rep 2020; 22:4265-4277. [PMID: 33000237 PMCID: PMC7533521 DOI: 10.3892/mmr.2020.11507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/10/2020] [Indexed: 01/21/2023] Open
Abstract
Mechanical ventilation (MV) and lipopolysaccharide (LPS) infection are common causes of acute lung injury. The aim of the present study was to identify the key genes and potential mechanisms involved in mechanical ventilation (MV) and lipopolysaccharide (LPS)-induced acute lung injury (ALI). Gene expression data of adult C57BL/6 mice with ALI induced by inhaling LPS, MV and LPS + MV were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) associated with MV, LPS and LPS + MV were screened, followed by functional enrichment analysis, protein-protein interaction network construction, and prediction of transcription factors and small molecule drugs. Finally, the expression of key genes was verified in vivo using reverse transcription-quantitative PCR. A total of 63, 538 and 1,635 DEGs were associated with MV, LPS and LPS + MV, respectively. MV-associated genes were significantly enriched in the ‘purine ribonucleotide metabolic process’. LPS and LPS + MV-associated genes were significantly enriched in ‘cellular response to cytokine stimulus’ and ‘cell chemotaxis’. All three conditions were enriched in ‘TNF signaling pathway’ and ‘IL-17 signaling pathway’. Expression levels of C-X-C motif chemokine ligand (CXCL)2, CXCL3 and CXCL10 were upregulated in the LPS and LPS + MV groups. Adenosine A2b receptor, zinc finger and BTB domain-containing 16 and hydroxycarboxylic acid receptor 2 were identified as DEGs in the MV group. Compared with the control group, Early growth response 1 and activating TF 3 was upregulated in all three groups. Similarities and differences were observed among the MV- and LPS-induced ALI, and MV may enhance the effects of LPS on gene expression. MV may affect urine ribonucleotide metabolic-related processes, whereas LPS may cause cell chemotaxis and cytokine stimulus responses in ALI progression. The inflammatory response was shared by MV and LPS. The results of the present study may provide insight into a theoretical basis for the study and treatment of ALI.
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Affiliation(s)
- Wen-Wen Dong
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Zhou Feng
- Department of Anesthesiology, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China
| | - Yun-Qian Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Zheng-Shang Ruan
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
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Wang RS, Loscalzo J. Illuminating drug action by network integration of disease genes: a case study of myocardial infarction. Mol Biosyst 2017; 12:1653-66. [PMID: 27004607 DOI: 10.1039/c6mb00052e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Drug discovery has produced many successful therapeutic agents; however, most of these drugs were developed without a deep understanding of the system-wide mechanisms of action responsible for their indications. Gene-disease associations produced by molecular and genetic studies of complex diseases provide great opportunities for a system-level understanding of drug activity. In this study, we focused on acute myocardial infarction (MI) and conducted an integrative network analysis to illuminate drug actions. We integrated MI drugs, MI drug interactors, drug targets, and MI disease genes into the human interactome and showed that MI drug targets are significantly proximate to MI disease proteins. We then constructed a bipartite network of MI-related drug targets and MI disease proteins and derived 12 drug-target-disease (DTD) modules. We assessed the biological relevance of these modules and demonstrated the benefits of incorporating disease genes. The results indicate that DTD modules provide insights into the mechanisms of action of MI drugs and the cardiovascular (side) effects of non-MI drugs.
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Affiliation(s)
- Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
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Zhang L, Li J, Liang A, Liu Y, Deng B, Wang H. Immune-related chemotactic factors were found in acute coronary syndromes by bioinformatics. Mol Biol Rep 2014; 41:4389-95. [PMID: 24599781 DOI: 10.1007/s11033-014-3310-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
DNA microarray data for thrombus-related leukocyte from patients with acute coronary syndrome (ACS) was analyzed to acquire key genes associated with ACS. Microarray data set GSE19339, including four ACS patients' samples and four normal samples, were downloaded from Gene Expression Omnibus database. Raw data was pre-processed and differentially expressed genes (DEGs) were identified by Affy packages of R. The interaction network was established with STRING. DrugBank was retrieved to obtain relevant small molecules. A total of 487 differentially expressed genes were identified as DEGs between normal and disease samples. Among which, ten up-regulated genes belonging to chemokine family (CCL2, CCR1, CXCL3, CXCL2, CCL8, CXCL11, CCL7, IL10, CCL22 and CCL20) were related to inflammatory response. In addition, two inhibitors of CCL2 (L-Mimosine) were retrieved from the DrugBank database. Considering the roles of inflammatory response in the progression of ACS and the functions of the ten up-regulated genes, we speculated that these genes might be related to ACS. Moreover, the inhibitors could provide guidelines for future drug design acting on these genes.
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Affiliation(s)
- Lei Zhang
- Department of Special Needs Medical Branch, Shanghai Tongji Hospital, School of Medicine, Tongji University, No. 389 Xincun Road, Putuo District, Shanghai, 200065, China,
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Abstract
BACKGROUND The recruitment of immune cells by chemokines and the regulation of endometrial cell apoptosis are critical aspects of endometriosis biology. Here, we review the local (paracrine) and systemic hormone (endocrine) modulation of these two specific, but highly related phenomena. METHODS We searched Pubmed for items published in English between September 1991 and September 2011 and selected the studies evaluating the effects of hormones on chemokines or apoptosis in normal human endometrium and endometriosis. RESULTS Estradiol has proinflammatory and antiapoptotic effects in endometrial cells, and these effects appear to be exacerbated in women with endometriosis. In these women, physiological estradiol concentrations are able to induce an enhanced inflammatory response mediated by local chemokine production and to reinforce mechanisms of cell survival mediated by extracellular signal-regulated kinases and Bcl-2. The main effect of progestogens is to inhibit interleukin-8 and other chemokines in stromal cells from both eutopic and ectopic endometrium. Progesterone is also effective in inducing apoptosis in endometrial and endometriotic cells through the inhibition of Bcl-2 and nuclear factor-κB. CONCLUSIONS Estrogens and progestogens modulate chemotaxis and apoptosis in human endometrium and endometriotic cells and tissues. These endocrine and paracrine pathways are perturbed in women with endometriosis, contributing to inflammatory responses, abnormal tissue remodeling, therapeutic refractoriness and disease persistence. Ultimately, they promote adhesion formation and the clinical symptoms of pelvic pain and infertility. A more detailed understanding of the molecular mechanisms involved will offer new opportunities for novel pharmacological strategies to diagnose and treat endometriosis.
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Affiliation(s)
- Fernando M Reis
- Department of Obstetrics and Gynecology, University of Minas Gerais, Belo Horizonte, Brazil
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Wu Y, Starzinski-Powitz A, Guo SW. Trichostatin A, a histone deacetylase inhibitor, attenuates invasiveness and reactivates E-cadherin expression in immortalized endometriotic cells. Reprod Sci 2007; 14:374-82. [PMID: 17644810 DOI: 10.1177/1933719107302913] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The objective of this study is to determine whether trichostatin A (TSA) can suppress the invasiveness of 2 endometriotic cell lines known to be invasive and E-cadherin negative. The membrane invasion culture system was used to assess cell invasion using invasive and a noninvasive bladder cancer cell lines as positive and negative controls, respectively. The E-cadherin mRNA levels and protein expression were evaluated by real-time reverse transcriptase polymerase chain reaction and Western blot analysis, respectively. The authors found that TSA attenuates the invasiveness of 2 cell lines in the presence or absence of tumor necrosis factor alpha (TNFalpha) stimulation. In addition, TSA treatment reactivates E-cadherin gene and protein expression in these cell lines. These results, along with recent findings that TSA suppresses proliferation, interleukin-1 beta-induced cyclo-oxygenase 2 expression, and constitutive or TNFalpha-stimulated nuclear factor kappa B activation in endometrial and endometriotic cells, makes histone deacetylase inhibitors a promising class of compounds for novel and more effective medical treatment of endometriosis, especially given the mounting evidence that endometrios be an epigenetic disease.
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Affiliation(s)
- Yan Wu
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226-0509, USA
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Huber AV, Saleh L, Prast J, Haslinger P, Knöfler M. Human chorionic gonadotrophin attenuates NF-kappaB activation and cytokine expression of endometriotic stromal cells. Mol Hum Reprod 2007; 13:595-604. [PMID: 17525069 DOI: 10.1093/molehr/gam032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, a clinical study provided evidence that treatment of endometriotic women with human chorionic gonadotrophin (hCG) alleviates disease-related pain and sleeplessness suggesting therapeutic effects of the hormone. Since endometriosis is associated with aberrant concentrations of inflammatory mediators in the peritoneal fluid, we investigated whether hCG may affect cytokine-dependent activation of the key-regulatory transcription factor NF-kappaB and expression of two nuclear factor kappa B (NF-kappaB)-inducible genes, tumour necrosing factor (TNF-alpha) and interleukin (IL)-1beta, in stromal cells isolated from ectopic endometriotic tissues. Electrophoretic mobility shift assay revealed that treatment of these cultures with the urinary preparation hCG-A suppressed TNF-alpha- or IL-1beta-induced NF-kappaB DNA-binding activity, whereas another urinary hCG preparation (hCG-B) was less effective. Recombinant alphahCG or epidermal growth factor (EGF), a contaminant of some urinary hCG preparations, did not alter cytokine-dependent NF-kappaB activation. Immunofluorescene of its p65 subunit revealed that pre-incubation with hCG-A strongly decreased TNF-alpha-dependent nuclear expression of NF-kappaB. Accordingly, hCG-A diminished IL-1beta-induced TNF-alpha transcript levels and protein release measured by quantitative real-time PCR and enzyme-linked immunosorbent assay. The hormone also attenuated TNF-alpha-dependent mRNA expression of IL-1beta. Western blot analyses revealed that hCG-A impaired TNF-alpha-mediated phosphorylation and degradation of the inhibitor IkappaBalpha suggesting that the hormone may reduce nuclear import of NF-kappaB by stabilizing its inhibitor. The data suggest that hCG attenuates inflammation-dependent NF-kappaB activation and cytokine expression that could provide one explanation for the beneficial role of the hormone in endometriotic patients.
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Affiliation(s)
- A V Huber
- Department of Obstetrics and Gynecology, Medical University of Vienna, AKH, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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Song M, Karabina SA, Kavtaradze N, Murphy AA, Parthasarathy S. Presence of endometrial epithelial cells in the peritoneal cavity and the mesothelial inflammatory response. Fertil Steril 2003; 79 Suppl 1:789-94. [PMID: 12620492 DOI: 10.1016/s0015-0282(02)04836-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To determine the contribution of endometrial cells in the development of endometriosis. Specifically the response of the mesothelium to endometrial cells in the production of monocyte chemotactic protein-1 (MCP-1), interleukin-6 (IL-6), and IL-8 was studied. DESIGN In vitro study. SETTING University Research Laboratory. PATIENT(S) None. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Cellular MCP-1, IL-6 secretion and MCP-1, and IL-6 and IL-8 messenger RNA expression were evaluated by ELISA and reverse transcription-polymerase chain reaction (RT-PCR) assay. RESULT(S) The mesothelial cells produced more MCP-1 and IL-6 than endometrial epithelial and stromal cells. Mesothelial cells cultured in the presence of endometrial epithelial cells produced even greater levels of MCP-1 and IL-6 than those cultured in the presence of stromal cells or cultured alone. The MCP-1, IL-6, and IL-8 mRNA expression also increased when mesothelial cells were co-cultured with endometrial epithelial cells. CONCLUSION(S) The results suggest that endometrial epithelial cells may be important in evoking the inflammatory reaction in the peritoneal cavity during retrograde menstruation and that mesothelial cells may play an important role in the chemotaxis of monocytes and in the inflammatory process during the development of endometriosis.
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Affiliation(s)
- Mingqing Song
- Emory Center for Advanced Research on Women's Health, Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Abstract
Monocyte chemoattractant protein-1 (MCP-1) has been implicated in many inflammatory and autoimmune diseases. The G-protein-coupled receptor CCR-2B is probably the most important MCP-1 receptor in vivo, and loss of MCP-1 effector function alone is sufficient to impair monocytic trafficking in inflammation models. MCP-1 signalling appears to be a relevant target, especially in rheumatoid arthritis (RA). In RA patients, MCP-1 is produced by synovial cells and infiltrating monocytes, plasma MCP-1 concentrations correlate with swollen joint count, and elevated serum MCP-1 concentrations were found in juvenile RA in patients with active disease. Modulation of MCP-1 signalling in experimental RA showed beneficial effects on inflammation and joint destruction. With respect to chronic neuroinflammation, a critical role for MCP-1 has been established in animal models for multiple sclerosis. In acute neuroinflammation, experimental evidence for a detrimental role of MCP-1 in stroke and excitotoxic injury has been found. Several selective small molecular weight CCR-2B antagonists and MCP-1-blocking antibodies have been described. The proof for the validity of targeting MCP-1 signalling in disease, however, has yet to be established in clinical trials.
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MESH Headings
- Alzheimer Disease/drug therapy
- Animals
- Anti-Inflammatory Agents/pharmacology
- Anti-Inflammatory Agents/therapeutic use
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Antirheumatic Agents/pharmacology
- Antirheumatic Agents/therapeutic use
- Arthritis, Rheumatoid/drug therapy
- Arthritis, Rheumatoid/physiopathology
- Central Nervous System/drug effects
- Central Nervous System/injuries
- Chemokine CCL2/antagonists & inhibitors
- Chemokine CCL2/deficiency
- Chemokine CCL2/genetics
- Chemokine CCL2/physiology
- Drug Design
- Encephalomyelitis, Autoimmune, Experimental/drug therapy
- Humans
- Inflammation/drug therapy
- Mice
- Mice, Inbred MRL lpr
- Mice, Knockout
- Models, Molecular
- Molecular Structure
- Multiple Sclerosis/drug therapy
- Obesity/drug therapy
- Receptors, CCR2
- Receptors, Chemokine/antagonists & inhibitors
- Receptors, Chemokine/deficiency
- Receptors, Chemokine/genetics
- Receptors, Chemokine/physiology
- Signal Transduction/drug effects
- Signal Transduction/physiology
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Affiliation(s)
- Janet Dawson
- Arthritis and Bone Metabolism Research, Novartis Pharma AG, Basel, Switzerland
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