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Travis J, Malone M, Hu H, Baten A, Johani K, Huygens F, Vickery K, Benkendorff K. The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing. BMC Microbiol 2020; 20:163. [PMID: 32546123 PMCID: PMC7296698 DOI: 10.1186/s12866-020-01843-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Health-care professionals need to collect wound samples to identify potential pathogens that contribute to wound infection. Obtaining appropriate samples from diabetic foot ulcers (DFUs) where there is a suspicion of infection is of high importance. Paired swabs and tissue biopsies were collected from DFUs and both sampling techniques were compared using 16S rRNA gene sequencing. Results Mean bacterial abundance determined using quantitative polymerase chain reaction (qPCR) was significantly lower in tissue biopsies (p = 0.03). The mean number of reads across all samples was significantly higher in wound swabs \documentclass[12pt]{minimal}
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\begin{document}$$ \Big(\overline{X} $$\end{document}(X¯ = 32,014) compared to tissue (\documentclass[12pt]{minimal}
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\begin{document}$$ \overline{X} $$\end{document}X¯ = 15,256, p = 0.001). Tissue biopsies exhibited greater overall diversity of bacteria relative to swabs (Shannon’s H diversity p = 0.009). However, based on a presence/absence analysis of all paired samples, the frequency of occurrence of bacteria from genera of known and potential pathogens was generally higher in wound swabs than tissue biopsies. Multivariate analysis identified significantly different bacterial communities in swabs compared to tissue (p = 0.001). There was minimal correlation between paired wound swabs and tissue biopsies in the number and types of microorganisms. RELATE analysis revealed low concordance between paired DFU swab and tissue biopsy samples (Rho = 0.043, p = 0.34). Conclusions Using 16S rRNA gene sequencing this study identifies the potential for using less invasive swabs to recover high relative abundances of known and potential pathogen genera from DFUs when compared to the gold standard collection method of tissue biopsy.
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Affiliation(s)
- J Travis
- School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - M Malone
- Limb Preservation and Wound Research Academic Unit, Western Sydney LHD, Liverpool, Sydney, NSW, 2170, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Campbelltown Campus, Liverpool, Sydney, 2170, Australia.,Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, 2170, Australia
| | - H Hu
- Surgical Infection Research Group Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - A Baten
- Agresearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - K Johani
- Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, 2170, Australia.,Central Military Laboratories and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - F Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Herston, QLD, Australia.,School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - K Vickery
- Surgical Infection Research Group Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - K Benkendorff
- School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia. .,National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, Australia.
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Wang C, Chen Y, Wang Y, Liu X, Liu Y, Li Y, Chen H, Fan C, Wu D, Yang J. Inhibition of COX-2, mPGES-1 and CYP4A by isoliquiritigenin blocks the angiogenic Akt signaling in glioma through ceRNA effect of miR-194-5p and lncRNA NEAT1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:371. [PMID: 31438982 PMCID: PMC6704644 DOI: 10.1186/s13046-019-1361-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/06/2019] [Indexed: 11/10/2022]
Abstract
Background Arachidonic acid (AA) metabolic enzymes including cyclooxygenase-2 (COX-2), microsomal prostaglandin E synthase-1 (mPGES-1) and cytochrome P450 (CYP) 4A11 play important roles in glioma angiogenesis. Thus, there is an urgent need to identify the underlying mechanisms and develop strategies to overcome them. Methods A homology model of human CYP4A11 was constructed using SYBYL-X 2.0. Structure-based virtual screening against COX-2, mPGES-1 and CYP4A11was performed using the Surflex-Dock of the SYBYL suite. The candidates were further evaluated their antiangiogenic activities in a zebrafish embryo and rabbit corneal angiogenesis model. Laser doppler analysis was used to measure tumor perfusion. The expression of CD31 and α-SMA was measured by immunofluorescence. Western blot was used to measure the expression of HIF-1, Akt and p-Akt. The gene expression of FGF-2, G-CSF, PDGF, TGF-β, Tie-2, VEGF, lncRNA NEAT1 and miR-194-5p were determined using qPCR. The production of FGF-2, TGF-β and VEGF were analyzed using ELISA. Bioinformatic analysis and luciferase reporter assays confirmed the interaction between lncRNA NEAT1 and miR-194-5p. Results The nearly 36,043 compounds from the Traditional Chinese Medicine (TCM) database were screened against COX-2, mPGES-1 and CYP4A11 3D models, and the 17 top flavonoids were identified. In zebrafish screening, isoliquiritigenin (ISL) exhibited the most potent antiangiogenic activities with the EC50 values of 5.9 μM. Conversely, the antiangiogenic effects of ISL in the zebrafish and rabbit corneal models were partly reversed by 20-hydroxyeicosatetraenoic acid (20-HETE) or prostaglandin E2 (PGE2). ISL normalized glioma vasculature and improved the efficacy of temozolomide therapy in the rat C6 glioma model. Inhibition of COX-2, mPGES-1 and CYP4A by ISL decreased FGF-2, TGF-β and VEGF production in the C6 and U87 glioma cells with p-Akt downregulation, which was reversed by Akt overexpression. Furthermore, ISL downregulated lncRNA NEAT1 but upregulated miR-194-5p in the U87 glioma cell. Importantly, lncRNA NEAT1 overexpression reversed ISL-mediated increase in miR-194-5p expression, and thereby attenuated FGF-2, TGF-β and VEGF production. Conclusions Reprogramming COX-2, mPGES-1 and CYP4A mediated-AA metabolism in glioma by flavonoid ISL inhibits the angiogenic Akt- FGF-2/TGF-β/VEGF signaling through ceRNA effect of miR-194-5p and lncRNA NEAT1, and may serve as a novel therapeutic strategy for human glioma. Electronic supplementary material The online version of this article (10.1186/s13046-019-1361-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chenlong Wang
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.,Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Yaxin Chen
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Yang Wang
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Xiaoxiao Liu
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Yanzhuo Liu
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Ying Li
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China
| | - Honglei Chen
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chengpeng Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Dongfang Wu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan, 430071, China.
| | - Jing Yang
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Donghu Road 185, Wuhan, 430071, China.
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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Wang C, Li Y, Chen H, Huang K, Liu X, Qiu M, Liu Y, Yang Y, Yang J. CYP4X1 Inhibition by Flavonoid CH625 Normalizes Glioma Vasculature through Reprogramming TAMs via CB2 and EGFR-STAT3 Axis. J Pharmacol Exp Ther 2018; 365:72-83. [PMID: 29437915 DOI: 10.1124/jpet.117.247130] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/29/2018] [Indexed: 01/03/2023] Open
Abstract
Tumor-associated macrophages (TAMs) are pivotal effector cells in angiogenesis. Here, we tested whether CYP4X1 inhibition in TAMs by flavonoid CH625 prolongs survival and normalizes glioma vasculature. CH625 was selected against the CYP4X1 3D model by virtual screening and showed inhibitory activity on the CYP4X1 catalytic production of 14,15-EET-EA in the M2-polarized human peripheral blood mononuclear cells (IC50 = 16.5 μM). CH625 improved survival and reduced tumor burden in the C6 and GL261 glioma intracranial and subcutaneous model. In addition, CH625 normalized vasculature (evidenced by a decrease in microvessel density and HIF-1α expression and an increase in tumor perfusion, pericyte coverage, and efficacy of temozolomide therapy) accompanied with the decreased secretion of 14,15-EET-EA, VEGF, and TGF-β in the TAMs. Furthermore, CH625 attenuated vascular abnormalization and immunosuppression induced by coimplantation of GL261 cells with CYP4X1high macrophages. In vitro TAM polarization away from the M2 phenotype by CH625 inhibited proliferation and migration of endothelial cells, enhanced pericyte migration and T cell proliferation, and decreased VEGF and TGF-β production accompanied with the downregulation of CB2 and EGFR-dependent downstream STAT3 expression. These effects were reversed by overexpression of CYP4X1 and STAT3 or exogenous addition of 14,15-EET-EA, VEGF, TGF-β, EGF, and CB2 inhibitor AM630. These results suggest that CYP4X1 inhibition in TAMs by CH625 prolongs survival and normalizes tumor vasculature in glioma via CB2 and EGFR-STAT3 axis and may serve as a novel therapeutic strategy for human glioma.
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Affiliation(s)
- Chenlong Wang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Ying Li
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Honglei Chen
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Keqing Huang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Xiaoxiao Liu
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Miao Qiu
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Yanzhuo Liu
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Yuqing Yang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
| | - Jing Yang
- Department of Pharmacology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases (C.W., Y.L., K.H., X.L., M.Q., Y.L., J.Y.), Experimental Teaching Center (J.Y.), and Department of Pathology and Pathophysiology (H.C.), School of Basic Medical Sciences, Wuhan University, Wuhan, China; Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, South-central University for Nationalities, Wuhan, China (C.W.); and Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey (Y.Y.)
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