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Lê-Bury P, Druart K, Savin C, Lechat P, Mas Fiol G, Matondo M, Bécavin C, Dussurget O, Pizarro-Cerdá J. Yersiniomics, a Multi-Omics Interactive Database for Yersinia Species. Microbiol Spectr 2023; 11:e0382622. [PMID: 36847572 PMCID: PMC10100798 DOI: 10.1128/spectrum.03826-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
The genus Yersinia includes a large variety of nonpathogenic and life-threatening pathogenic bacteria, which cause a broad spectrum of diseases in humans and animals, such as plague, enteritis, Far East scarlet-like fever (FESLF), and enteric redmouth disease. Like most clinically relevant microorganisms, Yersinia spp. are currently subjected to intense multi-omics investigations whose numbers have increased extensively in recent years, generating massive amounts of data useful for diagnostic and therapeutic developments. The lack of a simple and centralized way to exploit these data led us to design Yersiniomics, a web-based platform allowing straightforward analysis of Yersinia omics data. Yersiniomics contains a curated multi-omics database at its core, gathering 200 genomic, 317 transcriptomic, and 62 proteomic data sets for Yersinia species. It integrates genomic, transcriptomic, and proteomic browsers, a genome viewer, and a heatmap viewer to navigate within genomes and experimental conditions. For streamlined access to structural and functional properties, it directly links each gene to GenBank, the Kyoto Encyclopedia of Genes and Genomes (KEGG), UniProt, InterPro, IntAct, and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and each experiment to Gene Expression Omnibus (GEO), the European Nucleotide Archive (ENA), or the Proteomics Identifications Database (PRIDE). Yersiniomics provides a powerful tool for microbiologists to assist with investigations ranging from specific gene studies to systems biology studies. IMPORTANCE The expanding genus Yersinia is composed of multiple nonpathogenic species and a few pathogenic species, including the deadly etiologic agent of plague, Yersinia pestis. In 2 decades, the number of genomic, transcriptomic, and proteomic studies on Yersinia grew massively, delivering a wealth of data. We developed Yersiniomics, an interactive web-based platform, to centralize and analyze omics data sets on Yersinia species. The platform allows user-friendly navigation between genomic data, expression data, and experimental conditions. Yersiniomics will be a valuable tool to microbiologists.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Karen Druart
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | - Cyril Savin
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
| | - Pierre Lechat
- Institut Pasteur, Université Paris Cité, ALPS, Bioinformatic Hub, Paris, France
| | - Guillem Mas Fiol
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | | | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
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The effect of ciprofloxacin on doxorubicin cytotoxic activity in the acquired resistance to doxorubicin in DU145 prostate carcinoma cells. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:194. [PMID: 36071289 DOI: 10.1007/s12032-022-01787-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/28/2022] [Indexed: 10/14/2022]
Abstract
The present study aimed to assess the influence of ciprofloxacin (CIP) against the doxorubicin (DOX)-resistant androgen-independent prostate cancer DU145 cells. The DOX-resistant DU145 (DU145/DOX20) cells were established by exposing DU145 cells to the increasing concentrations of DOX. The antiproliferative effect of CIP was examined through employing MTT, colony formation, and 3D culture assays. DU145/DOX20 cells exhibited a twofold higher IC50 value for DOX, an increased ABCB1 transporter activity, and some morphological changes accompanied by a decrease in spheroid size, adhesive and migration potential compared to DU145 cells. CIP (5 and 25 µg mL-1) resulted in a higher reduction in the viability of DU145/DOX20 cells than in DU145 cells. DU145/DOX20 cells were more resistant to CIP in 3D culture compared to the 2D one. No spheroid formation was observed for DU145/DOX20 cells treated with DOX and CIP combination. CIP and DOX, alone or in combination, significantly reduced the growth of DU145 spheroids. CIP in combination with 20 nM DOX prevented the colony formation of DU145 cells. The clonogenicity of DU145/DOX20 cells could not be estimated due to their low adhesive potential. CIP alone caused a significant reduction in the migration of DU145 cells and resulted in a more severe decrease in the wound closure ability of DOX-exposed ones. We identified that CIP enhanced DOX sensitivity in DU145 and DU145/DOX20 cells. This study suggested the co-delivery of low concentrations of CIP and DOX may be a promising strategy in treating the DOX-resistant and -sensitive hormone-refractory prostate cancer.
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Evolutionary Instability of Collateral Susceptibility Networks in Ciprofloxacin-Resistant Clinical Escherichia coli Strains. mBio 2022; 13:e0044122. [PMID: 35862779 PMCID: PMC9426462 DOI: 10.1128/mbio.00441-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Collateral sensitivity and resistance occur when resistance development toward one antimicrobial either potentiates or deteriorates the effect of others. Previous reports on collateral effects on susceptibility focus on newly acquired resistance determinants and propose that novel treatment guidelines informed by collateral networks may reduce the evolution, selection, and spread of antimicrobial resistance. In this study, we investigate the evolutionary stability of collateral networks in five ciprofloxacin-resistant, clinical Escherichia coli strains. After 300 generations of experimental evolution without antimicrobials, we show complete fitness restoration in four of five genetic backgrounds and demonstrate evolutionary instability in collateral networks of newly acquired resistance determinants. We show that compensatory mutations reducing efflux expression are the main drivers destabilizing initial collateral networks and identify rpoS as a putative target for compensatory evolution. Our results add another layer of complexity to future predictions and clinical application of collateral networks.
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Souder K, Beatty EJ, McGovern SC, Whaby M, Young E, Pancake J, Weekley D, Rice J, Primerano DA, Denvir J, Horzempa J, Schmitt DM. Role of dipA and pilD in Francisella tularensis Susceptibility to Resazurin. Antibiotics (Basel) 2021; 10:antibiotics10080992. [PMID: 34439042 PMCID: PMC8388984 DOI: 10.3390/antibiotics10080992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 11/16/2022] Open
Abstract
The phenoxazine dye resazurin exhibits bactericidal activity against the Gram-negative pathogens Francisella tularensis and Neisseria gonorrhoeae. One resazurin derivative, resorufin pentyl ether, significantly reduces vaginal colonization by Neisseria gonorrhoeae in a mouse model of infection. The narrow spectrum of bacteria susceptible to resazurin and its derivatives suggests these compounds have a novel mode of action. To identify potential targets of resazurin and mechanisms of resistance, we isolated mutants of F. tularensis subsp. holarctica live vaccine strain (LVS) exhibiting reduced susceptibility to resazurin and performed whole genome sequencing. The genes pilD (FTL_0959) and dipA (FTL_1306) were mutated in half of the 46 resazurin-resistant (RZR) strains sequenced. Complementation of select RZR LVS isolates with wild-type dipA or pilD partially restored sensitivity to resazurin. To further characterize the role of dipA and pilD in resazurin susceptibility, a dipA deletion mutant, ΔdipA, and pilD disruption mutant, FTL_0959d, were generated. Both mutants were less sensitive to killing by resazurin compared to wild-type LVS with phenotypes similar to the spontaneous resazurin-resistant mutants. This study identified a novel role for two genes dipA and pilD in F. tularensis susceptibility to resazurin.
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Affiliation(s)
- Kendall Souder
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Emma J. Beatty
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Siena C. McGovern
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Michael Whaby
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Emily Young
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Jacob Pancake
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Daron Weekley
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Justin Rice
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Donald A. Primerano
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA; (D.A.P.); (J.D.)
| | - James Denvir
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA; (D.A.P.); (J.D.)
| | - Joseph Horzempa
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
| | - Deanna M. Schmitt
- Department of Biomedical Sciences, West Liberty University, West Liberty, WV 26074, USA; (K.S.); (E.J.B.); (S.C.M.); (M.W.); (E.Y.); (J.P.); (D.W.); (J.R.); (J.H.)
- Correspondence: ; Tel.: +1-304-336-8576
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Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T. A decade of advances in transposon-insertion sequencing. Nat Rev Genet 2020; 21:526-540. [PMID: 32533119 PMCID: PMC7291929 DOI: 10.1038/s41576-020-0244-x] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 01/12/2023]
Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
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Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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